EFI - Training Resources: Publications

5 US Patents

US2019/0144798A1, Cleaning composition. The Procter & Gamble Company, Cincinnati, OH. May 16, 2019.
US2019/0144801, Cleaning composition. The Procter & Gamble Company, Cincinnati, OH. May 16, 2019.
US2019/0194599A1, Methods for generating a bacterial hemoglobin library and uses thereof. Zymergen, Inc., Emeryville, CA. June 27, 2019.
US2019/0209625A1, Engineering therapeutic probiotic system and method. National University of Singapore, Singapore. July 11, 2019.
US2019/0225663A1, Discovery of cationic nonribosomal peptides as gram-negative antibiotics through global genome mining. Hong Kong University of Science and Technology, China Ocean Mineral Resources R&D Association, Hong Kong CN. July 25, 2019.

339 Journal Articles

Wichelecki, D. J., Graff, D. C., Al-Obaidi, N., Almo, S. C., Gerlt, J. A., Identification of the in vivo function of the high-efficiency D-mannonate dehydratase in Caulobacter crescentus NA1000 from the enolase superfamily. Biochemistry, 2014. 53(25): p. 4087-9. http://doi.org/10.1021/bi500683x
Wichelecki, D. J., Balthazor, B. M., Chau, A. C., Vetting, M. W., Fedorov, A. A., Fedorov, E. V., Lukk, T., Patskovsky, Y. V., Stead, M. B., Hillerich, B. S., Seidel, R. D., Almo, S. C., Gerlt, J. A., Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup. Biochemistry, 2014. 53(16): p. 2722-31. http://doi.org/10.1021/bi500264p
Dunbar, K. L., Chekan, J. R., Cox, C. L., Burkhart, B. J., Nair, S. K., Mitchell, D. A., Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis. Nat Chem Biol, 2014. 10(10): p. 823-9. http://doi.org/10.1038/nchembio.1608
Rao, G., O'Dowd, B., Li, J., Wang, K., Oldfield, E., IspH–RPS1 and IspH–UbiA:“Rosetta stone” proteins. Chemical science, 2015. 6(12): p. 6813-6822. http://doi.org/10.1039/C5SC02600H
Petronikolou, N., Nair, S. K., Biochemical Studies of Mycobacterial Fatty Acid Methyltransferase: A Catalyst for the Enzymatic Production of Biodiesel. Chem Biol, 2015. 22(11): p. 1480-1490. http://doi.org/10.1016/j.chembiol.2015.09.011
Cox, C. L., Doroghazi, J. R., Mitchell, D. A., The genomic landscape of ribosomal peptides containing thiazole and oxazole heterocycles. BMC Genomics, 2015. 16(1): p. 778. http://doi.org/10.1186/s12864-015-2008-0
Roche, D., Brackenridge, D., McGuffin, L., Proteins and their interacting partners: An introduction to protein–ligand binding site prediction methods. International journal of molecular sciences, 2015. 16(12): p. 29829-29842. http://doi.org/10.3390/ijms161226202
Huang, H., Carter, M. S., Vetting, M. W., Al-Obaidi, N., Patskovsky, Y., Almo, S. C., Gerlt, J. A., A General Strategy for the Discovery of Metabolic Pathways: d-Threitol, l-Threitol, and Erythritol Utilization in Mycobacterium smegmatis. J Am Chem Soc, 2015. 137(46): p. 14570-3. http://doi.org/10.1021/jacs.5b08968
Wichelecki, D. J., Vetting, M. W., Chou, L., Al-Obaidi, N., Bouvier, J. T., Almo, S. C., Gerlt, J. A., ATP-binding Cassette (ABC) Transport System Solute-binding Protein-guided Identification of Novel d-Altritol and Galactitol Catabolic Pathways in Agrobacterium tumefaciens C58. J Biol Chem, 2015. 290(48): p. 28963-76. http://doi.org/10.1074/jbc.M115.686857
San Francisco, B., Zhang, X., Whalen, K., Gerlt, J., A Novel Pathway for Bacterial Ethanolamine Metabolism. The FASEB Journal, 2015. 29(1_supplement): p. 573.45.
Vetting, M. W., Al-Obaidi, N., Zhao, S., San Francisco, B., Kim, J., Wichelecki, D. J., Bouvier, J. T., Solbiati, J. O., Vu, H., Zhang, X., Rodionov, D. A., Love, J. D., Hillerich, B. S., Seidel, R. D., Quinn, R. J., Osterman, A. L., Cronan, J. E., Jacobson, M. P., Gerlt, J. A., Almo, S. C., Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes. Biochemistry, 2015. 54(3): p. 909-31. http://doi.org/10.1021/bi501388y
Zhang, X., Kumar, R., Vetting, M. W., Zhao, S., Jacobson, M. P., Almo, S. C., Gerlt, J. A., A unique cis-3-hydroxy-l-proline dehydratase in the enolase superfamily. J Am Chem Soc, 2015. 137(4): p. 1388-91. http://doi.org/10.1021/ja5103986
Anders, K., Essen, L., The family of phytochrome-like photoreceptors: diverse, complex and multi-colored, but very useful. Current Opinion in Structural Biology, 2015. 35: p. 7-16. http://doi.org/10.1016/j.sbi.2015.07.005
Colin, P. Y., Kintses, B., Gielen, F., Miton, C. M., Fischer, G., Mohamed, M. F., Hyvonen, M., Morgavi, D. P., Janssen, D. B., Hollfelder, F., Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional metagenomics. Nat Commun, 2015. 6: p. 10008. http://doi.org/10.1038/ncomms10008
Burkhart, B. J., Hudson, G. A., Dunbar, K. L., Mitchell, D. A., A prevalent peptide-binding domain guides ribosomal natural product biosynthesis. Nat Chem Biol, 2015. 11(8): p. 564-70. http://doi.org/10.1038/nchembio.1856
Latham, J. A., Iavarone, A. T., Barr, I., Juthani, P. V., Klinman, J. P., PqqD is a novel peptide chaperone that forms a ternary complex with the radical S-adenosylmethionine protein PqqE in the pyrroloquinoline quinone biosynthetic pathway. J Biol Chem, 2015. 290(20): p. 12908-18. http://doi.org/10.1074/jbc.M115.646521
Celis, A. I., DuBois, J. L., Substrate, product, and cofactor: The extraordinarily flexible relationship between the CDE superfamily and heme. Arch Biochem Biophys, 2015. 574: p. 3-17. http://doi.org/10.1016/j.abb.2015.03.004
Liu, F., Geng, J., Gumpper, R. H., Barman, A., Davis, I., Ozarowski, A., Hamelberg, D., Liu, A., An Iron Reservoir to the Catalytic Metal: THE RUBREDOXIN IRON IN AN EXTRADIOL DIOXYGENASE. J Biol Chem, 2015. 290(25): p. 15621-34. http://doi.org/10.1074/jbc.M115.650259
Desai, J., Liu, Y. L., Wei, H., Liu, W., Ko, T. P., Guo, R. T., Oldfield, E., Structure, Function, and Inhibition of Staphylococcus aureus Heptaprenyl Diphosphate Synthase. ChemMedChem, 2016. 11(17): p. 1915-23. http://doi.org/10.1002/cmdc.201600311
Molloy, E. M, Tietz, J. I, Blair, P. M, Mitchell, D. A, Biological characterization of the hygrobafilomycin antibiotic JBIR-100 and bioinformatic insights into the hygrolide family of natural products. Bioorganic & medicinal chemistry, 2016. 24(24): p. 6276-6290. http://doi.org/10.1016/j.bmc.2016.05.021
Ghodge, S. V., Biernat, K. A., Bassett, S. J., Redinbo, M. R., Bowers, A. A., Post-translational Claisen Condensation and Decarboxylation en Route to the Bicyclic Core of Pantocin A. J Am Chem Soc, 2016. 138(17): p. 5487-90. http://doi.org/10.1021/jacs.5b13529
Plach, M. G, Reisinger, B., Sterner, R., Merkl, R., Long-term persistence of bi-functionality contributes to the robustness of microbial life through exaptation. PLoS genetics, 2016. 12(1): p. e1005836. http://doi.org/10.1371/journal.pgen.1005836
Thotsaporn, K., Tinikul, R., Maenpuen, S., Phonbuppha, J., Watthaisong, P., Chenprakhon, P., Chaiyen, P., Enzymes in the p-hydroxyphenylacetate degradation pathway of Acinetobacter baumannii. Journal of Molecular Catalysis B: Enzymatic, 2016. 134: p. 353-366. http://doi.org/10.1016/j.molcatb.2016.09.003
Kumar, G., Johnson, J. L, Frantom, P. A, Improving functional annotation in the DRE-TIM metallolyase superfamily through identification of active site fingerprints. Biochemistry, 2016. 55(12): p. 1863-1872. http://doi.org/10.1021/acs.biochem.5b01193
Davey, L., Halperin, S. A., Lee, S. F., Thiol-Disulfide Exchange in Gram-Positive Firmicutes. Trends Microbiol, 2016. 24(11): p. 902-915. http://doi.org/10.1016/j.tim.2016.06.010
Ding, W., Li, Q., Jia, Y., Ji, X., Qianzhu, H., Zhang, Q., Emerging Diversity of the Cobalamin-Dependent Methyltransferases Involving Radical-Based Mechanisms. Chembiochem, 2016. 17(13): p. 1191-7. http://doi.org/10.1002/cbic.201600107
Ahmed, F H., Mohamed, A E., Carr, P. D, Lee, B. M, Condic‐Jurkic, K., O'Mara, M. L, Jackson, C. J, Rv2074 is a novel F420H2‐dependent biliverdin reductase in Mycobacterium tuberculosis. Protein Science, 2016. 25(9): p. 1692-1709. http://doi.org/10.1002/pro.2975
Ji, X., Liu, W. Q., Yuan, S., Yin, Y., Ding, W., Zhang, Q., Mechanistic study of the radical SAM-dependent amine dehydrogenation reactions. Chem Commun (Camb), 2016. 52(69): p. 10555-8. http://doi.org/10.1039/c6cc05661j
Chekan, J. R., Koos, J. D., Zong, C., Maksimov, M. O., Link, A. J., Nair, S. K., Structure of the Lasso Peptide Isopeptidase Identifies a Topology for Processing Threaded Substrates. J Am Chem Soc, 2016. 138(50): p. 16452-16458. http://doi.org/10.1021/jacs.6b10389
Atkinson, J. T, Campbell, I., Bennett, G. N, Silberg, J. J, Cellular assays for ferredoxins: a strategy for understanding electron flow through protein carriers that link metabolic pathways. Biochemistry, 2016. 55(51): p. 7047-7064. http://doi.org/10.1021/acs.biochem.6b00831
Hao, Y., Pierce, E., Roe, D., Morita, M., McIntosh, J. A., Agarwal, V., Cheatham, T. E. 3rd, Schmidt, E. W., Nair, S. K., Molecular basis for the broad substrate selectivity of a peptide prenyltransferase. Proc Natl Acad Sci U S A, 2016. 113(49): p. 14037-14042. http://doi.org/10.1073/pnas.1609869113
Li, D., Moorman, R., Vanhercke, T., Petrie, J., Singh, S., Jackson, C. J., Classification and substrate head-group specificity of membrane fatty acid desaturases. Comput Struct Biotechnol J, 2016. 14: p. 341-349. http://doi.org/10.1016/j.csbj.2016.08.003
Rao, G., Oldfield, E., Structure and Function of Four Classes of the 4Fe-4S Protein, IspH. Biochemistry, 2016. 55(29): p. 4119-29. http://doi.org/10.1021/acs.biochem.6b00474
Baier, F., Copp, J. N., Tokuriki, N., Evolution of Enzyme Superfamilies: Comprehensive Exploration of Sequence-Function Relationships. Biochemistry, 2016. 55(46): p. 6375-6388. http://doi.org/10.1021/acs.biochem.6b00723
Ji, X., Li, Y., Xie, L., Lu, H., Ding, W., Zhang, Q., Expanding radical SAM chemistry by using radical addition reactions and SAM analogues. Angewandte Chemie International Edition, 2016. 55(39): p. 11845-11848. http://doi.org/10.1002/anie.201605917
Zallot, R., Harrison, K. J., Kolaczkowski, B., de Crecy-Lagard, V., Functional Annotations of Paralogs: A Blessing and a Curse. Life (Basel), 2016. 6(3): p. 39. http://doi.org/10.3390/life6030039
Zhang, X., Carter, M. S, Vetting, M. W, San Francisco, B., Zhao, S., Al-Obaidi, N. F, Solbiati, J. O, Thiaville, J. J, de Crécy-Lagard, V., Jacobson, M. P, Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proceedings of the National Academy of Sciences, 2016. 113(29): p. E4161-E4169. http://doi.org/10.1073/pnas.1605546113
I Tietz, J., Mitchell, A, Using genomics for natural product structure elucidation. Current topics in medicinal chemistry, 2016. 16(15): p. 1645-1694. http://doi.org/10.2174/1568026616666151012111439
Bhandari, D. M., Fedoseyenko, D., Begley, T. P., Tryptophan Lyase (NosL): A Cornucopia of 5'-Deoxyadenosyl Radical Mediated Transformations. J Am Chem Soc, 2016. 138(50): p. 16184-16187. http://doi.org/10.1021/jacs.6b06139
Prunetti, L., El Yacoubi, B., Schiavon, C. R, Kirkpatrick, E., Huang, L., Bailly, M., El Badawi-Sidhu, M., Harrison, K., Gregory 3rd, J. F, Fiehn, O., Evidence that COG0325 proteins are involved in PLP homeostasis. Microbiology, 2016. 162(4): p. 694-706. http://doi.org/10.1099/mic.0.000255
Gerlt, J. A, Tools and strategies for discovering novel enzymes and metabolic pathways. Perspectives in science, 2016. 9: p. 24-32. http://doi.org/10.1016/j.pisc.2016.07.001
Colabroy, K. L., Tearing down to build up: Metalloenzymes in the biosynthesis lincomycin, hormaomycin and the pyrrolo [1,4]benzodiazepines. Biochim Biophys Acta, 2016. 1864(6): p. 724-737. http://doi.org/10.1016/j.bbapap.2016.03.001
