John Alan Gerlt

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Article
2020

A bifunctional salvage pathway for two distinct S-adenosylmethionine by-products that is widespread in bacteria, including pathogenic Escherichia coli

North, J. A., Wildenthal, J. A., Erb, T. J., Evans, B. S., Byerly, K. M., Gerlt, J. A. & Tabita, F. R., May 1 2020, In : Molecular Microbiology. 113, 5, p. 923-937 15 p.

Research output: Contribution to journalArticle

Characterization of an l -Ascorbate Catabolic Pathway with Unprecedented Enzymatic Transformations

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., Jan 29 2020, In : Journal of the American Chemical Society. 142, 4, p. 1657-1661 5 p.

Research output: Contribution to journalArticle

The gastrointestinal pathogen Campylobacter jejuni metabolizes sugars with potential help from commensal Bacteroides vulgatus

Garber, J. M., Nothaft, H., Pluvinage, B., Stahl, M., Bian, X., Porfirio, S., Enriquez, A., Butcher, J., Huang, H., Glushka, J., Line, E., Gerlt, J. A., Azadi, P., Stintzi, A., Boraston, A. B. & Szymanski, C. M., Dec 1 2020, In : Communications biology. 3, 1, 2.

Research output: Contribution to journalArticle

Open Access
2019

Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens

Yuan, Y., Zallot, R., Grove, T. L., Payan, D. J., Martin-Verstraete, I., Šepić, S., Balamkundu, S., Neelakandan, R., Gadi, V. K., Liu, C. F., Swairjo, M. A., Dedon, P. C., Almo, S. C., Gerlt, J. A. & de Crécy-Lagard, V., Sep 17 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 38, p. 19126-19135 10 p.

Research output: Contribution to journalArticle

Open Access

Novel metabolic pathways and regulons for hexuronate utilization in Proteobacteria

Bouvier, J. T., Sernova, N. V., Ghasempur, S., Rodionova, I. A., Vetting, M. W., Al-Obaidi, N. F., Almo, S. C., Gerlt, J. A. & Rodionov, D. A., Jan 1 2019, In : Journal of bacteriology. 201, 2, e00431-18.

Research output: Contribution to journalArticle

The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways

Zallot, R., Oberg, N. & Gerlt, J. A., Oct 15 2019, In : Biochemistry. 58, 41, p. 4169-4182 14 p.

Research output: Contribution to journalArticle

Open Access
2018

Enzyme Architecture: Breaking Down the Catalytic Cage that Activates Orotidine 5′-Monophosphate Decarboxylase for Catalysis

Reyes, A. C., Plache, D. C., Koudelka, A. P., Amyes, T. L., Gerlt, J. A. & Richard, J. P., Dec 19 2018, In : Journal of the American Chemical Society. 140, 50, p. 17580-17590 11 p.

Research output: Contribution to journalArticle

Functional assignment of multiple catabolic pathways for d-apiose article

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., Jul 1 2018, In : Nature chemical biology. 14, 7, p. 696-705 10 p.

Research output: Contribution to journalArticle

Prediction of enzymatic pathways by integrative pathway mapping

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., Jan 29 2018, In : eLife. 7, e31097.

Research output: Contribution to journalArticle

2017
2016

Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars

Zhang, X., Carter, M. S., Vetting, M. W., Francisco, B. S., Zhao, S., Al-Obaidi, N. F., Solbiati, J. O., Thiaville, J. J., Crécy-Lagard, V. D., Jacobson, M. P., Almo, S. C. & Gerlt, J. A., Jul 19 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 29, p. E4161-E4169

Research output: Contribution to journalArticle

Members of a Novel Kinase Family (DUF1537) Can Recycle Toxic Intermediates into an Essential Metabolite

Thiaville, J. J., Flood, J., Yurgel, S., Prunetti, L., Elbadawi-Sidhu, M., Hutinet, G., Forouhar, F., Zhang, X., Ganesan, V., Reddy, P., Fiehn, O., Gerlt, J. A., Hunt, J. F., Copley, S. D. & De Crécy-Lagard, V., Aug 19 2016, In : ACS chemical biology. 11, 8, p. 2304-2311 8 p.

Research output: Contribution to journalArticle

Structure of an ABC transporter solute-binding protein specific for the amino sugars glucosamine and galactosamine

Yadava, U., Vetting, M. W., Al Obaidi, N., Carter, M. S., Gerlt, J. A. & Almo, S. C., Jan 1 2016, In : Acta Crystallographica Section:F Structural Biology Communications. 72, p. 467-472 6 p.

