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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 JA.

Biochemistry. 2019 Oct 15;58(41):4169-4182. doi: 10.1021/acs.biochem.9b00735. Epub 2019 Oct 4.


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

Yuan Y, Zallot R, Grove TL, Payan DJ, Martin-Verstraete I, Šepić S, Balamkundu S, Neelakandan R, Gadi VK, Liu CF, Swairjo MA, Dedon PC, Almo SC, Gerlt JA, de Crécy-Lagard V.

Proc Natl Acad Sci U S A. 2019 Sep 17;116(38):19126-19135. doi: 10.1073/pnas.1909604116. Epub 2019 Sep 3.


Editorial overview: Novel enzymes, coenzymes, and metabolic pathways.

Gerlt JA, Erb TJ.

Curr Opin Chem Biol. 2018 Dec;47:A4-A6. doi: 10.1016/j.cbpa.2018.11.008. Epub 2018 Nov 26. No abstract available.


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

Reyes AC, Plache DC, Koudelka AP, Amyes TL, Gerlt JA, Richard JP.

J Am Chem Soc. 2018 Dec 19;140(50):17580-17590. doi: 10.1021/jacs.8b09609. Epub 2018 Dec 7.


'Democratized' genomic enzymology web tools for functional assignment.

Zallot R, Oberg NO, Gerlt JA.

Curr Opin Chem Biol. 2018 Dec;47:77-85. doi: 10.1016/j.cbpa.2018.09.009. Epub 2018 Sep 27. Review.


Novel Metabolic Pathways and Regulons for Hexuronate Utilization in Proteobacteria.

Bouvier JT, Sernova NV, Ghasempur S, Rodionova IA, Vetting MW, Al-Obaidi NF, Almo SC, Gerlt JA, Rodionov DA.

J Bacteriol. 2018 Dec 20;201(2). pii: e00431-18. doi: 10.1128/JB.00431-18. Print 2019 Jan 15.


Functional assignment of multiple catabolic pathways for D-apiose.

Carter MS, Zhang X, Huang H, Bouvier JT, Francisco BS, Vetting MW, Al-Obaidi N, Bonanno JB, Ghosh A, Zallot RG, Andersen HM, Almo SC, Gerlt JA.

Nat Chem Biol. 2018 Jul;14(7):696-705. doi: 10.1038/s41589-018-0067-7. Epub 2018 Jun 4.


Special Issue: Current Topics in Mechanistic Enzymology.

Gerlt JA.

Biochemistry. 2018 Jun 5;57(22):3085-3086. doi: 10.1021/acs.biochem.8b00585. No abstract available.


Prediction of enzymatic pathways by integrative pathway mapping.

Calhoun S, Korczynska M, Wichelecki DJ, San Francisco B, Zhao S, Rodionov DA, Vetting MW, Al-Obaidi NF, Lin H, O'Meara MJ, Scott DA, Morris JH, Russel D, Almo SC, Osterman AL, Gerlt JA, Jacobson MP, Shoichet BK, Sali A.

Elife. 2018 Jan 29;7. pii: e31097. doi: 10.7554/eLife.31097.


Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence-Function Space and Genome Context to Discover Novel Functions.

Gerlt JA.

Biochemistry. 2017 Aug 22;56(33):4293-4308. doi: 10.1021/acs.biochem.7b00614. Review.


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

Zhang X, Carter MS, Vetting MW, San Francisco B, Zhao S, Al-Obaidi NF, Solbiati JO, Thiaville JJ, de Crécy-Lagard V, Jacobson MP, Almo SC, Gerlt JA.

Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):E4161-9. doi: 10.1073/pnas.1605546113. Epub 2016 Jul 11.


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

Yadava U, Vetting MW, Al Obaidi N, Carter MS, Gerlt JA, Almo SC.

Acta Crystallogr F Struct Biol Commun. 2016 Jun;72(Pt 6):467-72. doi: 10.1107/S2053230X16007500. Epub 2016 May 23.


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

Thiaville JJ, Flood J, Yurgel S, Prunetti L, Elbadawi-Sidhu M, Hutinet G, Forouhar F, Zhang X, Ganesan V, Reddy P, Fiehn O, Gerlt JA, Hunt JF, Copley SD, de Crécy-Lagard V.