Maxson, T., Tietz, J. I., Hudson, G. A., Guo, X. R., Tai, H. C., Mitchell, D. A., Targeting Reactive Carbonyls for Identifying Natural Products and Their Biosynthetic Origins. J Am Chem Soc, 2016. 138(46): p. 15157-15166. http://doi.org/10.1021/jacs.6b06848
Dassama, L. M., Kenney, G. E., Ro, S. Y., Zielazinski, E. L., Rosenzweig, A. C., Methanobactin transport machinery. Proc Natl Acad Sci U S A, 2016. 113(46): p. 13027-13032. http://doi.org/10.1073/pnas.1603578113
Machovina, M. M., Usselman, R. J., DuBois, J. L., Monooxygenase Substrates Mimic Flavin to Catalyze Cofactorless Oxygenations. J Biol Chem, 2016. 291(34): p. 17816-28. http://doi.org/10.1074/jbc.M116.730051
Chowdhary, J., Loffler, F. E., Smith, J. C., Community detection in sequence similarity networks based on attribute clustering. PLoS One, 2017. 12(7): p. e0178650. http://doi.org/10.1371/journal.pone.0178650
Kandlinger, F., Plach, M. G., Merkl, R., AGeNNT: annotation of enzyme families by means of refined neighborhood networks. BMC Bioinformatics, 2017. 18(1): p. 274. http://doi.org/10.1186/s12859-017-1689-6
McFarland, B. J, Online Tools for Teaching Large Laboratory Courses: How the GENI Website Facilitates Authentic Research. Teaching and the Internet: The Application of Web Apps, Networking, and Online Tech for Chemistry Education, 2017. http://doi.org/10.1021/bk-2017-1270.ch008
Vazquez, R., Domenech, M., Iglesias-Bexiga, M., Menendez, M., Garcia, P., Csl2, a novel chimeric bacteriophage lysin to fight infections caused by Streptococcus suis, an emerging zoonotic pathogen. Sci Rep, 2017. 7(1): p. 16506. http://doi.org/10.1038/s41598-017-16736-0
Hopkins, D. H, Fraser, N. J, Mabbitt, P. D, Carr, P. D, Oakeshott, J. G, Jackson, C. J, Structure of an insecticide sequestering carboxylesterase from the disease vector Culex quinquefasciatus: what makes an enzyme a good insecticide sponge?. Biochemistry, 2017. 56(41): p. 5512-5525. http://doi.org/10.1021/acs.biochem.7b00774
Schwalen, C. J., Feng, X., Liu, W., O. Dowd B, , Ko, T. P., Shin, C. J., Guo, R. T., Mitchell, D. A., Oldfield, E., Head-to-Head Prenyl Synthases in Pathogenic Bacteria. Chembiochem, 2017. 18(11): p. 985-991. http://doi.org/10.1002/cbic.201700099
Yuan, H., Zhang, J., Cai, Y., Wu, S., Yang, K., Chan, H. C. S., Huang, W., Jin, W. B., Li, Y., Yin, Y., Igarashi, Y., Yuan, S., Zhou, J., Tang, G. L., GyrI-like proteins catalyze cyclopropanoid hydrolysis to confer cellular protection. Nat Commun, 2017. 8(1): p. 1485. http://doi.org/10.1038/s41467-017-01508-1
Holliday, G. L, Brown, S. D, Akiva, E., Mischel, D., Hicks, M. A, Morris, J. H, Huang, C. C, Meng, E. C, Pegg, S. C., Ferrin, T. E, Biocuration in the structure–function linkage database: the anatomy of a superfamily. Database, 2017. 2017:. http://doi.org/10.1093/database/bax045
Wang, H., Chen, X., Li, C., Liu, Y., Yang, F., Wang, C., Sequence-based prediction of cysteine reactivity using machine learning. Biochemistry, 2017. 57(4): p. 451-460. http://doi.org/10.1021/acs.biochem.7b00897
Lohans, C. T, Wang, D. Y, Wang, J., Hamed, R. B, Schofield, C. J, Crotonases: nature’s exceedingly convertible catalysts. ACS Catalysis, 2017. 7(10): p. 6587-6599. http://doi.org/10.1021/acscatal.7b01699
Orth, C., Niemann, N., Hennig, L., Essen, L., Batschauer, A., Hyperactivity of the Arabidopsis cryptochrome (cry1) L407F mutant is caused by a structural alteration close to the cry1 ATP-binding site. Journal of Biological Chemistry, 2017. 292(31): p. 12906-12920. http://doi.org/10.1074/jbc.M117.788869
Ahmed, M. N., Reyna-Gonzalez, E., Schmid, B., Wiebach, V., Sussmuth, R. D., Dittmann, E., Fewer, D. P., Phylogenomic Analysis of the Microviridin Biosynthetic Pathway Coupled with Targeted Chemo-Enzymatic Synthesis Yields Potent Protease Inhibitors. ACS Chem Biol, 2017. 12(6): p. 1538-1546. http://doi.org/10.1021/acschembio.7b00124
Holliday, G. L, Davidson, R., Akiva, E., Babbitt, P. C, Evaluating functional annotations of enzymes using the gene ontology. The Gene Ontology Handbook, 2017. http://doi.org/10.1007/978-1-4939-3743-1_9
Ding, W., Ji, W., Wu, Y., Wu, R., Liu, W. Q., Mo, T., Zhao, J., Ma, X., Zhang, W., Xu, P., Deng, Z., Tang, B., Yu, Y., Zhang, Q., Biosynthesis of the nosiheptide indole side ring centers on a cryptic carrier protein NosJ. Nat Commun, 2017. 8(1): p. 437. http://doi.org/10.1038/s41467-017-00439-1
Jia, B., Zhu, X. F., Pu, Z. J., Duan, Y. X., Hao, L. J., Zhang, J., Chen, L. Q., Jeon, C. O., Xuan, Y. H., Integrative View of the Diversity and Evolution of SWEET and SemiSWEET Sugar Transporters. Front Plant Sci, 2017. 8: p. 2178. http://doi.org/10.3389/fpls.2017.02178
Wang, M., Moynié, L., Harrison, P. J, Kelly, V., Piper, A., Naismith, J. H, Campopiano, D. J, Using the pimeloyl-CoA synthetase adenylation fold to synthesize fatty acid thioesters. Nature chemical biology, 2017. 13(6): p. 660. http://doi.org/10.1038/nchembio.2361
Bearne, S. L, The interdigitating loop of the enolase superfamily as a specificity binding determinant or ‘flying buttress’. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 2017. 1865(5): p. 619-630. http://doi.org/10.1016/j.bbapap.2017.02.006
Essen, L. O., Franz, S., Banerjee, A., Structural and evolutionary aspects of algal blue light receptors of the cryptochrome and aureochrome type. J Plant Physiol, 2017. 217: p. 27-37. http://doi.org/10.1016/j.jplph.2017.07.005
Jia, B., Jia, X., Hyun Kim, K., Ji Pu, Z., Kang, M. S., Ok Jeon, C., Evolutionary, computational, and biochemical studies of the salicylaldehyde dehydrogenases in the naphthalene degradation pathway. Sci Rep, 2017. 7: p. 43489. http://doi.org/10.1038/srep43489
Zallot, R., Yuan, Y., de Crécy-Lagard, V., The Escherichia coli COG1738 member YhhQ is involved in 7-cyanodeazaguanine (preQ0) transport. Biomolecules, 2017. 7(1): p. 12. http://doi.org/10.3390/biom7010012
Plach, M. G., Semmelmann, F., Busch, F., Busch, M., Heizinger, L., Wysocki, V. H., Merkl, R., Sterner, R., Evolutionary diversification of protein-protein interactions by interface add-ons. Proc Natl Acad Sci U S A, 2017. 114(40): p. E8333-E8342. http://doi.org/10.1073/pnas.1707335114
Glasner, M. E., Finding enzymes in the gut metagenome. Science, 2017. 355(6325): p. 577-578. http://doi.org/10.1126/science.aam7446
Grim, K. P., San Francisco, B., Radin, J. N., Brazel, E. B., Kelliher, J. L., Parraga Solorzano, P. K., Kim, P. C., McDevitt, C. A., Kehl-Fie, T. E., The Metallophore Staphylopine Enables Staphylococcus aureus To Compete with the Host for Zinc and Overcome Nutritional Immunity. mBio, 2017. 8(5): p. e01281-17. http://doi.org/10.1128/mBio.01281-17
Dong, S. H., Frane, N. D., Christensen, Q. H., Greenberg, E. P., Nagarajan, R., Nair, S. K., Molecular basis for the substrate specificity of quorum signal synthases. Proc Natl Acad Sci U S A, 2017. 114(34): p. 9092-9097. http://doi.org/10.1073/pnas.1705400114
Jia, B., Jia, X., Kim, K. H., Jeon, C. O., Integrative view of 2-oxoglutarate/Fe(II)-dependent oxygenase diversity and functions in bacteria. Biochim Biophys Acta Gen Subj, 2017. 1861(2): p. 323-334. http://doi.org/10.1016/j.bbagen.2016.12.001
Jia, B., Tang, K., Chun, B. H., Jeon, C. O., Large-scale examination of functional and sequence diversity of 2-oxoglutarate/Fe(II)-dependent oxygenases in Metazoa. Biochim Biophys Acta Gen Subj, 2017. 1861(11 Pt A): p. 2922-2933. http://doi.org/10.1016/j.bbagen.2017.08.019
Wagner, D. T., Zeng, J., Bailey, C. B., Gay, D. C., Yuan, F., Manion, H. R., Keatinge-Clay, A. T., Structural and Functional Trends in Dehydrating Bimodules from trans-Acyltransferase Polyketide Synthases. Structure, 2017. 25(7): p. 1045-1055 e2. http://doi.org/10.1016/j.str.2017.05.011
Estrada, P., Manandhar, M., Dong, S. H., Deveryshetty, J., Agarwal, V., Cronan, J. E., Nair, S. K., The pimeloyl-CoA synthetase BioW defines a new fold for adenylate-forming enzymes. Nat Chem Biol, 2017. 13(6): p. 668-674. http://doi.org/10.1038/nchembio.2359
Pimviriyakul, P., Thotsaporn, K., Sucharitakul, J., Chaiyen, P., Kinetic Mechanism of the Dechlorinating Flavin-dependent Monooxygenase HadA. J Biol Chem, 2017. 292(12): p. 4818-4832. http://doi.org/10.1074/jbc.M116.774448
Liao, C., Seebeck, F. P., Convergent Evolution of Ergothioneine Biosynthesis in Cyanobacteria. Chembiochem, 2017. 18(21): p. 2115-2118. http://doi.org/10.1002/cbic.201700354
Tietz, J. I., Schwalen, C. J., Patel, P. S., Maxson, T., Blair, P. M., Tai, H. C., Zakai, U. I., Mitchell, D. A., A new genome-mining tool redefines the lasso peptide biosynthetic landscape. Nat Chem Biol, 2017. 13(5): p. 470-478. http://doi.org/10.1038/nchembio.2319
Erb, T. J., Jones, P. R., Bar-Even, A., Synthetic metabolism: metabolic engineering meets enzyme design. Curr Opin Chem Biol, 2017. 37: p. 56-62. http://doi.org/10.1016/j.cbpa.2016.12.023
Repka, L. M., Chekan, J. R., Nair, S. K., van der Donk, W. A., Mechanistic Understanding of Lanthipeptide Biosynthetic Enzymes. Chem Rev, 2017. 117(8): p. 5457-5520. http://doi.org/10.1021/acs.chemrev.6b00591
Levin, B. J., Huang, Y. Y., Peck, S. C., Wei, Y., Martinez-Del Campo, A., Marks, J. A., Franzosa, E. A., Huttenhower, C., Balskus, E. P., A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline. Science, 2017. 355(6325): p. eaai8386. http://doi.org/10.1126/science.aai8386
Rudolf, J. D., Chang, C. Y., Ma, M., Shen, B., Cytochromes P450 for natural product biosynthesis in Streptomyces: sequence, structure, and function. Nat Prod Rep, 2017. 34(9): p. 1141-1172. http://doi.org/10.1039/c7np00034k
Giessen, T. W., Silver, P. A., Widespread distribution of encapsulin nanocompartments reveals functional diversity. Nat Microbiol, 2017. 2(6): p. 17029. http://doi.org/10.1038/nmicrobiol.2017.29
Ney, B., Ahmed, F H., Carere, C. R, Biswas, A., Warden, A. C, Morales, S. E, Pandey, G., Watt, S. J, Oakeshott, J. G, Taylor, M. C, The methanogenic redox cofactor F 420 is widely synthesized by aerobic soil bacteria. The ISME journal, 2017. 11(1): p. 125. http://doi.org/10.1038/ismej.2016.100
Ortega, M. A., Cogan, D. P., Mukherjee, S., Garg, N., Li, B., Thibodeaux, G. N., Maffioli, S. I., Donadio, S., Sosio, M., Escano, J., Smith, L., Nair, S. K., van der Donk, W. A., Two Flavoenzymes Catalyze the Post-Translational Generation of 5-Chlorotryptophan and 2-Aminovinyl-Cysteine during NAI-107 Biosynthesis. ACS Chem Biol, 2017. 12(2): p. 548-557. http://doi.org/10.1021/acschembio.6b01031
Benjdia, A., Guillot, A., Ruffie, P., Leprince, J., Berteau, O., Post-translational modification of ribosomally synthesized peptides by a radical SAM epimerase in Bacillus subtilis. Nat Chem, 2017. 9(7): p. 698-707. http://doi.org/10.1038/nchem.2714
Cogan, D. P, Hudson, G. A, Zhang, Z., Pogorelov, T. V, van der Donk, W. A, Mitchell, D. A, Nair, S. K, Structural insights into enzymatic [4+ 2] aza-cycloaddition in thiopeptide antibiotic biosynthesis. Proceedings of the National Academy of Sciences, 2017. 114(49): p. 12928-12933. http://doi.org/10.1073/pnas.1716035114
Gerlt, J. A., Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence-Function Space and Genome Context to Discover Novel Functions. Biochemistry, 2017. 56(33): p. 4293-4308. http://doi.org/10.1021/acs.biochem.7b00614
Hetrick, K. J., van der Donk, W. A., Ribosomally synthesized and post-translationally modified peptide natural product discovery in the genomic era. Curr Opin Chem Biol, 2017. 38: p. 36-44. http://doi.org/10.1016/j.cbpa.2017.02.005
