J. Gerlt

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The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids.

G. H. Reed, P. Babbitt, D. Ringe, 1996, Biochemistry.

Heidi J. Imker, Karen N. Allen, A. Sali, 2011, Biochemistry.

Discovery of Function in the Enolase Superfamily: d-Mannonate and d-Gluconate Dehydratases in the d-Mannonate Dehydratase Subgroup

Steven C. Almo, Matthew W. Vetting, Ronald D. Seidel, 2014, Biochemistry.

A gold standard set of mechanistically diverse enzyme superfamilies

Shoshana D. Brown, P. Babbitt, J. Gerlt, 2006, Genome Biology.

Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies.

P. Babbitt, J. Gerlt, 2001, Annual review of biochemistry.

Roles of small laccases from Streptomyces in lignin degradation.

J. Gerlt, J. Cronan, S. Nair, 2014, Biochemistry.

Enzyme (re)design: lessons from natural evolution and computation.

P. Babbitt, J. Gerlt, 2009, Current opinion in chemical biology.

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

Heidi J. Imker, J. Gerlt, K. Whalen, 2015, Biochimica et biophysica acta.

On the origin of enzymatic species.

G. Petsko, D. Ringe, G. L. Kenyon, 1993, Trends in biochemical sciences.

Evolution of enzyme superfamilies.

P. Babbitt, M. E. Glasner, J. Gerlt, 2006, Current opinion in chemical biology.

Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily.

Ranyee A. Chiang, P. Babbitt, M. E. Glasner, 2006, Journal of molecular biology.

Evolutionary Potential of (β/α)8-Barrels: Stepwise Evolution of a “New” Reaction in the Enolase Superfamily†

J. Gerlt, J. E. Vick, 2007 .

Prediction and assignment of function for a divergent N-succinyl amino acid racemase.

Heidi J. Imker, Shoshana D. Brown, P. Babbitt, 2007, Nature chemical biology.

Divergent Evolution in Enolase Superfamily: Strategies for Assigning Functions*

P. Babbitt, J. Gerlt, S. Almo, 2011, The Journal of Biological Chemistry.

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

Shoshana D. Brown, P. Babbitt, J. Gerlt, 2012, Proceedings of the National Academy of Sciences.

Mechanistically diverse enzyme superfamilies: the importance of chemistry in the evolution of catalysis.

P C Babbitt, P. Babbitt, J. Gerlt, 1998, Current opinion in chemical biology.

Evolutionary Potential of (β/α)8-Barrels: Functional Promiscuity Produced by Single Substitutions in the Enolase Superfamily†

Patricia C. Babbitt, Jon E. Ness, Jeremy Minshull, 2003 .

Evolution of function in (β/α)8-barrel enzymes

John Alan Gerlt, J. Gerlt, F. Raushel, 2003 .

Mechanisms of protein evolution and their application to protein engineering.

Patricia C Babbitt, John A Gerlt, P. Babbitt, 2007, Advances in enzymology and related areas of molecular biology.

Understanding Enzyme Superfamilies

Patricia C. Babbitt, P. Babbitt, J. Gerlt, 1997, The Journal of Biological Chemistry.

Can sequence determine function?

Patricia C Babbitt, John A Gerlt, P. Babbitt, 2000, Genome Biology.

Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity.

Ivan Rayment, Patricia C Babbitt, John A Gerlt, 2005, Archives of biochemistry and biophysics.

Mechanism of UV endonuclease V cleavage of abasic sites in DNA determined by 13C labeling

M. Manoharan, J. Gerlt, S. Ransom, 1988 .

UV Endonuclease V from Bacteriophage T4 Catalyzes DNA Strand Cleavage at Aldehydic Abasic Sites by a Syn β-Elimination Reaction

J. Gerlt, M. Absalon, J. Stubbe, 1989 .

New wine from old barrels

J. Gerlt, John A. Gerlt, 2000, Nature Structural Biology.

Unexpected divergence of enzyme function and sequence: "N-acylamino acid racemase" is o-succinylbenzoate synthase.

P C Babbitt, P. Babbitt, D. R. Palmer, 1999, Biochemistry.

Evolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from Novosphingobium aromaticivorans.

P. Babbitt, M. E. Glasner, J. Gerlt, 2007, Biochemistry.

Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening.

Heidi J Imker, Matthew P Jacobson, Heidi J. Imker, 2008, Structure.

Evolution of enzymatic activities in the enolase superfamily: stereochemically distinct mechanisms in two families of cis,cis-muconate lactonizing enzymes.

Patricia C Babbitt, Stephen K Burley, Ayano Sakai, 2009, Biochemistry.

Integration of untargeted metabolomics with transcriptomics reveals active metabolic pathways

J. Gerlt, B. Evans, J. Sweedler, 2014, Metabolomics.

A method for the observation of selected proton NMR resonances of proteins

J. Gerlt, P. Bolton, N. Stolowich, 1986 .

The ompA signal peptide directed secretion of Staphylococcal nuclease A by Escherichia coli.

M. Inouye, J. Gerlt, P. Barr, 1985, The Journal of biological chemistry.

Relationships between enzymatic catalysis and active site structure revealed by applications of site-directed mutagenesis

J. Gerlt, 1987 .

Letter: A phosphodiesterase from Enterobacter aerogenes.

J. Gerlt, F. Westheimer, 1973, Journal of the American Chemical Society.

The enthalpies of hydrolysis of acyclic, monocyclic, and glycoside cyclic phosphate diesters.

J. Gerlt, J. Sturtevant, F. Westheimer, 1975, The Journal of biological chemistry.

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

Lawrence M. Goldman, J. Gerlt, J. Richard, 2013, Biochemistry.

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

J. Gerlt, A. Fedorov, E. Fedorov, 2011, Biochemistry.

Crystal structure of D-ribulose 5-phosphate 3-epimerase from Synechocystis to 1.6 angstrom resolution

I. Rayment, J. Gerlt, E. Wise, 2004 .

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

J. Gerlt, S. Almo, D. Wichelecki, 2015, The Journal of Biological Chemistry.

Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.

Heidi J. Imker, J. Gerlt, A. Fedorov, 2009, Biochemistry.

Mandelate racemase and class-related enzymes

G. Petsko, G. L. Kenyon, J. Gerlt, 1992 .

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

J. Gerlt, J. Richard, T. L. Amyes, 2009, Biochemistry.

Mandelate Racemase: Structure-Function Studies of a Pseudosymmetric Enzyme

G. Petsko, G. L. Kenyon, J. Gerlt, 1995 .

Electrophilic catalysis can explain the unexpected acidity of carbon acids in enzyme-catalyzed reactions

P. G. Gassman, G. L. Kenyon, J. Gerlt, 1991 .

Structure-Function Relationships in Mandelate Racemase and Muconate Lactonizing Enzyme

G. Petsko, G. L. Kenyon, J. Gerlt, 1990 .

Selection and characterization of a mutant of the cloned gene for mandelate racemase that confers resistance to an affinity label by greatly enhanced production of enzyme.

G. L. Kenyon, J. Gerlt, S. Ransom, 1989, Biochemistry.

Preliminary x-ray data on crystals of mandelate racemase.

G. Petsko, G. L. Kenyon, J. Gerlt, 1988, The Journal of biological chemistry.

The structural enzymology of proton-transfer reactions

John Alan Gerlt, Dagmar Ringe, Martin Karplus, 1993 .

Mandelate racemase and muconate lactonizing enzyme are mechanistically distinct and structurally homologous

Gregory A. Petsko, G. Petsko, G. L. Kenyon, 1990, Nature.

RadicalSAM.org: A Resource to Interpret Sequence-Function Space and Discover New Radical SAM Enzyme Chemistry

J. Gerlt, Nils Oberg, D. Mitchell, 2021, ACS bio & med chem Au.

Formation and stability of a vinyl carbanion at the active site of orotidine 5'-monophosphate decarboxylase: pKa of the C-6 proton of enzyme-bound UMP.

J. Gerlt, J. Richard, T. L. Amyes, 2008, Journal of the American Chemical Society.

Discovery of novel pathways for carbohydrate metabolism.