ACS Chem Biol. 2016 Aug 19;11(8):2304-11. doi: 10.1021/acschembio.6b00279. Epub 2016 Jun 24.


Correction to "A General Strategy for the Discovery of Metabolic Pathways: D-Threitol, L-Threitol, and Erythritol Utilization in Mycobacterium smegmatis".

Huang H, Carter MS, Vetting MW, Al-Obaidi N, Patskovsky Y, Almo SC, Gerlt JA.

J Am Chem Soc. 2016 Mar 30;138(12):4267. doi: 10.1021/jacs.6b01906. Epub 2016 Mar 15. No abstract available.


Purification, crystallization and structural elucidation of D-galactaro-1,4-lactone cycloisomerase from Agrobacterium tumefaciens involved in pectin degradation.

Vetting MW, Bouvier JT, Gerlt JA, Almo SC.

Acta Crystallogr F Struct Biol Commun. 2016 Jan;72(Pt 1):36-41. doi: 10.1107/S2053230X15023286. Epub 2016 Jan 1.


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

Huang H, Carter MS, Vetting MW, Al-Obaidi N, Patskovsky Y, Almo SC, Gerlt JA.

J Am Chem Soc. 2015 Nov 25;137(46):14570-3. doi: 10.1021/jacs.5b08968. Epub 2015 Nov 12. Erratum in: J Am Chem Soc. 2016 Mar 30;138(12):4267.


ATP-binding Cassette (ABC) Transport System Solute-binding Protein-guided Identification of Novel d-Altritol and Galactitol Catabolic Pathways in Agrobacterium tumefaciens C58.

Wichelecki DJ, Vetting MW, Chou L, Al-Obaidi N, Bouvier JT, Almo SC, Gerlt JA.

J Biol Chem. 2015 Nov 27;290(48):28963-76. doi: 10.1074/jbc.M115.686857. Epub 2015 Oct 15.


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

Goryanova B, Goldman LM, Ming S, Amyes TL, Gerlt JA, Richard JP.

Biochemistry. 2015 Jul 28;54(29):4555-64. doi: 10.1021/acs.biochem.5b00591. Epub 2015 Jul 14.


Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks.

Gerlt JA, Bouvier JT, Davidson DB, Imker HJ, Sadkhin B, Slater DR, Whalen KL.

Biochim Biophys Acta. 2015 Aug;1854(8):1019-37. doi: 10.1016/j.bbapap.2015.04.015. Epub 2015 Apr 18. Review.


Integration of untargeted metabolomics with transcriptomics reveals active metabolic pathways.

Cho K, Evans BS, Wood BM, Kumar R, Erb TJ, Warlick BP, Gerlt JA, Sweedler JV.

Metabolomics. 2014 Sep 3;2014(August). pii:


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

Zhang X, Kumar R, Vetting MW, Zhao S, Jacobson MP, Almo SC, Gerlt JA.

J Am Chem Soc. 2015 Feb 4;137(4):1388-91. doi: 10.1021/ja5103986. Epub 2015 Jan 26.


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

Vetting MW, Al-Obaidi N, Zhao S, San Francisco B, Kim J, Wichelecki DJ, Bouvier JT, Solbiati JO, Vu H, Zhang X, Rodionov DA, Love JD, Hillerich BS, Seidel RD, Quinn RJ, Osterman AL, Cronan JE, Jacobson MP, Gerlt JA, Almo SC.

Biochemistry. 2015 Jan 27;54(3):909-31. doi: 10.1021/bi501388y. Epub 2015 Jan 16.


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

Desai BJ, Goto Y, Cembran A, Fedorov AA, Almo SC, Gao J, Suga H, Gerlt JA.

Proc Natl Acad Sci U S A. 2014 Oct 21;111(42):15066-71. doi: 10.1073/pnas.1411772111. Epub 2014 Oct 1.


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 DJ, Vendiola JA, Jones AM, Al-Obaidi N, Almo SC, Gerlt JA.

Biochemistry. 2014 Sep 9;53(35):5692-9. doi: 10.1021/bi500837w. Epub 2014 Aug 27.