Blin, K., Wolf, T., Chevrette, M. G., Lu, X., Schwalen, C. J., Kautsar, S. A., Suarez Duran, H. G., de Los Santos, E. L. C., Kim, H. U., Nave, M., Dickschat, J. S., Mitchell, D. A., Shelest, E., Breitling, R., Takano, E., Lee, S. Y., Weber, T., Medema, M. H., antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res, 2017. 45(W1): p. W36-W41. http://doi.org/10.1093/nar/gkx319
Koppel, N., Maini Rekdal, V., Balskus, E. P., Chemical transformation of xenobiotics by the human gut microbiota. Science, 2017. 356(6344): p. eaag2770. http://doi.org/10.1126/science.aag2770
Welsh, M. A., Taguchi, A., Schaefer, K., Van Tyne, D., Lebreton, F., Gilmore, M. S., Kahne, D., Walker, S., Identification of a Functionally Unique Family of Penicillin-Binding Proteins. J Am Chem Soc, 2017. 139(49): p. 17727-17730. http://doi.org/10.1021/jacs.7b10170
Haase, E. M., Kou, Y., Sabharwal, A., Liao, Y. C., Lan, T., Lindqvist, C., Scannapieco, F. A., Comparative genomics and evolution of the amylase-binding proteins of oral streptococci. BMC Microbiol, 2017. 17(1): p. 94. http://doi.org/10.1186/s12866-017-1005-7
Pornsuwan, S., Maenpuen, S., Kamutira, P., Watthaisong, P., Thotsaporn, K., Tongsook, C., Juttulapa, M., Nijvipakul, S., Chaiyen, P., 3,4-Dihydroxyphenylacetate 2,3-dioxygenase from Pseudomonas aeruginosa: An Fe(II)-containing enzyme with fast turnover. PLoS One, 2017. 12(2): p. e0171135. http://doi.org/10.1371/journal.pone.0171135
Zhong, G., Zhao, Q., Zhang, Q., Liu, W., 4-alkyl-L-(Dehydro)proline biosynthesis in actinobacteria involves N-terminal nucleophile-hydrolase activity of gamma-glutamyltranspeptidase homolog for C-C bond cleavage. Nat Commun, 2017. 8: p. 16109. http://doi.org/10.1038/ncomms16109
Macaisne, N., Liu, F., Scornet, D., Peters, A. F., Lipinska, A., Perrineau, M. M., Henry, A., Strittmatter, M., Coelho, S. M., Cock, J. M., The Ectocarpus IMMEDIATE UPRIGHT gene encodes a member of a novel family of cysteine-rich proteins with an unusual distribution across the eukaryotes. Development, 2017. 144(3): p. 409-418. http://doi.org/10.1242/dev.141523
Stojkovic, V., Chu, T., Therizols, G., Weinberg, D. E., Fujimori, D. G., miCLIP-MaPseq, a Substrate Identification Approach for Radical SAM RNA Methylating Enzymes. J Am Chem Soc, 2018. 140(23): p. 7135-7143. http://doi.org/10.1021/jacs.8b02618
Yuenyao, A., Petchyam, N., Kamonsutthipaijit, N., Chaiyen, P., Pakotiprapha, D., Crystal structure of the flavin reductase of Acinetobacter baumannii p-hydroxyphenylacetate 3-hydroxylase (HPAH) and identification of amino acid residues underlying its regulation by aromatic ligands. Arch Biochem Biophys, 2018. 653: p. 24-38. http://doi.org/10.1016/j.abb.2018.06.010
Viana, A. T., Caetano, T., Covas, C., Santos, T., Mendo, S., Environmental superbugs: The case study of Pedobacter spp. Environ Pollut, 2018. 241: p. 1048-1055. http://doi.org/10.1016/j.envpol.2018.06.047
Roy, R., Samanta, S., Patra, S., Mahato, N. K., Saha, R. P., In silico identification and characterization of sensory motifs in the transcriptional regulators of the ArsR-SmtB family. Metallomics, 2018. 10(10): p. 1476-1500. http://doi.org/10.1039/c8mt00082d
Chakravarti, A., Selvadurai, K., Shahoei, R., Lee, H., Fatma, S., Tajkhorshid, E., Huang, R. H., Reconstitution and substrate specificity for isopentenyl pyrophosphate of the antiviral radical SAM enzyme viperin. J Biol Chem, 2018. 293(36): p. 14122-14133. http://doi.org/10.1074/jbc.RA118.003998
Jia, B., Pu, Z. J., Tang, K., Jia, X., Kim, K. H., Liu, X., Jeon, C. O., Catalytic, Computational, and Evolutionary Analysis of the d-Lactate Dehydrogenases Responsible for d-Lactic Acid Production in Lactic Acid Bacteria. J Agric Food Chem, 2018. 66(31): p. 8371-8381. http://doi.org/10.1021/acs.jafc.8b02454
Mallette, E., Kimber, M. S., Structure and Kinetics of the S-(+)-1-Amino-2-propanol Dehydrogenase from the RMM Microcompartment of Mycobacterium smegmatis. Biochemistry, 2018. 57(26): p. 3780-3789. http://doi.org/10.1021/acs.biochem.8b00464
Kim, K. H., Jia, X., Jia, B., Jeon, C. O., Identification and Characterization of l-Malate Dehydrogenases and the l-Lactate-Biosynthetic Pathway in Leuconostoc mesenteroides ATCC 8293. J Agric Food Chem, 2018. 66(30): p. 8086-8093. http://doi.org/10.1021/acs.jafc.8b02649
Vogt, M. S., Volpel, S. L., Albers, S. V., Essen, L. O., Banerjee, A., Crystal structure of an Lrs14-like archaeal biofilm regulator from Sulfolobus acidocaldarius. Acta Crystallogr D Struct Biol, 2018. 74(Pt 11): p. 1105-1114. http://doi.org/10.1107/S2059798318014146
An, L., Cogan, D. P., Navo, C. D., Jimenez-Oses, G., Nair, S. K., van der Donk, W. A., Substrate-assisted enzymatic formation of lysinoalanine in duramycin. Nat Chem Biol, 2018. 14(10): p. 928-933. http://doi.org/10.1038/s41589-018-0122-4
Ji, X., Mandalapu, D., Cheng, J., Ding, W., Zhang, Q., Expanding the Chemistry of the Class C Radical SAM Methyltransferase NosN by Using an Allyl Analogue of SAM. Angewandte Chemie International Edition, 2018. 57(22): p. 6601-6604. http://doi.org/10.1002/anie.201712224
Mukherjee, K., Narindoshvili, T., Raushel, F. M., Discovery of a Kojibiose Phosphorylase in Escherichia coli K-12. Biochemistry, 2018. 57(19): p. 2857-2867. http://doi.org/10.1021/acs.biochem.8b00392
Bridwell-Rabb, J., Grell, T. A. J., Drennan, C. L., A Rich Man, Poor Man Story of S-Adenosylmethionine and Cobalamin Revisited. Annu Rev Biochem, 2018. 87: p. 555-584. http://doi.org/10.1146/annurev-biochem-062917-012500
Yan, X. F., Xin, L., Yen, J. T., Zeng, Y., Jin, S., Cheang, Q. W., Fong, R., Chiam, K. H., Liang, Z. X., Gao, Y. G., Structural analyses unravel the molecular mechanism of cyclic di-GMP regulation of bacterial chemotaxis via a PilZ adaptor protein. J Biol Chem, 2018. 293(1): p. 100-111. http://doi.org/10.1074/jbc.M117.815704
Jeoung, J., Dobbek, H., ATP-dependent substrate reduction at an [Fe8S9] double-cubane cluster. Proceedings of the National Academy of Sciences, 2018. 115(12): p. 2994-2999. http://doi.org/10.1073/pnas.1720489115
Ongpipattanakul, C., Nair, S. K., Molecular Basis for Autocatalytic Backbone N-Methylation in RiPP Natural Product Biosynthesis. ACS Chem Biol, 2018. 13(10): p. 2989-2999. http://doi.org/10.1021/acschembio.8b00668
Liao, L., Schaefer, A. L., Coutinho, B. G., Brown, P. J. B., Greenberg, E. P., An aryl-homoserine lactone quorum-sensing signal produced by a dimorphic prosthecate bacterium. Proc Natl Acad Sci U S A, 2018. 115(29): p. 7587-7592. http://doi.org/10.1073/pnas.1808351115
Wood, B. M., Santa Maria, J. P. Jr., Matano, L. M., Vickery, C. R., Walker, S., A partial reconstitution implicates DltD in catalyzing lipoteichoic acid d-alanylation. J Biol Chem, 2018. 293(46): p. 17985-17996. http://doi.org/10.1074/jbc.RA118.004561
Chang, C. Y., Yan, X., Crnovcic, I., Annaval, T., Chang, C., Nocek, B., Rudolf, J. D., Yang, D., Hindra, , Babnigg, G., Joachimiak, A., Phillips, G. N. Jr., Shen, B., Resistance to Enediyne Antitumor Antibiotics by Sequestration. Cell Chem Biol, 2018. 25(9): p. 1075-1085 e4. http://doi.org/10.1016/j.chembiol.2018.05.012
Green, C. M., Novikova, O., Belfort, M., The dynamic intein landscape of eukaryotes. Mob DNA, 2018. 9(1): p. 4. http://doi.org/10.1186/s13100-018-0111-x
Qiu, B., Xia, B., Zhou, Q., Lu, Y., He, M., Hasegawa, K., Ma, Z., Zhang, F., Gu, L., Mao, Q., Succinate-acetate permease from Citrobacter koseri is an anion channel that unidirectionally translocates acetate. Cell research, 2018. 28(6): p. 644. http://doi.org/10.1038/s41422-018-0032-8
Mehrer, C. R., Incha, M. R., Politz, M. C., Pfleger, B. F., Anaerobic production of medium-chain fatty alcohols via a beta-reduction pathway. Metab Eng, 2018. 48: p. 63-71. http://doi.org/10.1016/j.ymben.2018.05.011
Taylor, Z. W., Raushel, F. M., Cytidine Diphosphoramidate Kinase: An Enzyme Required for the Biosynthesis of the O-Methyl Phosphoramidate Modification in the Capsular Polysaccharides of Campylobacter jejuni. Biochemistry, 2018. 57(15): p. 2238-2244. http://doi.org/10.1021/acs.biochem.8b00279
Kenney, G. E., Dassama, L. M. K., Pandelia, M. E., Gizzi, A. S., Martinie, R. J., Gao, P., DeHart, C. J., Schachner, L. F., Skinner, O. S., Ro, S. Y., Zhu, X., Sadek, M., Thomas, P. M., Almo, S. C., Bollinger, J. M. Jr., Krebs, C., Kelleher, N. L., Rosenzweig, A. C., The biosynthesis of methanobactin. Science, 2018. 359(6382): p. 1411-1416. http://doi.org/10.1126/science.aap9437
Koppel, N., Bisanz, J. E., Pandelia, M. E., Turnbaugh, P. J., Balskus, E. P., Discovery and characterization of a prevalent human gut bacterial enzyme sufficient for the inactivation of a family of plant toxins. Elife, 2018. 7: p. e33953. http://doi.org/10.7554/eLife.33953
Lei, L., Cherukuri, K. P., Alcolombri, U., Meltzer, D., Tawfik, D. S, The dimethylsulfoniopropionate (DMSP) lyase and lyase-like cupin family consists of bona fide DMSP lyases as well as other enzymes with unknown function. Biochemistry, 2018. 57(24): p. 3364-3377. http://doi.org/10.1021/acs.biochem.8b00097
Ho, C. L., Tan, H. Q., Chua, K. J., Kang, A., Lim, K. H., Ling, K. L., Yew, W. S., Lee, Y. S., Thiery, J. P., Chang, M. W., Engineered commensal microbes for diet-mediated colorectal-cancer chemoprevention. Nat Biomed Eng, 2018. 2(1): p. 27-37. http://doi.org/10.1038/s41551-017-0181-y
Li, Y., Zhong, Z., Zhang, W., Qian, P., Discovery of cationic nonribosomal peptides as Gram-negative antibiotics through global genome mining. Nature communications, 2018. 9(1): p. 3273. http://doi.org/10.1038/s41467-018-05781-6
Calhoun, S., Korczynska, M., Wichelecki, D. J., San Francisco, B., Zhao, S., Rodionov, D. A., Vetting, M. W., Al-Obaidi, N. F., Lin, H., O'Meara, M. J., Scott, D. A., Morris, J. H., Russel, D., Almo, S. C., Osterman, A. L., Gerlt, J. A., Jacobson, M. P., Shoichet, B. K., Sali, A., Prediction of enzymatic pathways by integrative pathway mapping. Elife, 2018. 7: p. e31097. http://doi.org/10.7554/eLife.31097
Dunkle, J. A, Bruno, M. R, Outten, F W., Frantom, P. A, Structural Evidence for Dimer-Interface-Driven Regulation of the Type II Cysteine Desulfurase, SufS. Biochemistry, 2018. 58(6): p. 687-696. http://doi.org/10.1021/acs.biochem.8b01122
Han, L., Yuan, J., Ao, X., Lin, S., Han, X., Ye, H., Biochemical Characterization and Phylogenetic Analysis of the Virulence Factor Lysine Decarboxylase From Vibrio vulnificus. Front Microbiol, 2018. 9: p. 3082. http://doi.org/10.3389/fmicb.2018.03082
Dalponte, L., Parajuli, A., Younger, E., Mattila, A., Jokela, J., Wahlsten, M., Leikoski, N., Sivonen, K., Jarmusch, S. A., Houssen, W. E., Fewer, D. P., N-Prenylation of Tryptophan by an Aromatic Prenyltransferase from the Cyanobactin Biosynthetic Pathway. Biochemistry, 2018. 57(50): p. 6860-6867. http://doi.org/10.1021/acs.biochem.8b00879
Bastard, K., Isabet, T., Stura, E. A, Legrand, P., Zaparucha, A., Structural studies based on two lysine dioxygenases with distinct regioselectivity brings insights into enzyme specificity within the clavaminate synthase-like family. Scientific reports, 2018. 8(1): p. 16587. http://doi.org/10.1038/s41598-018-34795-9
Mallette, E., Kimber, M. S., Structural and kinetic characterization of (S)-1-amino-2-propanol kinase from the aminoacetone utilization microcompartment of Mycobacterium smegmatis. J Biol Chem, 2018. 293(51): p. 19909-19918. http://doi.org/10.1074/jbc.RA118.005485
Liu, D., Wei, Y., Liu, X., Zhou, Y., Jiang, L., Yin, J., Wang, F., Hu, Y., Urs, A. N N., Liu, Y., Indoleacetate decarboxylase is a glycyl radical enzyme catalysing the formation of malodorant skatole. Nature communications, 2018. 9(1): p. 4224. http://doi.org/10.1038/s41467-018-06627-x.