J. Gerlt, T. Stack, 2020, Current opinion in chemical biology.

d-Ribulose 5-Phosphate 3-Epimerase: Functional and Structural Relationships to Members of the Ribulose-Phosphate Binding (β/α)8-Barrel Superfamily,

P. Babbitt, J. Gerlt, A. Fedorov, 2006 .

D-Ribulose 5-phosphate 3-epimerase: functional and structural relationships to members of the ribulose-phosphate binding (beta/alpha)8-barrel superfamily.

P. Babbitt, J. Gerlt, A. Fedorov, 2006, Biochemistry.

A roadmap for the functional annotation of protein families: a community perspective

Benjamin M. Gyori, Lucy J. Colwell, Ian K. Blaby, 2022, Database J. Biol. Databases Curation.

Discovery of new enzymatic functions and metabolic pathways using genomic enzymology web tools.

J. Gerlt, Nils Oberg, Rémi Zallot, 2021, Current opinion in biotechnology.

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

J. Gerlt, J. Richard, T. L. Amyes, 2018, Journal of the American Chemical Society.

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

Lawrence M. Goldman, J. Gerlt, J. Richard, 2015, Biochemistry.

Kinetic and magnetic resonance studies of the glutamate-43 to serine mutant of staphylococcal nuclease.

J. Gerlt, A. Mildvan, E. Serpersu, 1989, Biochemistry.

A General Procedure for Assigning the 31P Spectra of Nucleic Acids

J. Gerlt, M. Petersheim, S. Mehdi, 2002 .

Understanding enzyme-catalyzed proton abstraction from carbon acids: Details of stepwise mechanisms for β-elimination reactions

P. G. Gassman, J. Gerlt, 1992 .

Oxygen chiral phosphodiesters. 4. Stereochemical course of the hydrolysis of 2'-deoxyadenosine cyclic 3',5'-[17O, 18O]monophosphate in water(oxygen-16) catalyzed by bovine heart cyclic nucleotide phosphodiesterase

J. Gerlt, J. Coderre, S. Mehdi, 1981 .

Discovering new enzymes and metabolic pathways: conversion of succinate to propionate by Escherichia coli.

J. Gerlt, T. Buckel, J. Rétey, 2000, Biochemistry.

Novel Metabolic Pathways and Regulons for Hexuronate Utilization in Proteobacteria

J. Gerlt, S. Almo, D. Rodionov, 2018, Journal of bacteriology.

1 Mechanistic Principles of Enzyme-catalyzed Cleavage of Phosphodiester Bonds

J. Gerlt, 1993 .

Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: structural basis for catalytic promiscuity in wild-type and designed mutants of 3-keto-L-gulonate 6-phosphate decarboxylase.

I. Rayment, J. Gerlt, E. Wise, 2005, Biochemistry.

Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: mechanistic evidence for a proton relay system in the active site of 3-keto-L-gulonate 6-phosphate decarboxylase.

I. Rayment, J. Gerlt, E. Wise, 2004, Biochemistry.

Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: crystallographic evidence for a proton relay system in the active site of 3-keto-L-gulonate 6-phosphate decarboxylase.

I. Rayment, J. Gerlt, E. Wise, 2004, Biochemistry.

Product deuterium isotope effects for orotidine 5'-monophosphate decarboxylase: effect of changing substrate and enzyme structure on the partitioning of the vinyl carbanion reaction intermediate.

J. Gerlt, J. Richard, T. L. Amyes, 2010, Journal of the American Chemical Society.

Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: effect of solvent viscosity on kinetic constants.

J. Gerlt, J. Richard, T. L. Amyes, 2009, Biochemistry.

Evolution of enzymatic activities in the enolase superfamily: D-tartrate dehydratase from Bradyrhizobium japonicum.

J. Gerlt, A. Fedorov, E. Fedorov, 2006, Biochemistry.

Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli.

P. Babbitt, D. R. Palmer, J. Gerlt, 1998, Biochemistry.

The lesser "burden borne" by o-succinylbenzoate synthase: an "easy" reaction involving a carboxylate carbon acid.