Research output: Contribution to journalArticle

2015

A General Strategy for the Discovery of Metabolic Pathways: D -Threitol, l -Threitol, and Erythritol Utilization in Mycobacterium smegmatis

Huang, H., Carter, M. S., Vetting, M. W., Al-Obaidi, N., Patskovsky, Y., Almo, S. C. & Gerlt, J. A., Nov 25 2015, In : Journal of the American Chemical Society. 137, 46, p. 14570-14573 4 p.

Research output: Contribution to journalArticle

ATP-binding cassette (ABC) transport system solute-binding protein-guided identification of novel D-altritol and galactitol catabolic pathways in Agrobacterium tumefaciens C58

Wichelecki, D. J., Vetting, M. W., Chou, L., Al-Obaidi, N., Bouvier, J. T., Almo, S. C. & Gerlt, J. A., Nov 27 2015, In : Journal of Biological Chemistry. 290, 48, p. 28963-28976 14 p.

Research output: Contribution to journalArticle

A unique cis -3-hydroxy- l -proline dehydratase in the enolase superfamily

Zhang, X., Kumar, R., Vetting, M. W., Zhao, S., Jacobson, M. P., Almo, S. C. & Gerlt, J. A., Feb 4 2015, In : Journal of the American Chemical Society. 137, 4, p. 1388-1391 4 p.

Research output: Contribution to journalArticle

Experimental strategies for functional annotation and metabolism discovery: Targeted screening of solute binding proteins and unbiased panning of metabolomes

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., Jan 27 2015, In : Biochemistry. 54, 3, p. 909-931 23 p.

Research output: Contribution to journalArticle

Integration of untargeted metabolomics with transcriptomics reveals active metabolic pathways

Cho, K., Evans, B. S., Wood, B. M. K., Kumar, R., Erb, T. J., Warlick, B. P., Gerlt, J. A. & Sweedler, J. V., Jun 1 2015, In : Metabolomics. 11, 3, p. 503-517 15 p.

Research output: Contribution to journalArticle

Rate and Equilibrium Constants for an Enzyme Conformational Change during Catalysis by Orotidine 5′-Monophosphate Decarboxylase

Goryanova, B., Goldman, L. M., Ming, S., Amyes, T. L., Gerlt, J. A. & Richard, J. P., Jul 28 2015, In : Biochemistry. 54, 29, p. 4555-4564 10 p.

Research output: Contribution to journalArticle

2014

Discovery of a novel l -lyxonate degradation pathway in Pseudomonas aeruginosa PAO1

Ghasempur, S., Eswaramoorthy, S., Hillerich, B. S., Seidel, R. D., Swaminathan, S., Almo, S. C. & Gerlt, J. A., May 27 2014, In : Biochemistry. 53, 20, p. 3357-3366 10 p.

Research output: Contribution to journalArticle

Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the d-mannonate dehydratase subgroup

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., Apr 29 2014, In : Biochemistry. 53, 16, p. 2722-2731 10 p.

Research output: Contribution to journalArticle

Enzymatic and structural characterization of rTSγ provides insights into the function of rTSβ

Wichelecki, D. J., Froese, D. S., Kopec, J., Muniz, J. R. C., Yue, W. W. & Gerlt, J. A., Apr 29 2014, In : Biochemistry. 53, 16, p. 2732-2738 7 p.

Research output: Contribution to journalArticle

Enzyme architecture: Deconstruction of the enzyme-activating phosphodianion interactions of orotidine 5′-monophosphate decarboxylase

Goldman, L. M., Amyes, T. L., Goryanova, B., Gerlt, J. A. & Richard, J. P., Jul 16 2014, In : Journal of the American Chemical Society. 136, 28, p. 10156-10165 10 p.

Research output: Contribution to journalArticle

Evolution of enzymatic activities in the enolase superfamily: Galactarate dehydratase III from agrobacterium tumefaciens C58

Groninger-Poe, F. P., Bouvier, J. T., Vetting, M. W., Kalyanaraman, C., Kumar, R., Almo, S. C., Jacobson, M. P. & Gerlt, J. A., Jul 1 2014, In : Biochemistry. 53, 25, p. 4192-4203 12 p.

Research output: Contribution to journalArticle

Galactaro δ-lactone isomerase: Lactone isomerization by a member of the amidohydrolase superfamily

Bouvier, J. T., Groninger-Poe, F. P., Vetting, M., Almo, S. C. & Gerlt, J. A., Feb 4 2014, In : Biochemistry. 53, 4, p. 614-616 3 p.

Research output: Contribution to journalArticle

Identification of the in vivo function of the high-efficiency d -mannonate dehydratase in caulobacter crescentus NA1000 from the enolase superfamily

Wichelecki, D. J., Graff, D. C., Al-Obaidi, N., Almo, S. C. & Gerlt, J. A., Jul 1 2014, In : Biochemistry. 53, 25, p. 4087-4089 3 p.