Nemmara, V. V., Xiang, D. F., Fedorov, A. A., Fedorov, E. V., Bonanno, J. B., Almo, S. C., Raushel, F. M., Substrate Profile of the Phosphotriesterase Homology Protein from Escherichia coli. Biochemistry, 2018. 57(43): p. 6219-6227. http://doi.org/10.1021/acs.biochem.8b00935
Blair, P. M., Land, M. L., Piatek, M. J., Jacobson, D. A., Lu, T. S., Doktycz, M. J., Pelletier, D. A., Exploration of the Biosynthetic Potential of the Populus Microbiome. mSystems, 2018. 3(5): p. e00045-18. http://doi.org/10.1128/mSystems.00045-18
Ward, A. C., Allenby, N. E., Genome mining for the search and discovery of bioactive compounds: the Streptomyces paradigm. FEMS Microbiol Lett, 2018. 365(24): p. fny240. http://doi.org/10.1093/femsle/fny240
Hogancamp, T. N., Mabanglo, M. F., Raushel, F. M., Structure and Reaction Mechanism of the LigJ Hydratase: An Enzyme Critical for the Bacterial Degradation of Lignin in the Protocatechuate 4,5-Cleavage Pathway. Biochemistry, 2018. 57(40): p. 5841-5850. http://doi.org/10.1021/acs.biochem.8b00713
Ayikpoe, R., Salazar, J., Majestic, B., Latham, J. A, Mycofactocin biosynthesis proceeds through 3-amino-5-[(p-hydroxyphenyl) methyl]-4, 4-dimethyl-2-pyrrolidinone (AHDP); direct observation of MftE specificity toward MftA. Biochemistry, 2018. 57(37): p. 5379-5383. http://doi.org/10.1021/acs.biochem.8b00816
Jiang, S., Network analysis of RAD51 proteins in Metazoa and the evolutionary relationships with their archaeal homologs. Frontiers in genetics, 2018. 9: p. 383. http://doi.org/10.3389/fgene.2018.00383
Fisher, O. S., Kenney, G. E., Ross, M. O., Ro, S. Y., Lemma, B. E., Batelu, S., Thomas, P. M., Sosnowski, V. C., DeHart, C. J., Kelleher, N. L., Stemmler, T. L., Hoffman, B. M., Rosenzweig, A. C., Characterization of a long overlooked copper protein from methane- and ammonia-oxidizing bacteria. Nat Commun, 2018. 9(1): p. 4276. http://doi.org/10.1038/s41467-018-06681-5
Reichelt, R., Grohmann, D., Willkomm, S., A journey through the evolutionary diversification of archaeal Lsm and Hfq proteins. Emerging Topics in Life Sciences, 2018. 2(4): p. 647-657. http://doi.org/10.1042/etls20180034
Luo, S., Huang, H., Discovering a new catabolic pathway of D-ribonate in Mycobacterium smegmatis. Biochem Biophys Res Commun, 2018. 505(4): p. 1107-1111. http://doi.org/10.1016/j.bbrc.2018.10.033
Punekar, N., Future of Enzymology: An Appraisal. ENZYMES: Catalysis, Kinetics and Mechanisms, 2018. ; . ;
Leong, R., Urano, D., Molecular Breeding for Plant Factory: Strategies and Technology. Smart Plant Factory, 2018. http://doi.org/10.1007/978-981-13-1065-2_19
Bushin, L. B., Clark, K. A., Pelczer, I., Seyedsayamdost, M. R., Charting an Unexplored Streptococcal Biosynthetic Landscape Reveals a Unique Peptide Cyclization Motif. J Am Chem Soc, 2018. 140(50): p. 17674-17684. http://doi.org/10.1021/jacs.8b10266
Annaval, T., Han, L., Rudolf, J. D., Xie, G., Yang, D., Chang, C. Y., Ma, M., Crnovcic, I., Miller, M. D., Soman, J., Xu, W., Phillips, G. N. Jr., Shen, B., Biochemical and Structural Characterization of TtnD, a Prenylated FMN-Dependent Decarboxylase from the Tautomycetin Biosynthetic Pathway. ACS Chem Biol, 2018. 13(9): p. 2728-2738. http://doi.org/10.1021/acschembio.8b00673
Dong, L. B., Rudolf, J. D., Deng, M. R., Yan, X., Shen, B., Discovery of the Tiancilactone Antibiotics by Genome Mining of Atypical Bacterial Type II Diterpene Synthases. Chembiochem, 2018. 19(16): p. 1727-1733. http://doi.org/10.1002/cbic.201800285
Gilchrist, C. L. M., Li, H., Chooi, Y. H., Panning for gold in mould: can we increase the odds for fungal genome mining?. Org Biomol Chem, 2018. 16(10): p. 1620-1626. http://doi.org/10.1039/c7ob03127k
Purohit, R., Ross, M. O., Batelu, S., Kusowski, A., Stemmler, T. L., Hoffman, B. M., Rosenzweig, A. C., Cu(+)-specific CopB transporter: Revising P1B-type ATPase classification. Proc Natl Acad Sci U S A, 2018. 115(9): p. 2108-2113. http://doi.org/10.1073/pnas.1721783115
Ryu, H., Grove, T. L., Almo, S. C., Kim, J., Identification of a novel tRNA wobble uridine modifying activity in the biosynthesis of 5-methoxyuridine. Nucleic Acids Res, 2018. 46(17): p. 9160-9169. http://doi.org/10.1093/nar/gky592
Mahanta, N., Liu, A., Dong, S., Nair, S. K., Mitchell, D. A., Enzymatic reconstitution of ribosomal peptide backbone thioamidation. Proc Natl Acad Sci U S A, 2018. 115(12): p. 3030-3035. http://doi.org/10.1073/pnas.1722324115
Rose, H. R., Ghosh, M. K., Maggiolo, A. O., Pollock, C. J., Blaesi, E. J., Hajj, V., Wei, Y., Rajakovich, L. J., Chang, W. C., Han, Y., Hajj, M., Krebs, C., Silakov, A., Pandelia, M. E., Bollinger, J. M. Jr., Boal, A. K., Structural Basis for Superoxide Activation of Flavobacterium johnsoniae Class I Ribonucleotide Reductase and for Radical Initiation by Its Dimanganese Cofactor. Biochemistry, 2018. 57(18): p. 2679-2693. http://doi.org/10.1021/acs.biochem.8b00247
Wang, S. C., Cobalamin-dependent radical S-adenosyl-l-methionine enzymes in natural product biosynthesis. Nat Prod Rep, 2018. 35(8): p. 707-720. http://doi.org/10.1039/c7np00059f
Hossain, G. S., Nadarajan, S. P., Zhang, L., Ng, T. K., Foo, J. L., Ling, H., Choi, W. J., Chang, M. W., Rewriting the Metabolic Blueprint: Advances in Pathway Diversification in Microorganisms. Front Microbiol, 2018. 9: p. 155. http://doi.org/10.3389/fmicb.2018.00155
Copp, J. N., Akiva, E., Babbitt, P. C., Tokuriki, N., Revealing Unexplored Sequence-Function Space Using Sequence Similarity Networks. Biochemistry, 2018. 57(31): p. 4651-4662. http://doi.org/10.1021/acs.biochem.8b00473
Carter, M. S., Zhang, X., Huang, H., Bouvier, J. T., Francisco, B. S., Vetting, M. W., Al-Obaidi, N., Bonanno, J. B., Ghosh, A., Zallot, R. G., Andersen, H. M., Almo, S. C., Gerlt, J. A., Functional assignment of multiple catabolic pathways for D-apiose. Nat Chem Biol, 2018. 14(7): p. 696-705. http://doi.org/10.1038/s41589-018-0067-7
Li, B. C., Zhang, T., Li, Y. Q., Ding, G. B., Target Discovery of Novel alpha-L-Rhamnosidases from Human Fecal Metagenome and Application for Biotransformation of Natural Flavonoid Glycosides. Appl Biochem Biotechnol, 2019. 189(4): p. 1245-1261. http://doi.org/10.1007/s12010-019-03063-5
Erb, T. J, Back to the future: Why we need enzymology to build a synthetic metabolism of the future. Beilstein journal of organic chemistry, 2019. 15(1): p. 551-557. http://doi.org/10.3762/bjoc.15.49
Ji, X., Mo, T., Liu, W. Q., Ding, W., Deng, Z., Zhang, Q., Revisiting the Mechanism of the Anaerobic Coproporphyrinogen III Oxidase HemN. Angew Chem Int Ed Engl, 2019. 58(19): p. 6235-6238. http://doi.org/10.1002/anie.201814708
Harrison, A. O, Moore, R. M, Polson, S. W., Wommack, K E., Reannotation of the ribonucleotide reductase in a cyanophage reveals life history strategies within the virioplankton. Frontiers in microbiology, 2019. 10: p. 134. http://doi.org/10.3389/fmicb.2019.00134
Vu, V. V., Hangasky, J. A., Detomasi, T. C., Henry, S. J. W., Ngo, S. T., Span, E. A., Marletta, M. A., Substrate selectivity in starch polysaccharide monooxygenases. J Biol Chem, 2019. 294(32): p. 12157-12166. http://doi.org/10.1074/jbc.RA119.009509
Guo, J., Higgins, M. A, Daniel-Ivad, P., Ryan, K. S, An Asymmetric Reductase that Intercepts Acyclic Imino Acids Produced In Situ by a Partner Oxidase. Journal of the American Chemical Society, 2019. 141(31): p. 12258-12267. http://doi.org/10.1021/jacs.9b03307
Pongpamorn, P., Watthaisong, P., Pimviriyakul, P., Jaruwat, A., Lawan, N., Chitnumsub, P., Chaiyen, P., Identification of a Hotspot Residue for Improving the Thermostability of a Flavin-Dependent Monooxygenase. Chembiochem, 2019. 20(24): p. 3020-3031. http://doi.org/10.1002/cbic.201900413
Giessen, T. W., Orlando, B. J., Verdegaal, A. A., Chambers, M. G., Gardener, J., Bell, D. C., Birrane, G., Liao, M., Silver, P. A., Large protein organelles form a new iron sequestration system with high storage capacity. Elife, 2019. 8:. http://doi.org/10.7554/eLife.46070
Sutzl, L., Foley, G., Gillam, E. M. J., Boden, M., Haltrich, D., The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductases. Biotechnol Biofuels, 2019. 12(1): p. 118. http://doi.org/10.1186/s13068-019-1457-0
Hangasky, J. A, Detomasi, T. C, Marletta, M. A, Glycosidic bond hydroxylation by polysaccharide monooxygenases. Trends in Chemistry, 2019. http://doi.org/10.1016/j.trechm.2019.01.007
Bobeica, S. C, Dong, S., Huo, L., Mazo, N., McLaughlin, M. I, Jimenez-Oses, G., Nair, S. K, van der Donk, W. A, Insights into AMS/PCAT transporters from biochemical and structural characterization of a double Glycine motif protease. eLife, 2019. 8: p. e42305. http://doi.org/10.7554/eLife.42305
Yin, L., Harwood, C. S., Functional divergence of annotated l-isoaspartate O-methyltransferases in an alpha-proteobacterium. J Biol Chem, 2019. 294(8): p. 2854-2861. http://doi.org/10.1074/jbc.RA118.006546
Wu, Y., Wu, R., Mandalapu, D., Ji, X., Chen, T., Ding, W., Zhang, Q., Radical SAM-dependent adenosylation catalyzed by l-tyrosine lyases. Org Biomol Chem, 2019. 17(7): p. 1809-1812. http://doi.org/10.1039/c8ob02906g
Rajakovich, L. J., Balskus, E. P., Metabolic functions of the human gut microbiota: the role of metalloenzymes. Nat Prod Rep, 2019. 36(4): p. 593-625. http://doi.org/10.1039/c8np00074c
Mandalapu, D., Ji, X., Zhang, Q., Reductive Cleavage of Sulfoxide and Sulfone by Two Radical S-Adenosyl-l-methionine Enzymes. Biochemistry, 2019. 58(1): p. 36-39. http://doi.org/10.1021/acs.biochem.8b00844
Lin, G., Warden-Rothman, R., Voigt, C. A, Retrosynthetic design of metabolic pathways to chemicals not found in nature. Current Opinion in Systems Biology, 2019. http://doi.org/10.1016/j.coisb.2019.04.004
Malik, A., Kim, S. B., A comprehensive in silico analysis of sortase superfamily. J Microbiol, 2019. 57(6): p. 431-443. http://doi.org/10.1007/s12275-019-8545-5
Jia, B., Yuan, D. P., Lan, W. J., Xuan, Y. H., Jeon, C. O., New insight into the classification and evolution of glucose transporters in the Metazoa. The FASEB Journal, 2019. 33(6): p. 7519-7528. http://doi.org/10.1096/fj.201802617R
Rose, H. R., Maggiolo, A. O., McBride, M. J., Palowitch, G. M., Pandelia, M. E., Davis, K. M., Yennawar, N. H., Boal, A. K., Structures of Class Id Ribonucleotide Reductase Catalytic Subunits Reveal a Minimal Architecture for Deoxynucleotide Biosynthesis. Biochemistry, 2019. 58(14): p. 1845-1860. http://doi.org/10.1021/acs.biochem.8b01252
Rizzolo, K., Cohen, S. E, Weitz, A. C, Muñoz, M. M L., Hendrich, M. P, Drennan, C. L, Elliott, S. J, A widely distributed diheme enzyme from Burkholderia that displays an atypically stable bis-Fe (IV) state. Nature communications, 2019. 10(1): p. 1101. http://doi.org/10.1038/s41467-019-09020-4
Blaby-Haas, C. E., Merchant, S. S., Comparative and Functional Algal Genomics. Annu Rev Plant Biol, 2019. 70: p. 605-638. http://doi.org/10.1146/annurev-arplant-050718-095841
Gama, S. R, Vogt, M., Kalina, T., Hupp, K., Hammerschmidt, F., Pallitsch, K., Zechel, D. L, An oxidative pathway for microbial utilization of methylphosphonic acid as a phosphate source. ACS chemical biology, 2019. 14(4): p. 735-741. http://doi.org/10.1021/acschembio.9b00024