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

Zhao S, Sakai A, Zhang X, Vetting MW, Kumar R, Hillerich B, San Francisco B, Solbiati J, Steves A, Brown S, Akiva E, Barber A, Seidel RD, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP.

Elife. 2014 Jun 30;3. doi: 10.7554/eLife.03275.


Enzyme architecture: deconstruction of the enzyme-activating phosphodianion interactions of orotidine 5'-monophosphate decarboxylase.

Goldman LM, Amyes TL, Goryanova B, Gerlt JA, Richard JP.

J Am Chem Soc. 2014 Jul 16;136(28):10156-65. doi: 10.1021/ja505037v. Epub 2014 Jul 2.


Identification of the in vivo function of the high-efficiency D-mannonate dehydratase in Caulobacter crescentus NA1000 from the enolase superfamily.

Wichelecki DJ, Graff DC, Al-Obaidi N, Almo SC, Gerlt JA.

Biochemistry. 2014 Jul 1;53(25):4087-9. doi: 10.1021/bi500683x. Epub 2014 Jun 20.


Evolution of enzymatic activities in the enolase superfamily: galactarate dehydratase III from Agrobacterium tumefaciens C58.

Groninger-Poe FP, Bouvier JT, Vetting MW, Kalyanaraman C, Kumar R, Almo SC, Jacobson MP, Gerlt JA.

Biochemistry. 2014 Jul 1;53(25):4192-203. doi: 10.1021/bi5005377. Epub 2014 Jun 19.


Roles of small laccases from Streptomyces in lignin degradation.

Majumdar S, Lukk T, Solbiati JO, Bauer S, Nair SK, Cronan JE, Gerlt JA.

Biochemistry. 2014 Jun 24;53(24):4047-58.


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

Ghasempur S, Eswaramoorthy S, Hillerich BS, Seidel RD, Swaminathan S, Almo SC, Gerlt JA.

Biochemistry. 2014 May 27;53(20):3357-66. doi: 10.1021/bi5004298. Epub 2014 May 15.


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

Wichelecki DJ, Balthazor BM, Chau AC, Vetting MW, Fedorov AA, Fedorov EV, Lukk T, Patskovsky YV, Stead MB, Hillerich BS, Seidel RD, Almo SC, Gerlt JA.

Biochemistry. 2014 Apr 29;53(16):2722-31. doi: 10.1021/bi500264p. Epub 2014 Apr 15.


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

Wichelecki DJ, Froese DS, Kopec J, Muniz JR, Yue WW, Gerlt JA.

Biochemistry. 2014 Apr 29;53(16):2732-8. doi: 10.1021/bi500349e. Epub 2014 Apr 15.


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

Kumar R, Zhao S, Vetting MW, Wood BM, Sakai A, Cho K, Solbiati J, Almo SC, Sweedler JV, Jacobson MP, Gerlt JA, Cronan JE.

MBio. 2014 Feb 11;5(1):e00933-13. doi: 10.1128/mBio.00933-13.


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

Bouvier JT, Groninger-Poe FP, Vetting M, Almo SC, Gerlt JA.

Biochemistry. 2014 Feb 4;53(4):614-6. doi: 10.1021/bi5000492. Epub 2014 Jan 24.


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

Zhao S, Kumar R, Sakai A, Vetting MW, Wood BM, Brown S, Bonanno JB, Hillerich BS, Seidel RD, Babbitt PC, Almo SC, Sweedler JV, Gerlt JA, Cronan JE, Jacobson MP.

Nature. 2013 Oct 31;502(7473):698-702. doi: 10.1038/nature12576. Epub 2013 Sep 22.


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

Goryanova B, Goldman LM, Amyes TL, Gerlt JA, Richard JP.

Biochemistry. 2013 Oct 22;52(42):7500-11. doi: 10.1021/bi401117y. Epub 2013 Oct 8.


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

Kellett WF, Brunk E, Desai BJ, Fedorov AA, Almo SC, Gerlt JA, Rothlisberger U, Richards NG.

Biochemistry. 2013 Mar 19;52(11):1842-4. doi: 10.1021/bi400093y. Epub 2013 Mar 5.