Research output: Contribution to journalArticle

Investigating the physiological roles of low-efficiency D-mannonate and D-gluconate dehydratases in the enolase superfamily: Pathways for the catabolism of L-gulonate and L-idonate

Wichelecki, D. J., Vendiola, J. A. F., Jones, A. M., Al-Obaidi, N., Almo, S. C. & Gerlt, J. A., Sep 9 2014, In : Biochemistry. 53, 35, p. 5692-5699 8 p.

Research output: Contribution to journalArticle

Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution

Desai, B. J., Goto, Y., Cembran, A., Fedorov, A. A., Almo, S. C., Gao, J., Suga, H. & Gerlt, J. A., Oct 21 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 42, p. 15066-15071 6 p.

Research output: Contribution to journalArticle

Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine

Kumar, R., Zhao, S., Vetting, M. W., Wood, B. M. K., Sakai, A., Cho, K., Solbiati, J., Almo, S. C., Sweedler, J. V., Jacobson, M. P., Gerlt, J. A. & Cronan, J. E., Feb 11 2014, In : mBio. 5, 1, e00933-13.

Research output: Contribution to journalArticle

Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks

Zhao, S., Sakai, A., Zhang, X., Vetting, M. W., Kumar, R., Hillerich, B., Francisco, B. S., Solbiati, J., Steves, A., Brown, S., Akiva, E., Barber, A., Seidel, R. D., Babbitt, P. C., Almo, S. C., Gerlt, J. A. & Jacobson, M. P., Jun 30 2014, In : eLife. 2014, 3, 03275.

Research output: Contribution to journalArticle

Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks

Zhao, S., Sakai, A., Zhang, X., Vetting, M. W., Kumar, R., Hillerich, B., San Francisco, B., Solbiati, J., Steves, A., Brown, S., Akiva, E., Barber, A., Seidel, R. D., Babbitt, P. C., Almo, S. C., Gerlt, J. A. & Jacobson, M. P., Jan 1 2014, In : eLife. 3

Research output: Contribution to journalArticle

Roles of small laccases from streptomyces in lignin degradation

Majumdar, S., Lukk, T., Solbiati, J. O., Bauer, S., Nair, S. K., Cronan, J. E. & Gerlt, J. A., Jun 24 2014, In : Biochemistry. 53, 24, p. 4047-4058 12 p.

Research output: Contribution to journalArticle

2013

Computational, structural, and kinetic evidence that Vibrio vulnificus FrsA is not a cofactor-independent pyruvate decarboxylase

Kellett, W. F., Brunk, E., Desai, B. J., Fedorov, A. A., Almo, S. C., Gerlt, J. A., Rothlisberger, U. & Richards, N. G. J., Mar 19 2013, In : Biochemistry. 52, 11, p. 1842-1844 3 p.

Research output: Contribution to journalArticle

Discovery of new enzymes and metabolic pathways by using structure and genome context

Zhao, S., Kumar, R., Sakai, A., Vetting, M. W., Wood, B. M. K., Brown, S., Bonanno, J. B., Hillerich, B. S., Seidel, R. D., Babbitt, P. C., Almo, S. C., Sweedler, J. V., Gerlt, J. A., Cronan, J. E. & Jacobson, M. P., Sep 24 2013, In : Nature. 502, 7473, p. 698-702 5 p.

Research output: Contribution to journalArticle

Role of a guanidinium cation-phosphodianion pair in stabilizing the vinyl carbanion intermediate of orotidine 5′-phosphate decarboxylase-catalyzed reactions

Goryanova, B., Goldman, L. M., Amyes, T. L., Gerlt, J. A. & Richard, J. P., Nov 6 2013, In : Biochemistry. 52, 42, p. 7500-7511 12 p.

Research output: Contribution to journalArticle

2012

1-methylthio-d-xylulose 5-phosphate methylsulfurylase: A novel route to 1-deoxy-d-xylulose 5-phosphate in Rhodospirillum rubrum

Warlick, B. P., Evans, B. S., Erb, T. J., Ramagopal, U. A., Sriram, J., Imker, H. J., Sauder, J. M., Bonanno, J. B., Burley, S. K., Tabita, F. R., Almo, S. C., Sweedler, J. S. & Gerlt, J. A., Oct 23 2012, In : Biochemistry. 51, 42, p. 8324-8326 3 p.

Research output: Contribution to journalArticle

A RubisCO-like protein links SAM metabolism with isoprenoid biosynthesis

Erb, T. J., Evans, B. S., Cho, K., Warlick, B. P., Sriram, J., Wood, B. M. K., Imker, H. J., Sweedler, J. V., Tabita, F. R. & Gerlt, J. A., Nov 2012, In : Nature chemical biology. 8, 11, p. 926-932 7 p.