Rajakovich, L. J., Pandelia, M. E., Mitchell, A. J., Chang, W. C., Zhang, B., Boal, A. K., Krebs, C., Bollinger, J. M. Jr., A New Microbial Pathway for Organophosphonate Degradation Catalyzed by Two Previously Misannotated Non-Heme-Iron Oxygenases. Biochemistry, 2019. 58(12): p. 1627-1647. http://doi.org/10.1021/acs.biochem.9b00044
Rolf, J., Rosenthal, K., Lütz, S., Application of Cell-Free Protein Synthesis for Faster Biocatalyst Development. Catalysts, 2019. 9(2): p. 190. http://doi.org/10.3390/catal9020190
Pellock, S. J, Walton, W. G, Redinbo, M. R, Selecting a Single Stereocenter: The Molecular Nuances That Differentiate β-Hexuronidases in the Human Gut Microbiome. Biochemistry, 2019. 58(9): p. 1311-1317. http://doi.org/10.1021/acs.biochem.8b01285
Zhang, Y., Blaby-Haas, C. E, Steimle, S., Verissimo, A. F, Garcia-Angulo, V. A, Koch, H., Daldal, F., Khalfaoui-Hassani, B., Cu Transport by the Extended Family of C co A-l ike T ransporters (CalT) in Proteobacteria. Scientific reports, 2019. 9(1): p. 1208. http://doi.org/10.1038/s41598-018-37988-4
Zhou, Y., Wei, Y., Lin, L., Xu, T., Ang, E. L., Zhao, H., Yuchi, Z., Zhang, Y., Biochemical and structural investigation of sulfoacetaldehyde reductase from Klebsiella oxytoca. Biochem J, 2019. 476(4): p. 733-746. http://doi.org/10.1042/BCJ20190005
Biernat, K. A., Pellock, S. J., Bhatt, A. P., Bivins, M. M., Walton, W. G., Tran, B. N. T., Wei, L., Snider, M. C., Cesmat, A. P., Tripathy, A., Erie, D. A., Redinbo, M. R., Structure, function, and inhibition of drug reactivating human gut microbial beta-glucuronidases. Sci Rep, 2019. 9(1): p. 825. http://doi.org/10.1038/s41598-018-36069-w
Maresca, J. A., Keffer, J. L., Hempel, P. P., Polson, S. W., Shevchenko, O., Bhavsar, J., Powell, D., Miller, K. J., Singh, A., Hahn, M. W., Light Modulates the Physiology of Nonphototrophic Actinobacteria. J Bacteriol, 2019. 201(10): p. e00740-18. http://doi.org/10.1128/JB.00740-18
Pellock, S. J., Walton, W. G., Ervin, S. M., Torres-Rivera, D., Creekmore, B. C., Bergan, G., Dunn, Z. D., Li, B., Tripathy, A., Redinbo, M. R., Discovery and Characterization of FMN-Binding beta-Glucuronidases in the Human Gut Microbiome. J Mol Biol, 2019. 431(5): p. 970-980. http://doi.org/10.1016/j.jmb.2019.01.013
Gonzalez, J. M., Hernandez, L., Manzano, I., Pedros-Alio, C., Functional annotation of orthologs in metagenomes: a case study of genes for the transformation of oceanic dimethylsulfoniopropionate. ISME J, 2019. 13(5): p. 1183-1197. http://doi.org/10.1038/s41396-019-0347-6
Dong, L. B., Liu, Y. C., Cepeda, A. J., Kalkreuter, E., Deng, M. R., Rudolf, J. D., Chang, C., Joachimiak, A., Phillips, G. N. Jr., Shen, B., Characterization and Crystal Structure of a Nonheme Diiron Monooxygenase Involved in Platensimycin and Platencin Biosynthesis. J Am Chem Soc, 2019. 141(31): p. 12406-12412. http://doi.org/10.1021/jacs.9b06183
Dunbar, K. L, Dell, M., Molloy, E. M, Kloss, F., Hertweck, C., Reconstitution of Iterative Thioamidation in Closthioamide Biosynthesis Reveals a Novel Nonribosomal Peptide Backbone‐Tailoring Strategy. Angewandte Chemie, 2019. 58(37): p. 13014-13018. http://doi.org/10.1002/anie.201905992
Gumkowski, J. D, Martinie, R. J, Corrigan, P., Pan, J., Bauerle, M. R, Almarei, M., Booker, S. J, Silakov, A., Krebs, C., Boal, A. K, Analysis of RNA methylation by phylogenetically diverse Cfr radical SAM enzymes reveals an iron-binding accessory domain in a clostridial enzyme. Biochemistry, 2019. 58(29): p. 3169-3184. http://doi.org/10.1021/acs.biochem.9b00197
Khavrutskii, I. V, Compton, J. R, Jurkouich, K., Legler, P. M, Paired Carboxylic Acids in Enzymes and their Role in Selective Substrate Binding, Catalysis, and Unusually Shifted pKa Values. Biochemistry, 2019. 58(52): p. 5351-5365. http://doi.org/10.1021/acs.biochem.9b00429
Jaroensuk, J., Intasian, P., Kiattisewee, C., Munkajohnpon, P., Chunthaboon, P., Buttranon, S., Trisrivirat, D., Wongnate, T., Maenpuen, S., Tinikul, R., Chaiyen, P., Addition of formate dehydrogenase increases the production of renewable alkane from an engineered metabolic pathway. J Biol Chem, 2019. 294(30): p. 11536-11548. http://doi.org/10.1074/jbc.RA119.008246
Kraberger, S., Schmidlin, K., Fontenele, R. S., Walters, M., Varsani, A., Unravelling the Single-Stranded DNA Virome of the New Zealand Blackfly. Viruses, 2019. 11(6): p. 532. http://doi.org/10.3390/v11060532
Morgan, G. L., Kretsch, A. M., Santa Maria, K. C., Weeks, S. J., Li, B., Specificity of Nonribosomal Peptide Synthetases in the Biosynthesis of the Pseudomonas virulence factor. Biochemistry, 2019. 58(52): p. 5249-5254. http://doi.org/10.1021/acs.biochem.9b00360
Tong, Y., Wei, Y., Hu, Y., Ang, E. L., Zhao, H., Zhang, Y., A Pathway for Isethionate Dissimilation in Bacillus krulwichiae. Appl Environ Microbiol, 2019. 85(15): p. AEM. 00793-19. http://doi.org/10.1128/AEM.00793-19
Chekan, J. R., Lee, G. Y., El Gamal, A., Purdy, T. N., Houk, K. N., Moore, B. S., Bacterial Tetrabromopyrrole Debrominase Shares a Reductive Dehalogenation Strategy with Human Thyroid Deiodinase. Biochemistry, 2019. 58(52): p. 5329-5338. http://doi.org/10.1021/acs.biochem.9b00318
Radle, M. I, Miller, D. V, Laremore, T. N, Booker, S. J, Methanogenesis marker protein 10 (Mmp10) from Methanosarcina acetivorans is a radical S-adenosylmethionine methylase that unexpectedly requires cobalamin. Journal of Biological Chemistry, 2019. 294(11712-11725): p. jbc. RA119. 007609. http://doi.org/10.1074/jbc.RA119.007609
Hepowit, N. L., Maupin-Furlow, J. A., Rhodanese-Like Domain Protein UbaC and Its Role in Ubiquitin-Like Protein Modification and Sulfur Mobilization in Archaea. J Bacteriol, 2019. 201(15): p. JB. 00254-19. http://doi.org/10.1128/JB.00254-19
Clark, J., Terwilliger, A., Nguyen, C., Green, S., Nobles, C., Maresso, A., Heme catabolism in the causative agent of anthrax. Mol Microbiol, 2019. 112(2): p. 515-531. http://doi.org/10.1111/mmi.14270
Hudson, G. A, Burkhart, B. J, DiCaprio, A. J, Schwalen, C., Kille, B., Pogorelov, T. V, Mitchell, D. A, Bioinformatic mapping of radical SAM-dependent RiPPs identifies new Cα, Cβ, and Cγ-linked thioether-containing peptides. Journal of the American Chemical Society, 2019. 141(20): p. 8228-8238. http://doi.org/10.1021/jacs.9b01519.
Dong, S. H., Liu, A., Mahanta, N., Mitchell, D. A., Nair, S. K., Mechanistic Basis for Ribosomal Peptide Backbone Modifications. ACS Cent Sci, 2019. 5(5): p. 842-851. http://doi.org/10.1021/acscentsci.9b00124
Bashiri, G., Antoney, J., Jirgis, E. N., Shah, M. V, Ney, B., Copp, J., Stuteley, S. M, Sreebhavan, S., Palmer, B., Middleditch, M., A revised biosynthetic pathway for the cofactor F 420 in prokaryotes. Nature communications, 2019. 10(1): p. 1558. http://doi.org/10.1038/s41467-019-09534-x
Chen, W., Frantom, P. A., Distinct mechanisms of substrate selectivity in the DRE-TIM metallolyase superfamily: A role for the LeuA dimer regulatory domain. Arch Biochem Biophys, 2019. 664: p. 1-8. http://doi.org/10.1016/j.abb.2019.01.021
Mahanta, N., Hicks, K. A., Naseem, S., Zhang, Y., Fedoseyenko, D., Ealick, S. E., Begley, T. P., Menaquinone Biosynthesis: Biochemical and Structural Studies of Chorismate Dehydratase. Biochemistry, 2019. 58(14): p. 1837-1840. http://doi.org/10.1021/acs.biochem.9b00105
Scott, T. A., Piel, J., The hidden enzymology of bacterial natural product biosynthesis. Nat Rev Chem, 2019. 3(7): p. 404-425. http://doi.org/10.1038/s41570-019-0107-1
Copp, J. N, Anderson, D. W, Akiva, E., Babbitt, P. C, Tokuriki, N., Exploring the sequence, function, and evolutionary space of protein superfamilies using sequence similarity networks and phylogenetic reconstructions. Methods in enzymology, 2019. 620: p. 315-347. http://doi.org/10.1016/bs.mie.2019.03.015
Hai, Y., Huang, A. M., Tang, Y., Structure-guided function discovery of an NRPS-like glycine betaine reductase for choline biosynthesis in fungi. Proc Natl Acad Sci U S A, 2019. 116(21): p. 10348-10353. http://doi.org/10.1073/pnas.1903282116
Shi, J., Liu, C. L., Zhang, B., Guo, W. J., Zhu, J., Chang, C., Zhao, E. J., Jiao, R. H., Tan, R. X., Ge, H. M., Genome mining and biosynthesis of kitacinnamycins as a STING activator. Chemical science, 2019. 10(18): p. 4839-4846. http://doi.org/10.1039/c9sc00815b
Morishita, Y., Zhang, H., Taniguchi, T., Mori, K., Asai, T., The Discovery of Fungal Polyene Macrolides via a Postgenomic Approach Reveals a Polyketide Macrocyclization by trans-Acting Thioesterase in Fungi. Org Lett, 2019. 21(12): p. 4788-4792. http://doi.org/10.1021/acs.orglett.9b01674
Chekan, J. R., Ongpipattanakul, C., Wright, T. R., Zhang, B., Bollinger, J. M. Jr., Rajakovich, L. J., Krebs, C., Cicchillo, R. M., Nair, S. K., Molecular basis for enantioselective herbicide degradation imparted by aryloxyalkanoate dioxygenases in transgenic plants. Proc Natl Acad Sci U S A, 2019. 116(27): p. 13299-13304. http://doi.org/10.1073/pnas.1900711116
Ting, C. P, Funk, M. A, Halaby, S. L, Zhang, Z., Gonen, T., van der Donk, W. A, Use of a scaffold peptide in the biosynthesis of amino acid–derived natural products. Science, 2019. 365(6450): p. 280-284. http://doi.org/10.1126/science.aau6232
Lefeuvre, P., Martin, D. P., Elena, S. F., Shepherd, D. N., Roumagnac, P., Varsani, A., Evolution and ecology of plant viruses. Nat Rev Microbiol, 2019. 17(10): p. 632-644. http://doi.org/10.1038/s41579-019-0232-3
Mo, T., Yuan, H., Wang, F., Ma, S., Wang, J., Li, T., Liu, G., Yu, S., Tan, X., Ding, W., Zhang, Q., Convergent evolution of the Cys decarboxylases involved in aminovinyl-cysteine (AviCys) biosynthesis. FEBS Lett, 2019. 593(6): p. 573-580. http://doi.org/10.1002/1873-3468.13341
Chen, D., Zhao, Q., Liu, W., Discovery of caerulomycin/collismycin-type 2,2'-bipyridine natural products in the genomic era. J Ind Microbiol Biotechnol, 2019. 46(3-4): p. 459-468. http://doi.org/10.1007/s10295-018-2092-7
Amatuni, A., Renata, H., Identification of a lysine 4-hydroxylase from the glidobactin biosynthesis and evaluation of its biocatalytic potential. Org Biomol Chem, 2019. 17(7): p. 1736-1739. http://doi.org/10.1039/c8ob02054j
Niehs, S. P., Dose, B., Scherlach, K., Pidot, S. J., Stinear, T. P., Hertweck, C., Genome Mining Reveals Endopyrroles from a Nonribosomal Peptide Assembly Line Triggered in Fungal-Bacterial Symbiosis. ACS Chem Biol, 2019. 14(8): p. 1811-1818. http://doi.org/10.1021/acschembio.9b00406
Liu, J., Lin, Z., Li, Y., Zheng, Q., Chen, D., Liu, W., Insights into the thioamidation of thiopeptins to enhance the understanding of the biosynthetic logic of thioamide-containing thiopeptides. Org Biomol Chem, 2019. 17(15): p. 3727-3731. http://doi.org/10.1039/c9ob00402e
Clark, K. A., Bushin, L. B., Seyedsayamdost, M. R., Aliphatic Ether Bond Formation Expands the Scope of Radical SAM Enzymes in Natural Product Biosynthesis. J Am Chem Soc, 2019. 141(27): p. 10610-10615. http://doi.org/10.1021/jacs.9b05151
Zhi, Y., Narindoshvili, T., Bogomolnaya, L., Talamantes, M., El Saadi, A., Andrews-Polymenis, H., Raushel, F. M., Deciphering the Enzymatic Function of the Bovine Enteric Infection-Related Protein YfeJ from Salmonella enterica Serotype Typhimurium. Biochemistry, 2019. 58(9): p. 1236-1245. http://doi.org/10.1021/acs.biochem.8b01283
Mukherjee, K., Huddleston, J. P., Narindoshvili, T., Nemmara, V. V., Raushel, F. M., Functional Characterization of the ycjQRS Gene Cluster from Escherichia coli: A Novel Pathway for the Transformation of d-Gulosides to d-Glucosides. Biochemistry, 2019. 58(10): p. 1388-1399. http://doi.org/10.1021/acs.biochem.8b01278