D. R. Palmer, J. Gerlt, E. Taylor, 2001, Journal of the American Chemical Society.

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

Lawrence M. Goldman, J. Gerlt, J. Richard, 2012, Biochemistry.

Stereochemical studies of the beta-elimination reactions at aldehydic abasic sites in DNA: endonuclease III from Escherichia coli, sodium hydroxide, and Lys-Trp-Lys.

J. Gerlt, M. Absalon, R. Cunningham, 1991, Biochemistry.

3'- and 5'-strand cleavage reactions catalyzed by the Fpg protein from Escherichia coli occur via successive beta- and delta-elimination mechanisms, respectively.

J. Gerlt, M. Bhagwat, 1996, Biochemistry.

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

J. Gerlt, S. Almo, D. Wichelecki, 2020 .

ENZYME-CATALYZED ENOLIZATION REACTIONS : A THEORETICAL STUDY ON THE ENERGETICS OF CONCERTED AND STEPWISE PATHWAYS

P. G. Gassman, J. Gerlt, J. Almlöf, 1996 .

The characterization of abasic sites in DNA heteroduplexes by site specific labeling with 13C

M. Manoharan, J. Gerlt, S. Ransom, 1988 .

Identification of residues involved in a conformational change accompanying substitutions for glutamate-43 in staphylococcal nuclease.

J. Gerlt, P. H. Bolton, T. Pourmotabbed, 1988, Biochemistry.

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

Heidi J. Imker, J. M. Sauder, J. Gerlt, 2012, Biochemistry.

The role of lysine 166 in the mechanism of mandelate racemase from Pseudomonas putida: mechanistic and crystallographic evidence for stereospecific alkylation by (R)-alpha-phenylglycidate.

G L Kenyon, G A Petsko, G. Petsko, 1994, Biochemistry.

Chemical and Enzymatic Synthesis of Fluorinated‐Dehydroalanine‐Containing Peptides

J. Gerlt, W. A. van der Donk, D. M. Schmidt, 2003, Chembiochem : a European journal of chemical biology.

Evolution of enzymatic activities in the enolase superfamily: crystal structures of the L-Ala-D/L-Glu epimerases from Escherichia coli and Bacillus subtilis.

I. Rayment, J. Gerlt, D. M. Schmidt, 2001, Biochemistry.

Evolution of enzymatic activities in the enolase superfamily: functional assignment of unknown proteins in Bacillus subtilis and Escherichia coli as L-Ala-D/L-Glu epimerases.

J. Gerlt, B. Hubbard, D. M. Schmidt, 2001, Biochemistry.

Oxygen chiral phosphodiesters. 7. Stereochemical course of a reaction catalyzed by staphylococcal nuclease

J. Gerlt, S. Mehdi, 1982 .

Identification of the alkaline-labile product accompanying cytosine release during bleomycin-mediated degradation of d(CGCGCG)

J. Gerlt, J. Stubbe, J. Kozarich, 1986 .

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

Nils Oberg, Rémi Zallot, John A Gerlt, 2019, Biochemistry.

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

J. Gerlt, A. Fedorov, S. Almo, 2014, Proceedings of the National Academy of Sciences.

The Low Barrier Hydrogen Bond in Enzymatic Catalysis*

P A Frey, P. Frey, J. Gerlt, 1998, The Journal of Biological Chemistry.

Oxygen-17 NMR spectral properties of simple phosphate esters and adenine nucleotides

J. Gerlt, P. Demou, S. Mehdi, 1982 .

Evolution of enzymatic activities in the enolase superfamily: crystallographic and mutagenesis studies of the reaction catalyzed by D-glucarate dehydratase from Escherichia coli.

I. Rayment, J. Gerlt, B. Hubbard, 2000, Biochemistry.

Evolution of enzymatic activities in the enolase superfamily: Identification of a 'new' general acid catalyst in the active site of D- galactonate dehydratase from Escherichia coli

G. Petsko, J. Clifton, D. Ringe, 1999 .

5.02 – Stabilization of Reactive Intermediates and Transition States in Enzyme Active Sites by Hydrogen Bonding

J. Gerlt, 1999 .

The crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes.