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

Warlick BP, Imker HJ, Sriram J, Tabita FR, Gerlt JA.

Biochemistry. 2012 Nov 27;51(47):9470-9. doi: 10.1021/bi301311t. Epub 2012 Nov 14.


A RubisCO-like protein links SAM metabolism with isoprenoid biosynthesis.

Erb TJ, Evans BS, Cho K, Warlick BP, Sriram J, Wood BM, Imker HJ, Sweedler JV, Tabita FR, Gerlt JA.

Nat Chem Biol. 2012 Nov;8(11):926-32. doi: 10.1038/nchembio.1087. Epub 2012 Oct 7.


1-methylthio-D-xylulose 5-phosphate methylsulfurylase: a novel route to 1-deoxy-D-xylulose 5-phosphate in Rhodospirillum rubrum.

Warlick BP, Evans BS, Erb TJ, Ramagopal UA, Sriram J, Imker HJ, Sauder JM, Bonanno JB, Burley SK, Tabita FR, Almo SC, Sweedler JS, Gerlt JA.

Biochemistry. 2012 Oct 23;51(42):8324-6. doi: 10.1021/bi301215g. Epub 2012 Oct 8.


Conformational changes in orotidine 5'-monophosphate decarboxylase: a structure-based explanation for how the 5'-phosphate group activates the enzyme.

Desai BJ, Wood BM, Fedorov AA, Fedorov EV, Goryanova B, Amyes TL, Richard JP, Almo SC, Gerlt JA.

Biochemistry. 2012 Oct 30;51(43):8665-78. doi: 10.1021/bi301188k. Epub 2012 Oct 17.


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 WY, Wood BM, Wong FM, Wu W, Gerlt JA, Amyes TL, Richard JP.

J Am Chem Soc. 2012 Sep 5;134(35):14580-94. doi: 10.1021/ja3058474. Epub 2012 Aug 21.


Orotidine 5'-monophosphate decarboxylase: transition state stabilization from remote protein-phosphodianion interactions.

Amyes TL, Ming SA, Goldman LM, Wood BM, Desai BJ, Gerlt JA, Richard JP.

Biochemistry. 2012 Jun 12;51(23):4630-2. doi: 10.1021/bi300585e. Epub 2012 May 31.


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

Lukk T, Sakai A, Kalyanaraman C, Brown SD, Imker HJ, Song L, Fedorov AA, Fedorov EV, Toro R, Hillerich B, Seidel R, Patskovsky Y, Vetting MW, Nair SK, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP.

Proc Natl Acad Sci U S A. 2012 Mar 13;109(11):4122-7. doi: 10.1073/pnas.1112081109. Epub 2012 Mar 5.


Divergent evolution in enolase superfamily: strategies for assigning functions.

Gerlt JA, Babbitt PC, Jacobson MP, Almo SC.

J Biol Chem. 2012 Jan 2;287(1):29-34. doi: 10.1074/jbc.R111.240945. Epub 2011 Nov 8. Review.


The Enzyme Function Initiative.

Gerlt JA, Allen KN, Almo SC, Armstrong RN, Babbitt PC, Cronan JE, Dunaway-Mariano D, Imker HJ, Jacobson MP, Minor W, Poulter CD, Raushel FM, Sali A, Shoichet BK, Sweedler JV.

Biochemistry. 2011 Nov 22;50(46):9950-62. doi: 10.1021/bi201312u. Epub 2011 Oct 26. Review.


Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: importance of residues in the orotate binding site.

Iiams V, Desai BJ, Fedorov AA, Fedorov EV, Almo SC, Gerlt JA.

Biochemistry. 2011 Oct 4;50(39):8497-507. doi: 10.1021/bi2012355. Epub 2011 Sep 6.


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

Goryanova B, Amyes TL, Gerlt JA, Richard JP.

J Am Chem Soc. 2011 May 4;133(17):6545-8. doi: 10.1021/ja201734z. Epub 2011 Apr 12.


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

Wood BM, Amyes TL, Fedorov AA, Fedorov EV, Shabila A, Almo SC, Richard JP, Gerlt JA.

Biochemistry. 2010 May 4;49(17):3514-6. doi: 10.1021/bi100443a.

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