Tsui, H. S., Pham, N. V. B., Amer, B. R., Bradley, M. C., Gosschalk, J. E., Gallagher-Jones, M., Ibarra, H., Clubb, R. T., Blaby-Haas, C. E., Clarke, C. F., Human COQ10A and COQ10B are distinct lipid-binding START domain proteins required for coenzyme Q function. J Lipid Res, 2019. 60(7): p. 1293-1310. http://doi.org/10.1194/jlr.M093534
Zhang, R., Xu, X., Cao, H., Yuan, C., Yuminaga, Y., Zhao, S., Shi, J., Zhang, B., Purification, characterization, and application of a high activity 3-ketosteroid-Delta(1)-dehydrogenase from Mycobacterium neoaurum DSM 1381. Appl Microbiol Biotechnol, 2019. 103(16): p. 6605-6616. http://doi.org/10.1007/s00253-019-09988-5
Coscolin, C., Katzke, N., Garcia-Moyano, A., Navarro-Fernandez, J., Almendral, D., Martinez-Martinez, M., Bollinger, A., Bargiela, R., Gertler, C., Chernikova, T. N., Rojo, D., Barbas, C., Tran, H., Golyshina, O. V., Koch, R., Yakimov, M. M., Bjerga, G. E. K., Golyshin, P. N., Jaeger, K. E., Ferrer, M., Bioprospecting Reveals Class III omega-Transaminases Converting Bulky Ketones and Environmentally Relevant Polyamines. Appl Environ Microbiol, 2019. 85(2):. http://doi.org/10.1128/AEM.02404-18
Sikandar, A., Franz, L., Melse, O., Antes, I., Koehnke, J., Thiazoline-Specific Amidohydrolase PurAH Is the Gatekeeper of Bottromycin Biosynthesis. J Am Chem Soc, 2019. 141(25): p. 9748-9752. http://doi.org/10.1021/jacs.8b12231
Wang, Y., Shin, I., Fu, Y., Colabroy, K. L., Liu, A., Crystal Structures of L-DOPA Dioxygenase from Streptomyces sclerotialus. Biochemistry, 2019. 58(52): p. 5339-5350. http://doi.org/10.1021/acs.biochem.9b00396
Lee, S., Kang, J., Kim, J., Structural and biochemical characterization of Rv0187, an O-methyltransferase from Mycobacterium tuberculosis. Sci Rep, 2019. 9(1): p. 8059. http://doi.org/10.1038/s41598-019-44592-7
DiCaprio, A. J, Firouzbakht, A., Hudson, G. A., Mitchell, D. A., Enzymatic Reconstitution and Biosynthetic Investigation of the Lasso Peptide Fiusilassin. J Am Chem Soc, 2019. 141(1): p. 290-297. http://doi.org/10.1021/jacs.8b09928
Peck, S. C., Denger, K., Burrichter, A., Irwin, S. M., Balskus, E. P., Schleheck, D., A glycyl radical enzyme enables hydrogen sulfide production by the human intestinal bacterium Bilophila wadsworthia. Proc Natl Acad Sci U S A, 2019. 116(8): p. 3171-3176. http://doi.org/10.1073/pnas.1815661116
Caruso, A., Bushin, L. B., Clark, K. A., Martinie, R. J., Seyedsayamdost, M. R., Radical Approach to Enzymatic beta-Thioether Bond Formation. J Am Chem Soc, 2019. 141(2): p. 990-997. http://doi.org/10.1021/jacs.8b11060
Hermenau, R., Mehl, J. L., Ishida, K., Dose, B., Pidot, S. J., Stinear, T. P., Hertweck, C., Genomics-Driven Discovery of NO-Donating Diazeniumdiolate Siderophores in Diverse Plant-Associated Bacteria. Angew Chem Int Ed Engl, 2019. 58(37): p. 13024-13029. http://doi.org/10.1002/anie.201906326
Zhang, D., Zhang, F., Liu, W., A KAS-III Heterodimer in Lipstatin Biosynthesis Nondecarboxylatively Condenses C8 and C14 Fatty Acyl-CoA Substrates by a Variable Mechanism during the Establishment of a C22 Aliphatic Skeleton. J Am Chem Soc, 2019. 141(9): p. 3993-4001. http://doi.org/10.1021/jacs.8b12843
Helfrich, E. J. N., Ueoka, R., Dolev, A., Rust, M., Meoded, R. A., Bhushan, A., Califano, G., Costa, R., Gugger, M., Steinbeck, C., Moreno, P., Piel, J., Automated structure prediction of trans-acyltransferase polyketide synthase products. Nat Chem Biol, 2019. 15(8): p. 813-821. http://doi.org/10.1038/s41589-019-0313-7
Sieow, B. F., Nurminen, T. J., Ling, H., Chang, M. W., Meta-Omics- and Metabolic Modeling-Assisted Deciphering of Human Microbiota Metabolism. Biotechnol J, 2019. 14(9): p. e1800445. http://doi.org/10.1002/biot.201800445
Fontenele, R. S., Lacorte, C., Lamas, N. S., Schmidlin, K., Varsani, A., Ribeiro, S. G., Single Stranded DNA Viruses Associated with Capybara Faeces Sampled in Brazil. Viruses, 2019. 11(8):. http://doi.org/10.3390/v11080710
Desmarais, J. J., Flamholz, A. I., Blikstad, C., Dugan, E. J., Laughlin, T. G., Oltrogge, L. M., Chen, A. W., Wetmore, K., Diamond, S., Wang, J. Y., Savage, D. F., DABs are inorganic carbon pumps found throughout prokaryotic phyla. Nat Microbiol, 2019. 4(12): p. 2204-2215. http://doi.org/10.1038/s41564-019-0520-8
You, J., Lin, S., Jiang, T., Origins and Evolution of the alpha-L-Fucosidases: From Bacteria to Metazoans. Front Microbiol, 2019. 10: p. 1756. http://doi.org/10.3389/fmicb.2019.01756
Huddleston, J. P., Raushel, F. M., Biosynthesis of GDP-d-glycero-alpha-d-manno-heptose for the Capsular Polysaccharide of Campylobacter jejuni. Biochemistry, 2019. 58(37): p. 3893-3902. http://doi.org/10.1021/acs.biochem.9b00548
Huddleston, J. P., Raushel, F. M., Functional Characterization of YdjH, a Sugar Kinase of Unknown Specificity in Escherichia coli K12. Biochemistry, 2019. 58(31): p. 3354-3364. http://doi.org/10.1021/acs.biochem.9b00327
Huddleston, J. P., Thoden, J. B., Dopkins, B. J., Narindoshvili, T., Fose, B. J., Holden, H. M., Raushel, F. M., Structural and Functional Characterization of YdjI, an Aldolase of Unknown Specificity in Escherichia coli K12. Biochemistry, 2019. 58(31): p. 3340-3353. http://doi.org/10.1021/acs.biochem.9b00326
Neupane, D. P., Fullam, S. H., Chacon, K. N., Yukl, E. T., Crystal structures of AztD provide mechanistic insights into direct zinc transfer between proteins. Commun Biol, 2019. 2: p. 308. http://doi.org/10.1038/s42003-019-0542-z
Yuan, Y., Zallot, R., Grove, T. L., Payan, D. J., Martin-Verstraete, I., Sepic, S., Balamkundu, S., Neelakandan, R., Gadi, V. K., Liu, C. F., Swairjo, M. A., Dedon, P. C., Almo, S. C., Gerlt, J. A., de Crecy-Lagard, V., Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens. Proc Natl Acad Sci U S A, 2019. 116(38): p. 19126-19135. http://doi.org/10.1073/pnas.1909604116
Danczak, R. E., Johnston, M. D., Kenah, C., Slattery, M., Wilkins, M. J., Capability for arsenic mobilization in groundwater is distributed across broad phylogenetic lineages. PLoS One, 2019. 14(9): p. e0221694. http://doi.org/10.1371/journal.pone.0221694
Umana, A., Sanders, B. E., Yoo, C. C., Casasanta, M. A., Udayasuryan, B., Verbridge, S. S., Slade, D. J., Utilizing Whole Fusobacterium Genomes To Identify, Correct, and Characterize Potential Virulence Protein Families. J Bacteriol, 2019. 201(23):. http://doi.org/10.1128/JB.00273-19
Ganley, J. G., D'Ambrosio, H. K., Shieh, M., Derbyshire, E. R., Coculturing of Mosquito-Microbiome Bacteria Promotes Heme Degradation in Elizabethkingia anophelis. Chembiochem, 2019. http://doi.org/10.1002/cbic.201900675
Hutinet, G., Kot, W., Cui, L., Hillebrand, R., Balamkundu, S., Gnanakalai, S., Neelakandan, R., Carstens, A. B., Fa Lui, C., Tremblay, D., Jacobs-Sera, D., Sassanfar, M., Lee, Y. J., Weigele, P., Moineau, S., Hatfull, G. F., Dedon, P. C., Hansen, L. H., de Crecy-Lagard, V., 7-Deazaguanine modifications protect phage DNA from host restriction systems. Nat Commun, 2019. 10(1): p. 5442. http://doi.org/10.1038/s41467-019-13384-y
Liu, Y., Su, L., Fang, Q., Tabudravu, J., Yang, X., Rickaby, K., Trembleau, L., Kyeremeh, K., Deng, Z., Deng, H., Yu, Y., Enzymatic Reconstitution and Biosynthetic Investigation of the Bacterial Carbazole Neocarazostatin A. J Org Chem, 2019. 84(24): p. 16323-16328. http://doi.org/10.1021/acs.joc.9b02688
Rodriguez Benitez, A., Narayan, A. R. H., Frontiers in Biocatalysis: Profiling Function across Sequence Space. ACS Cent Sci, 2019. 5(11): p. 1747-1749. http://doi.org/10.1021/acscentsci.9b01112
Pyser, J. B., Baker Dockrey, S. A., Benitez, A. R., Joyce, L. A., Wiscons, R. A., Smith, J. L., Narayan, A. R. H., Stereodivergent, Chemoenzymatic Synthesis of Azaphilone Natural Products. J Am Chem Soc, 2019. 141(46): p. 18551-18559. http://doi.org/10.1021/jacs.9b09385
Ervin, S. M., Hanley, R. P., Lim, L., Walton, W. G., Pearce, K. H., Bhatt, A. P., James, L. I., Redinbo, M. R., Targeting Regorafenib-Induced Toxicity through Inhibition of Gut Microbial beta-Glucuronidases. ACS Chem Biol, 2019. 14(12): p. 2737-2744. http://doi.org/10.1021/acschembio.9b00663
Bell, A., Brunt, J., Crost, E., Vaux, L., Nepravishta, R., Owen, C. D., Latousakis, D., Xiao, A., Li, W., Chen, X., Walsh, M. A., Claesen, J., Angulo, J., Thomas, G. H., Juge, N., Elucidation of a sialic acid metabolism pathway in mucus-foraging Ruminococcus gnavus unravels mechanisms of bacterial adaptation to the gut. Nat Microbiol, 2019. 4(12): p. 2393-2404. http://doi.org/10.1038/s41564-019-0590-7
Zwick, C. R. 3rd, Sosa, M. B., Renata, H., Characterization of a Citrulline 4-Hydroxylase from Nonribosomal Peptide GE81112 Biosynthesis and Engineering of Its Substrate Specificity for the Chemoenzymatic Synthesis of Enduracididine. Angew Chem Int Ed Engl, 2019. 58(52): p. 18854-18858. http://doi.org/10.1002/anie.201910659
Hager, F. F., Sutzl, L., Stefanovic, C., Blaukopf, M., Schaffer, C., Pyruvate Substitutions on Glycoconjugates. Int J Mol Sci, 2019. 20(19):. http://doi.org/10.3390/ijms20194929
Travis, S., Shay, Madeline R., Manabe, S., Gilbert, Nathaniel C., Frantom, Patrick A., Thompson, Matthew K., Characterization of the genomically encoded fosfomycin resistance enzyme from Mycobacterium abscessus. MedChemComm, 2019. 10(11): p. 1948-1957. http://doi.org/10.1039/c9md00372j
Ervin, S. M., Li, H., Lim, L., Roberts, L. R., Liang, X., Mani, S., Redinbo, M. R., Gut microbial beta-glucuronidases reactivate estrogens as components of the estrobolome that reactivate estrogens. J Biol Chem, 2019. 294(49): p. 18586-18599. http://doi.org/10.1074/jbc.RA119.010950
Gomez-Escribano, J. P., Castro, J. F., Razmilic, V., Jarmusch, S. A., Saalbach, G., Ebel, R., Jaspars, M., Andrews, B., Asenjo, J. A., Bibb, M. J., Heterologous Expression of a Cryptic Gene Cluster from Streptomyces leeuwenhoekii C34(T) Yields a Novel Lasso Peptide, Leepeptin. Appl Environ Microbiol, 2019. 85(23):. http://doi.org/10.1128/AEM.01752-19
Ji, Z. Y., Nie, Q. Y., Yin, Y., Zhang, M., Pan, H. X., Hou, X. F., Tang, G. L., Activation and Characterization of Cryptic Gene Cluster: Two Series of Aromatic Polyketides Biosynthesized by Divergent Pathways. Angew Chem Int Ed Engl, 2019. 58(50): p. 18046-18054. http://doi.org/10.1002/anie.201910882
Neugebauer, M.E., Sumida, K.H., Pelton, J.G., McMurry, J.L., Marchand, J.A., Chang, M.C.Y., A family of radical halogenases for the engineering of amino-acid-based products. Nature chemical biology, 2019. 15(10): p. 1009-1016. http://doi.org/10.1038/s41589-019-0355-x
Weiz, G., Mazzaferro, L. S., Kotik, M., Neher, B. D., Halada, P., Kren, V., Breccia, J. D., The flavonoid degrading fungus Acremonium sp. DSM 24697 produces two diglycosidases with different specificities. Appl Microbiol Biotechnol, 2019. 103(23-24): p. 9493-9504. http://doi.org/10.1007/s00253-019-10180-y
Campbell, I. J., Bennett, G. N., Silberg, J. J., Evolutionary Relationships Between Low Potential Ferredoxin and Flavodoxin Electron Carriers. Front Energy Res, 2019. 7:. http://doi.org/10.3389/fenrg.2019.00079
Fisher, B. F., Snodgrass, H. M., Jones, K. A., Andorfer, M. C., Lewis, J. C., Site-Selective C-H Halogenation Using Flavin-Dependent Halogenases Identified via Family-Wide Activity Profiling. ACS Cent Sci, 2019. 5(11): p. 1844-1856. http://doi.org/10.1021/acscentsci.9b00835