G. Petsko, D. Ringe, M. Hasson, 1998, Biochemistry.

Mechanism of the reaction catalyzed by mandelate racemase: structure and mechanistic properties of the D270N mutant.

G L Kenyon, G A Petsko, G. Petsko, 1995, Biochemistry.

Characterization of an L-Ascorbate Catabolic Pathway with Unprecedented Enzymatic Transformations.

J. Gerlt, Michael S. Carter, Brian San Francisco, 2019, Journal of the American Chemical Society.

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

J. Gerlt, J. Richard, T. L. Amyes, 2011, Journal of the American Chemical Society.

The crotonase superfamily: divergently related enzymes that catalyze different reactions involving acyl coenzyme a thioesters.

H M Holden, J. Gerlt, H. Holden, 2001, Accounts of chemical research.

Mechanism of the reaction catalyzed by acetoacetate decarboxylase. Importance of lysine 116 in determining the pKa of active-site lysine 115.

G. L. Kenyon, J. Gerlt, L. Highbarger, 1996, Biochemistry.

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

J. Gerlt, S. Almo, M. Vetting, 2016, Acta crystallographica. Section F, Structural biology communications.

Characterization of the equilibrating forms of the aldehydic abasic site in duplex DNA by 17O NMR

M. Manoharan, J. Gerlt, P. Bolton, 1989 .

An explanation for rapid enzyme-catalyzed proton abstraction from carbon acids: importance of late transition states in concerted mechanisms

John Alan Gerlt, P. G. Gassman, J. Gerlt, 1993 .

Utilization of l-Ascorbate by Escherichia coli K-12: Assignments of Functions to Products of the yjf-sga and yia-sgb Operons

J. Gerlt, W. Yew, 2002, Journal of bacteriology.

Purification and properties of a phosphohydrolase from Enterobacter aerogenes.

J. Gerlt, G. Whitman, 1975, The Journal of biological chemistry.

The mechanism of action of 5'-adenylic acid-activated threonine dehydrase. V. Relation between ligand-induced allosteric activation and the protomeroligomer interconversion.

J. Gerlt, W. Wood, C. Dunne, 1973, The Journal of biological chemistry.

'Democratized' genomic enzymology web tools for functional assignment.

Rémi Zallot, John A Gerlt, J. Gerlt, 2018, Current opinion in chemical biology.

Oxygen chiral phosphate esters.

J. Gerlt, J. Coderre, S. Mehdi, 1983, Advances in enzymology and related areas of molecular biology.

Mechanistic diversity in the RuBisCO superfamily: the "enolase" in the methionine salvage pathway in Geobacillus kaustophilus.

Heidi J Imker, Heidi J. Imker, Steven C Almo, 2007, Biochemistry.

Oxygen chiral phosphodiesters. 3. Use of 17O NMR spectroscopy to demonstrate configurational differences in the diastereomers of cyclic 2′-deoxyadenosine 3′,5′-[17O,18O]monophosphate

J. Gerlt, D. Traficante, J. Coderre, 1981 .

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

V. de Crécy-Lagard, J. Gerlt, S. Almo, 2019, Proceedings of the National Academy of Sciences.

Oxygen chiral phosphodiesters. 1. Synthesis and configurational analysis of cyclic [18O]-2'-deoxyadenosine 3',5'-monophosphate

J. Gerlt, J. Coderre, 1980 .

Theoretical calculations on the geometric destabilization of 3′,5′- and 2′,3′-cyclic nucleotides

P. Kollman, P. Weiner, G. L. Kenyon, 1980 .

Thermochemical identification of the structural factors responsible for the thermodynamic instability of 3',5'-cyclic nucleotides

J. Gerlt, N. Gutterson, B. Belleau, 1980 .

Stereochemistry of the hydrolysis of the endo isomer of uridine 2',3'-cyclic phosphorothioate catalyzed by the nonspecific phosphohydrolase from Enterobacter aerogenes.