Research output: Contribution to journalArticle

Conformational changes in orotidine 5′-monophosphate decarboxylase: A structure-based explanation for how the 5′-phosphate group activates the enzyme

Desai, B. J., Wood, B. M. K., Fedorov, A. A., Fedorov, E. V., Goryanova, B., Amyes, T. L., Richard, J. P., Almo, S. C. & Gerlt, J. A., Oct 30 2012, In : Biochemistry. 51, 43, p. 8665-8678 14 p.

Research output: Contribution to journalArticle

Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily

Lukk, T., Sakai, A., Kalyanaraman, C., Brown, S. D., Imker, H. J., Song, L., Fedorov, A. A., Fedorov, E. V., Toro, R., Hillerich, B., Seidel, R., Patskovsky, Y., Vetting, M. W., Nair, S. K., Babbitt, P. C., Almo, S. C., Gerlt, J. A. & Jacobson, M. P., Mar 13 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 11, p. 4122-4127 6 p.

Research output: Contribution to journalArticle

Mechanistic diversity in the RuBisCO superfamily: RuBisCO from rhodospirillum rubrum is not promiscuous for reactions catalyzed by RuBisCO-like proteins

Warlick, B. P. E., Imker, H. J., Sriram, J., Tabita, F. R. & Gerlt, J. A., Nov 27 2012, In : Biochemistry. 51, 47, p. 9470-9479 10 p.

Research output: Contribution to journalArticle

Orotidine 5′-monophosphate decarboxylase: Transition state stabilization from remote protein-phosphodianion interactions

Amyes, T. L., Ming, S. A., Goldman, L. M., Wood, B. M. K., Desai, B. J., Gerlt, J. A. & Richard, J. P., Jun 12 2012, In : Biochemistry. 51, 23, p. 4630-4632 3 p.

Research output: Contribution to journalArticle

Proton transfer from C-6 of uridine 5′-monophosphate catalyzed by orotidine 5′-monophosphate decarboxylase: Formation and stability of a vinyl carbanion intermediate and the effect of a 5-fluoro substituent

Tsang, W. Y., Wood, B. M. K., Wong, F. M., Wu, W., Gerlt, J. A., Amyes, T. L. & Richard, J. P., Sep 5 2012, In : Journal of the American Chemical Society. 134, 35, p. 14580-14594 15 p.

Research output: Contribution to journalArticle

2011

Mechanism of the orotidine 5′-monophosphate decarboxylase-catalyzed reaction: Importance of residues in the orotate binding site

Iiams, V., Desai, B. J., Fedorov, A. A., Fedorov, E. V., Almo, S. C. & Gerlt, J. A., Oct 4 2011, In : Biochemistry. 50, 39, p. 8497-8507 11 p.

Research output: Contribution to journalArticle

OMP decarboxylase: Phosphodianion binding energy is used to stabilize a vinyl carbanion intermediate

Goryanova, B., Amyes, T. L., Gerlt, J. A. & Richard, J. P., May 4 2011, In : Journal of the American Chemical Society. 133, 17, p. 6545-6548 4 p.

Research output: Contribution to journalArticle

2010

Activation of R235A mutant orotidine 5′-monophosphate decarboxylase by the guanidinium cation: Effective molarity of the cationic side chain of Arg-235

Barnett, S. A., Amyes, T. L., Wood, B. M., Gerlt, J. A. & Richard, J. P., Feb 9 2010, In : Biochemistry. 49, 5, p. 824-826 3 p.

Research output: Contribution to journalArticle

Conformational changes in orotidine 5′-monophosphate decarboxylase: "remote" residues that stabilize the active conformation

Wood, B. M. K., Amyes, T. L., Fedorov, A. A., Fedorov, E. V., Shabila, A., Almo, S. C., Richard, J. P. & Gerlt, J. A., May 4 2010, In : Biochemistry. 49, 17, p. 3514-3516 3 p.

Research output: Contribution to journalArticle

2009

An examination of the relationship between active site loop size and thermodynamic activation parameters for orotidine 5′-monophosphate decarboxylase from mesophilic and thermophilic organisms

Toth, K., Amyes, T. L., Wood, B. M. K., Chan, K. K., Gerlt, J. A. & Richard, J. P., Aug 25 2009, In : Biochemistry. 48, 33, p. 8006-8013 8 p.

Research output: Contribution to journalArticle

Computation-facilitated assignment of the function in the enolase superfamily: A regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis

Rakus, J. F., Kalyanaraman, C., Fedorov, A. A., Fedorov, E. V., Mills-Groninger, F. P., Toro, R., Bonanno, J., Bain, K., Sauder, J. M., Burley, S. K., Almo, S. C., Jacobson, M. P. & Gerlt, J. A., Dec 8 2009, In : Biochemistry. 48, 48, p. 11546-11558 13 p.

Research output: Contribution to journalArticle