Marckmann, D., Trasnea, P. I., Schimpf, J., Winterstein, C., Andrei, A., Schmollinger, S., Blaby-Haas, C. E., Friedrich, T., Daldal, F., Koch, H. G., The cbb 3-type cytochrome oxidase assembly factor CcoG is a widely distributed cupric reductase. Proc Natl Acad Sci U S A, 2019. 116(42): p. 21166-21175. http://doi.org/10.1073/pnas.1913803116
Kenney, G. E., Dassama, L. M. K., Manesis, A. C., Ross, M. O., Chen, S., Hoffman, B. M., Rosenzweig, A. C., MbnH is a diheme MauG-like protein associated with microbial copper homeostasis. J Biol Chem, 2019. 294(44): p. 16141-16151. http://doi.org/10.1074/jbc.RA119.010202
Reis, R. A. G., Salvi, F., Williams, I., Gadda, G., Kinetic Investigation of a Presumed Nitronate Monooxygenase from Pseudomonas aeruginosa PAO1 Establishes a New Class of NAD(P)H:Quinone Reductases. Biochemistry, 2019. 58(22): p. 2594-2607. http://doi.org/10.1021/acs.biochem.9b00207
Chekan, J. R., Ongpipattanakul, C., Nair, S. K., Steric complementarity directs sequence promiscuous leader binding in RiPP biosynthesis. Proc Natl Acad Sci U S A, 2019. 116(48): p. 24049-24055. http://doi.org/10.1073/pnas.1908364116
Bruno, S., Coppola, D., di Prisco, G., Giordano, D., Verde, C., Enzymes from Marine Polar Regions and Their Biotechnological Applications. Mar Drugs, 2019. 17(10):. http://doi.org/10.3390/md17100544
Xing, M., Wei, Y., Zhou, Y., Zhang, J., Lin, L., Hu, Y., Hua, G., N. Nanjaraj Urs A, , Liu, D., Wang, F., Guo, C., Tong, Y., Li, M., Liu, Y., Ang, E. L., Zhao, H., Yuchi, Z., Zhang, Y., Radical-mediated C-S bond cleavage in C2 sulfonate degradation by anaerobic bacteria. Nat Commun, 2019. 10(1): p. 1609. http://doi.org/10.1038/s41467-019-09618-8
Canu, N., Moutiez, M., Belin, P., Gondry, M., Cyclodipeptide synthases: a promising biotechnological tool for the synthesis of diverse 2,5-diketopiperazines. Nat Prod Rep, 2020. 37(3): p. 312-321. http://doi.org/10.1039/c9np00036d
Rajendran, A., Vaidya, K., Mendoza, J., Bridwell-Rabb, J., Kamat, S. S., Functional Annotation of ABHD14B, an Orphan Serine Hydrolase Enzyme. Biochemistry, 2020. 59(2): p. 183-196. http://doi.org/10.1021/acs.biochem.9b00703
Surger, M., Angelov, A., Liebl, W., Distribution and diversity of olefins and olefin-biosynthesis genes in Gram-positive bacteria. Biotechnol Biofuels, 2020. 13: p. 70. http://doi.org/10.1186/s13068-020-01706-y
Rocker, A., Lacey, J. A., Belousoff, M. J., Wilksch, J. J., Strugnell, R. A., Davies, M. R., Lithgow, T., Global Trends in Proteome Remodeling of the Outer Membrane Modulate Antimicrobial Permeability in Klebsiella pneumoniae. mBio, 2020. 11(2):. http://doi.org/10.1128/mBio.00603-20
Fontenele, R. S., Salywon, A. M., Majure, L. C., Cobb, I. N., Bhaskara, A., Avalos-Calleros, J. A., Arguello-Astorga, G. R., Schmidlin, K., Khalifeh, A., Smith, K., Schreck, J., Lund, M. C., Kohler, M., Wojciechowski, M. F., Hodgson, W. C., Puente-Martinez, R., Van Doorslaer, K., Kumari, S., Verniere, C., Filloux, D., Roumagnac, P., Lefeuvre, P., Ribeiro, S. G., Kraberger, S., Martin, D. P., Varsani, A., A Novel Divergent Geminivirus Identified in Asymptomatic New World Cactaceae Plants. Viruses, 2020. 12(4):. http://doi.org/10.3390/v12040398
Zhang, C., Chen, X., Orban, A., Shukal, S., Birk, F., Too, H. P., Ruhl, M., Agrocybe aegerita Serves As a Gateway for Identifying Sesquiterpene Biosynthetic Enzymes in Higher Fungi. ACS Chem Biol, 2020. http://doi.org/10.1021/acschembio.0c00155
Tararina, M. A., Allen, K. N., Bioinformatic Analysis of the Flavin-Dependent Amine Oxidase Superfamily: Adaptations for Substrate Specificity and Catalytic Diversity. J Mol Biol, 2020. http://doi.org/10.1016/j.jmb.2020.03.007
Jeoung, J. H., Martins, B. M., Dobbek, H., Double-Cubane [8Fe9S] Clusters: A Novel Nitrogenase-Related Cofactor in Biology. Chembiochem, 2020. http://doi.org/10.1002/cbic.202000016
Ghebreamlak, S. M., Mansoorabadi, S. O., Divergent Members of the Nitrogenase Superfamily: Tetrapyrrole Biosynthesis and Beyond. Chembiochem, 2020. http://doi.org/10.1002/cbic.201900782
Huddleston, J. P., Raushel, F. M., Functional Characterization of Cj1427, a Unique Ping-Pong Dehydrogenase Responsible for the Oxidation of GDP-d-glycero-alpha-d-manno-heptose in Campylobacter jejuni. Biochemistry, 2020. 59(13): p. 1328-1337. http://doi.org/10.1021/acs.biochem.0c00097
Mukhopadhyay, R., Chacon, K. N., Jarvis, J. M., Talipov, M. R., Yukl, E. T., Structural insights into the mechanism of oxidative activation of heme-free H-NOX from Vibrio cholerae. Biochem J, 2020. 477(6): p. 1123-1136. http://doi.org/10.1042/BCJ20200124
Waldern, J., Schiraldi, N. J., Belfort, M., Novikova, O., Bacterial group II intron genomic neighborhoods reflect survival strategies: hiding and hijacking. Mol Biol Evol, 2020. http://doi.org/10.1093/molbev/msaa055
Dhawi, F., Plant Growth Promoting Rhizobacteria (PGPR) Regulated Phyto and Microbial Beneficial Protein Interactions. Open Life Sciences, 2020. 15(1): p. 68-78. http://doi.org/10.1515/biol-2020-0008
Caetano, T., van der Donk, W., Mendo, S., Bacteroidetes can be a rich source of novel lanthipeptides: The case study of Pedobacter lusitanus. Microbiol Res, 2020. 235: p. 126441. http://doi.org/10.1016/j.micres.2020.126441
Ding, W., Ji, X., Zhong, Y., Xu, K., Zhang, Q., Adenosylation reactions catalyzed by the radical S-adenosylmethionine superfamily enzymes. Curr Opin Chem Biol, 2020. 55: p. 86-95. http://doi.org/10.1016/j.cbpa.2020.01.007
Li, J., Amatuni, A., Renata, H., Recent advances in the chemoenzymatic synthesis of bioactive natural products. Curr Opin Chem Biol, 2020. 55: p. 111-118. http://doi.org/10.1016/j.cbpa.2020.01.005
Gorecki, K., McEvoy, M. M., Phylogenetic analysis reveals an ancient gene duplication as the origin of the MdtABC efflux pump. PLoS One, 2020. 15(2): p. e0228877. http://doi.org/10.1371/journal.pone.0228877
Orton, J. P., Morales, M., Fontenele, R. S., Schmidlin, K., Kraberger, S., Leavitt, D. J., Webster, T. H., Wilson, M. A., Kusumi, K., Dolby, G. A., Varsani, A., Virus Discovery in Desert Tortoise Fecal Samples: Novel Circular Single-Stranded DNA Viruses. Viruses, 2020. 12(2):. http://doi.org/10.3390/v12020143
Yun, B. R., Malik, A., Kim, S. B., Genome based characterization of Kitasatospora sp. MMS16-BH015, a multiple heavy metal resistant soil actinobacterium with high antimicrobial potential. Gene, 2020. 733: p. 144379. http://doi.org/10.1016/j.gene.2020.144379
Steiningerova, L., Kamenik, Z., Gazak, R., Kadlcik, S., Bashiri, G., Man, P., Kuzma, M., Pavlikova, M., Janata, J., Different Reaction Specificities of F420H2-Dependent Reductases Facilitate Pyrrolobenzodiazepines and Lincomycin To Fit Their Biological Targets. J Am Chem Soc, 2020. 142(7): p. 3440-3448. http://doi.org/10.1021/jacs.9b11234
Huang, J. Q., Fang, X., Tian, X., Chen, P., Lin, J. L., Guo, X. X., Li, J. X., Fan, Z., Song, W. M., Chen, F. Y., Ahati, R., Wang, L. J., Zhao, Q., Martin, C., Chen, X. Y., Aromatization of natural products by a specialized detoxification enzyme. Nat Chem Biol, 2020. 16(3): p. 250-256. http://doi.org/10.1038/s41589-019-0446-8
Wang, Z., Tauzin, A. S., Laville, E., Tedesco, P., Letisse, F., Terrapon, N., Lepercq, P., Mercade, M., Potocki-Veronese, G., Harvesting of Prebiotic Fructooligosaccharides by Nonbeneficial Human Gut Bacteria. mSphere, 2020. 5(1):. http://doi.org/10.1128/mSphere.00771-19
Dunbar, K. L., Dell, M., Gude, F., Hertweck, C., Reconstitution of polythioamide antibiotic backbone formation reveals unusual thiotemplated assembly strategy. Proc Natl Acad Sci U S A, 2020. 117(16): p. 8850-8858. http://doi.org/10.1073/pnas.1918759117
Thierbach, S., Sartor, P., Yucel, O., Fetzner, S., Efficient modification of the Pseudomonas aeruginosa toxin 2-heptyl-1-hydroxyquinolin-4-one by three Bacillus glycosyltransferases with broad substrate ranges. J Biotechnol, 2020. 308: p. 74-81. http://doi.org/10.1016/j.jbiotec.2019.11.015
Zhu, D., Wei, Y., Yin, J., Liu, D., Ang, E. L., Zhao, H., Zhang, Y., A Pathway for Degradation of Uracil to Acetyl Coenzyme A in Bacillus megaterium. Appl Environ Microbiol, 2020. 86(7):. http://doi.org/10.1128/AEM.02837-19
Stack, T. M. M., Morrison, K. N., Dettmer, T. M., Wille, B., Kim, C., Joyce, R., Jermain, M., Naing, Y. T., Bhatti, K., Francisco, B. S., Carter, M. S., Gerlt, J. A., Characterization of an l-Ascorbate Catabolic Pathway with Unprecedented Enzymatic Transformations. J Am Chem Soc, 2020. 142(4): p. 1657-1661. http://doi.org/10.1021/jacs.9b09863
Martinez-Rodriguez, S., Soriano-Maldonado, P., Gavira, J. A., N-succinylamino acid racemases: Enzymatic properties and biotechnological applications. Biochim Biophys Acta Proteins Proteom, 2020. 1868(4): p. 140377. http://doi.org/10.1016/j.bbapap.2020.140377
Fang, Q., Maglangit, F., Wu, L., Ebel, R., Kyeremeh, K., Andersen, J. H., Annang, F., Perez-Moreno, G., Reyes, F., Deng, H., Signalling and Bioactive Metabolites from Streptomyces sp. RK44. Molecules, 2020. 25(3):. http://doi.org/10.3390/molecules25030460
Bosch, N., Mariana, B., Greczmiel, U., Morinaka, B., Gugger, M., Oxenius, A., Vagstad, A. L., Piel, J., Landornamides, antiviral ornithine-containing ribosomal peptides discovered by proteusin mining. Angew Chem Int Ed Engl, 2020. http://doi.org/10.1002/anie.201916321
Sekula, B., Ruszkowski, M., Dauter, Z., S-adenosylmethionine synthases in plants: Structural characterization of type I and II isoenzymes from Arabidopsis thaliana and Medicago truncatula. Int J Biol Macromol, 2020. 151: p. 554-565. http://doi.org/10.1016/j.ijbiomac.2020.02.100
Ueoka, R., Meoded, R. A., Gran-Scheuch, A., Bhushan, A., Fraaije, M. W., Piel, J., Genome Mining of Oxidation Modules in trans-Acyltransferase Polyketide Synthases Reveals a Culturable Source for Lobatamides. Angew Chem Int Ed Engl, 2020. http://doi.org/10.1002/anie.201916005
Esch, R., Merkl, R., Conserved genomic neighborhood is a strong but no perfect indicator for a direct interaction of microbial gene products. BMC Bioinformatics, 2020. 21(1): p. 5. http://doi.org/10.1186/s12859-019-3200-z
Athukoralage, J. S., McMahon, S. A., Zhang, C., Gruschow, S., Graham, S., Krupovic, M., Whitaker, R. J., Gloster, T. M., White, M. F., An anti-CRISPR viral ring nuclease subverts type III CRISPR immunity. Nature, 2020. 577(7791): p. 572-575. http://doi.org/10.1038/s41586-019-1909-5
Wang, B., Guo, F., Huang, C., Zhao, H., Unraveling the iterative type I polyketide synthases hidden in Streptomyces. Proc Natl Acad Sci U S A, 2020. 117(15): p. 8449-8454. http://doi.org/10.1073/pnas.1917664117
Wu, H., Rebello, O., Crost, E. H., Owen, C. D., Walpole, S., Bennati-Granier, C., Ndeh, D., Monaco, S., Hicks, T., Colvile, A., Urbanowicz, P. A., Walsh, M. A., Angulo, J., Spencer, D. I. R., Juge, N., Fucosidases from the human gut symbiont Ruminococcus gnavus. Cell Mol Life Sci, 2020. http://doi.org/10.1007/s00018-020-03514-x
Jia, B., Park, D., Hahn, Y., Jeon, C. O., Metagenomic analysis of the human microbiome reveals the association between the abundance of gut bile salt hydrolases and host health. Gut Microbes, 2020. http://doi.org/10.1080/19490976.2020.1748261
Manck, L. E., Espinoza, J. L., Dupont, C. L., Barbeau, K. A., Transcriptomic Study of Substrate-Specific Transport Mechanisms for Iron and Carbon in the Marine Copiotroph Alteromonas macleodii. mSystems, 2020. 5(2):. http://doi.org/10.1128/mSystems.00070-20
Jones, C. S., Sychantha, D., Howell, P. L., Clarke, A. J., Structural basis for the O-acetyltransferase function of the extracytoplasmic domain of OatA from Staphylococcus aureus. J Biol Chem, 2020. http://doi.org/10.1074/jbc.RA120.013108
Bisanz, J. E., Soto-Perez, P., Noecker, C., Aksenov, A. A., Lam, K. N., Kenney, G. E., Bess, E. N., Haiser, H. J., Kyaw, T. S., Yu, F. B., Rekdal, V. M., Ha, C. W. Y., Devkota, S., Balskus, E. P., Dorrestein, P. C., Allen-Vercoe, E., Turnbaugh, P. J., A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria. Cell Host Microbe, 2020. http://doi.org/10.1016/j.chom.2020.04.006
Suplatov, D., Sharapova, Y., Geraseva, E., Svedas, V., Zebra2: advanced and easy-to-use web-server for bioinformatic analysis of subfamily-specific and conserved positions in diverse protein superfamilies. Nucleic Acids Res, 2020. http://doi.org/10.1093/nar/gkaa276
Williamson, A., Leiros, H. S., Structural insight into DNA joining: from conserved mechanisms to diverse scaffolds. Nucleic Acids Res, 2020. http://doi.org/10.1093/nar/gkaa307
Wullich, S. C., Arranz San Martin, A., Fetzner, S., An alpha/beta-Hydrolase Fold Subfamily Comprising Pseudomonas Quinolone Signal-Cleaving Dioxygenases. Appl Environ Microbiol, 2020. 86(9):. http://doi.org/10.1128/AEM.00279-20
Hon, J., Borko, S., Stourac, J., Prokop, Z., Zendulka, J., Bednar, D., Martinek, T., Damborsky, J., EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities. Nucleic Acids Res, 2020. http://doi.org/10.1093/nar/gkaa372
Wu, X., Zhou, H., Li, L., Wang, E., Zhou, X., Gu, Y., Wu, X., Shen, L., Zeng, W., Whole Genome Sequencing and Comparative Genomic Analyses of Lysinibacillus pakistanensis LZH-9, a Halotolerant Strain with Excellent COD Removal Capability. Microorganisms, 2020. 8(5):. http://doi.org/10.3390/microorganisms8050716
Santos, C. R., Costa, P., Vieira, P. S., Gonzalez, S. E. T., Correa, T. L. R., Lima, E. A., Mandelli, F., Pirolla, R. A. S., Domingues, M. N., Cabral, L., Martins, M. P., Cordeiro, R. L., Junior, A. T., Souza, B. P., Prates, E. T., Gozzo, F. C., Persinoti, G. F., Skaf, M. S., Murakami, M. T., Structural insights into beta-1,3-glucan cleavage by a glycoside hydrolase family. Nat Chem Biol, 2020. http://doi.org/10.1038/s41589-020-0554-5
Wang, J., Dai, W., Li, J., Xie, R., Dunstan, R. A., Stubenrauch, C., Zhang, Y., Lithgow, T., PaCRISPR: a server for predicting and visualizing anti-CRISPR proteins. Nucleic Acids Res, 2020. http://doi.org/10.1093/nar/gkaa432
ShylajaNaciyar, M., Karthick, L., Prakasam, P. A., Deviram, G., Uma, L., Prabaharan, D., Saha, S. K., Diversity of Glutathione S-Transferases (GSTs) in Cyanobacteria with Reference to Their Structures, Substrate Recognition and Catalytic Functions. Microorganisms, 2020. 8(5):. http://doi.org/10.3390/microorganisms8050712
Campbell, I. J., Olmos, J. L. Jr., Xu, W., Kahanda, D., Atkinson, J. T., Sparks, O. N., Miller, M. D., Phillips, G. N. Jr., Bennett, G. N., Silberg, J. J., Prochlorococcus phage ferredoxin: Structural characterization and electron transfer to cyanobacterial sulfite reductases. J Biol Chem, 2020. http://doi.org/10.1074/jbc.RA120.013501
Lukowski, A. L., Liu, J., Bridwell-Rabb, J., Narayan, A. R. H., Structural basis for divergent C-H hydroxylation selectivity in two Rieske oxygenases. Nat Commun, 2020. 11(1): p. 2991. http://doi.org/10.1038/s41467-020-16729-0
Sun, S., Pandelia, M. E., The HD-[HD-GYP] Phosphodiesterases; Activities and Evolutionary Diversification within the HD-GYP family. Biochemistry, 2020. http://doi.org/10.1021/acs.biochem.0c00257
Ma, S., Zhang, Q., Linaridin natural products. Nat Prod Rep, 2020. http://doi.org/10.1039/c9np00074g
Mabanglo, M. F., Huddleston, J. P., Mukherjee, K., Taylor, Z. W., Raushel, F. M., Structure and Reaction Mechanism of YcjR, an Epimerase That Facilitates the Interconversion of d-Gulosides to d-Glucosides in Escherichia coli. Biochemistry, 2020. 59(22): p. 2069-2077. http://doi.org/10.1021/acs.biochem.0c00334
Grzechowiak, M., Sliwiak, J., Jaskolski, M., Ruszkowski, M., Structural Studies of Glutamate Dehydrogenase (Isoform 1) from Arabidopsis thaliana, an Important Enzyme at the Branch-Point Between Carbon and Nitrogen Metabolism. Front Plant Sci, 2020. 11:754:. http://doi.org/10.3389/fpls.2020.00754
Perfumo, A., Freiherr von Sass, G. J., Nordmann, E. L., Budisa, N., Wagner, D., Discovery and Characterization of a New Cold-Active Protease From an Extremophilic Bacterium via Comparative Genome Analysis and in vitro Expression. Front Microbiol, 2020. 11: p. 881. http://doi.org/10.3389/fmicb.2020.00881
Liu, J., Wei, Y., Lin, L., Teng, L., Yin, J., Lu, Q., Chen, J., Zheng, Y., Li, Y., Xu, R., Zhai, W., Liu, Y., Liu, Y., Cao, P., Ang, E. L., Zhao, H., Yuchi, Z., Zhang, Y., Two radical-dependent mechanisms for anaerobic degradation of the globally abundant organosulfur compound dihydroxypropanesulfonate. Proc Natl Acad Sci U S A, 2020. http://doi.org/10.1073/pnas.2003434117
Ly, L. K., Rowles, J. L. 3rd, Paul, H. M., Alves, J. M. P., Yemm, C., Wolf, P. M., Devendran, S., Hudson, M. E., Morris, D. J., Erdman, J. W. Jr., Ridlon, J. M., Bacterial steroid-17,20-desmolase is a taxonomically rare enzymatic pathway that converts prednisone to 1,4-androstanediene-3,11,17-trione, a metabolite that causes proliferation of prostate cancer cells. J Steroid Biochem Mol Biol, 2020. 199: p. 105567. http://doi.org/10.1016/j.jsbmb.2019.105567
Niehs, S. P., Kumpfmuller, J., Dose, B., Little, R. F., Ishida, K., Florez, L. V., Kaltenpoth, M., Hertweck, C., Insect-Associated Bacteria Assemble the Antifungal Butenolide Gladiofungin by Non-Canonical Polyketide Chain Termination. Angew Chem Int Ed Engl, 2020. http://doi.org/10.1002/anie.202005711
Li, A., Laville, E., Tarquis, L., Lombard, V., Ropartz, D., Terrapon, N., Henrissat, B., Guieysse, D., Esque, J., Durand, J., Morgavi, D. P., Potocki-Veronese, G., Analysis of the diversity of the glycoside hydrolase family 130 in mammal gut microbiomes reveals a novel mannoside-phosphorylase function. Microb Genom, 2020. http://doi.org/10.1099/mgen.0.000404
Bleckwedel, J., Mohamed, F., Mozzi, F., Raya, R. R., Major role of lactate dehydrogenase D-LDH1 for the synthesis of lactic acid in Fructobacillus tropaeoli CRL 2034. Appl Microbiol Biotechnol, 2020. http://doi.org/10.1007/s00253-020-10776-9
Raut, P., Glass, J. B., Lieberman, R. L., Archaeal roots of intramembrane aspartyl protease siblings signal peptide peptidase and presenilin. Proteins, 2020. http://doi.org/10.1002/prot.26009
Le Chevalier, F., Correia, I., Matheron, L., Babin, M., Moutiez, M., Canu, N., Gondry, M., Lequin, O., Belin, P., In vivo characterization of the activities of novel cyclodipeptide oxidases: new tools for increasing chemical diversity of bioproduced 2,5-diketopiperazines in Escherichia coli. Microb Cell Fact, 2020. 19(1): p. 178. http://doi.org/10.1186/s12934-020-01432-y
Foflonker, F., Blaby-Haas, C. E., Co-locality to co-functionality: Eukaryotic gene neighborhoods as a resource for function discovery. Mol Biol Evol, 2020. http://doi.org/10.1093/molbev/msaa221
Hecht, N., Monteil, C. L., Perriere, G., Vishkautzan, M., Gur, E., Exploring protein space: From hydrolase to ligase by substitution. Mol Biol Evol, 2020. http://doi.org/10.1093/molbev/msaa215
Bushin, L. B., Covington, B. C., Rued, B. E., Federle, M. J., Seyedsayamdost, M. R., Discovery and Biosynthesis of Streptosactin, a Sactipeptide with an Alternative Topology Encoded by Commensal Bacteria in the Human Microbiome. J Am Chem Soc, 2020. http://doi.org/10.1021/jacs.0c05546
Vogt, M. S., Schmitz, G. F., Varon Silva, D., Mosch, H. U., Essen, L. O., Structural base for the transfer of GPI-anchored glycoproteins into fungal cell walls. Proc Natl Acad Sci U S A, 2020. 117(36): p. 22061-22067. http://doi.org/10.1073/pnas.2010661117
Morgan, K. T., Zheng, J., McCafferty, D., Discovery of Six Ramoplanin Family Gene Clusters and the Lipoglycodepsipeptide Chersinamycin. Chembiochem, 2020. http://doi.org/10.1002/cbic.202000555
Prahlad, J., Yuan, Y., Lin, J., Chang, C. W., Iwata-Reuyl, D., Liu, Y., de Crecy-Lagard, V., Wilson, M. A., The DUF328 family member YaaA is a DNA-binding protein with a novel fold. J Biol Chem, 2020. http://doi.org/10.1074/jbc.RA120.015055
Schneider, N. O., Tassoulas, L. J., Zeng, D., Laseke, A. J., Reiter, N. J., Wackett, L. P., Maurice, M. S., Solving the Conundrum: Widespread Proteins Annotated for Urea Metabolism in Bacteria Are Carboxyguanidine Deiminases Mediating Nitrogen Assimilation from Guanidine. Biochemistry, 2020. 59(35): p. 3258-3270. http://doi.org/10.1021/acs.biochem.0c00537
Conte, J. V., Frantom, P. A., Biochemical characterization of 2-phosphinomethylmalate synthase from Streptomyces hygroscopicus: A member of the DRE-TIM metallolyase superfamily. Arch Biochem Biophys, 2020. 691: p. 108489. http://doi.org/10.1016/j.abb.2020.108489
Shaffer, M., Borton, M. A., McGivern, B. B., Zayed, A. A., La Rosa, S. L., Solden, L. M., Liu, P., Narrowe, A. B., Rodriguez-Ramos, J., Bolduc, B., Gazitua, M. C., Daly, R. A., Smith, G. J., Vik, D. R., Pope, P. B., Sullivan, M. B., Roux, S., Wrighton, K. C., DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Res, 2020. 48(16): p. 8883-8900. http://doi.org/10.1093/nar/gkaa621
Morey, J. R., Kehl-Fie, T. E., Bioinformatic Mapping of Opine-Like Zincophore Biosynthesis in Bacteria. mSystems, 2020. 5(4):. http://doi.org/10.1128/mSystems.00554-20
Wang, F., Wei, Y., Lu, Q., Ang, E. L., Zhao, H., Zhang, Y., A ferredoxin-dependent dihydropyrimidine dehydrogenase in Clostridium chromiireducens. Biosci Rep, 2020. 40(7):. http://doi.org/10.1042/BSR20201642
Marques, W. L., Anderson, L. A., Sandoval, L., Hicks, M. A., Prather, K. L. J., Sequence-based bioprospecting of myo-inositol oxygenase (Miox) reveals new homologues that increase glucaric acid production in Saccharomyces cerevisiae. Enzyme Microb Technol, 2020. 140: p. 109623. http://doi.org/10.1016/j.enzmictec.2020.109623
Levy, H., Fontenele, R. S., Harding, C., Suazo, C., Kraberger, S., Schmidlin, K., Djurhuus, A., Black, C. E., Hart, T., Smith, A. L., Varsani, A., Identification and Distribution of Novel Cressdnaviruses and Circular molecules in Four Penguin Species in South Georgia and the Antarctic Peninsula. Viruses, 2020. 12(9):. http://doi.org/10.3390/v12091029
Shi, Q., Wang, H., Liu, J., Li, S., Guo, J., Li, H., Jia, X., Huo, H., Zheng, Z., You, S., Qin, B., Old yellow enzymes: structures and structure-guided engineering for stereocomplementary bioreduction. Appl Microbiol Biotechnol, 2020. 104(19): p. 8155-8170. http://doi.org/10.1007/s00253-020-10845-z
Nguyen, T. Q. N., Tooh, Y. W., Sugiyama, R., Nguyen, T. P. D., Purushothaman, M., Leow, L. C., Hanif, K., Yong, R. H. S., Agatha, I., Winnerdy, F. R., Gugger, M., Phan, A. T., Morinaka, B. I., Post-translational formation of strained cyclophanes in bacteria. Nat Chem, 2020. http://doi.org/10.1038/s41557-020-0519-z
Vobruba, S., Kamenik, Z., Kadlcik, S., Janata, J., N-Deacetylation in Lincosamide Biosynthesis is Catalyzed byy a TldD/PmbA Family Protein. ACS Chem Biol, 2020. 15(8): p. 2048-2054. http://doi.org/10.1021/acschembio.0c00224

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