J. Gerlt, W. Wan, Winnie H. Y. Wan, 1979, Biochemistry.

Syntheses and configurational assignments of the diastereomers of the 4-nitrophenyl esters of thymidine 3′-(N-phenyl phosphoramidate) and thymidine 5′-(N-phenyl phosphoramidate)

J. Gerlt, W. Rogers, J. Coderre, 1980 .

Understanding enzymic catalysis: the importance of short, strong hydrogen bonds.

P. Frey, J. Gerlt, W. Cleland, 1997, Chemistry & biology.

Structure of D-ribulose 5-phosphate 3-epimerase from Synechocystis to 1.6 A resolution.

I. Rayment, J. Gerlt, E. Wise, 2004, Acta crystallographica. Section D, Biological crystallography.

Use of Chiral [16O,17O,18O]Phosphate Esters to Determine the Stereochemical Course of Enzymatic Phosphoryl Transfer Reactions

J. Gerlt, 2012 .

Syntheses and configurational analyses of thymidine 4-nitrophenyl [17O,18O]phosphates and the stereochemical course of a reaction catalyzed by bovine pancreatic deoxyribonuclease I.

J. Gerlt, S. Mehdi, 1984, Biochemistry.

Oxygen chiral phosphodiesters—8 : Stereochemical course of the base-catalyzed hydrolysis of cyclic 2'-deoxyadenosine 3',5'-[17O, 18O]monophosphate

J. Gerlt, J. Coderre, S. Mehdi, 1983 .

OXYGEN CHIRAL PHOSPHODIESTERS. 3. USE OF OXYGEN-17 NMR SPECTROSCOPY TO DEMONSTRATE CONFIGURATIONAL DIFFERENCES IN THE DIASTEREOMERS OF CYCLIC 2′-DEOXYADENOSINE 3′,5′-(17O,18O)MONOPHOSPHATE

J. Gerlt, D. Traficante, J. Coderre, 1981 .

Evolution of enzymatic activities in the enolase superfamily: L-fuconate dehydratase from Xanthomonas campestris.

Steven C Almo, John A Gerlt, Wen Shan Yew, 2006, Biochemistry.

Evolution of Enzyme Function and the Development of Catalytic Efficiency: Triosephosphate Isomerase, Jeremy R. Knowles, and W. John Albery.

J. Gerlt, 2021, Biochemistry.

Experimental Strategies for Functional Annotation and Metabolism Discovery: Targeted Screening of Solute Binding Proteins and Unbiased Panning of Metabolomes

Ronald J. Quinn, Steven C. Almo, Matthew P. Jacobson, 2014, Biochemistry.

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

J. Gerlt, S. Almo, D. Wichelecki, 2014, Biochemistry.

Identification of the in Vivo Function of the High-Efficiency d-Mannonate Dehydratase in Caulobacter crescentus NA1000 from the Enolase Superfamily

J. Gerlt, S. Almo, D. Wichelecki, 2014 .

Enzyme Architecture: Deconstruction of the Enzyme-Activating Phosphodianion Interactions of Orotidine 5′-Monophosphate Decarboxylase

Lawrence M. Goldman, J. Gerlt, J. Richard, 2014, Journal of the American Chemical Society.

Evolution of enzymatic activity in the enolase superfamily: structural studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis.

I. Rayment, J. Gerlt, J. Thoden, 2004, Biochemistry.

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

Matthew P Jacobson, Suwen Zhao, Brian San Francisco, 2016, Proceedings of the National Academy of Sciences.

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

Matthew P Jacobson, Chakrapani Kalyanaraman, Stephen K Burley, 2009, Biochemistry.

Crystal structure and functional assignment of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12.

John A Gerlt, V. Fülöp, J. Gerlt, 2008, Biochemistry.

Evolution of enzymatic activities in the enolase superfamily: structure of a substrate-liganded complex of the L-Ala-D/L-Glu epimerase from Bacillus subtilis.

I. Rayment, J. Gerlt, V. A. Klenchin, 2004, Biochemistry.

Pyridoxal 5’-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes

V. de Crécy-Lagard, J. Gerlt, R. Denise, 2023, Microbial genomics.

Evolutionary potential of (beta/alpha)8-barrels: stepwise evolution of a "new" reaction in the enolase superfamily.

John A Gerlt, J. Gerlt, J. E. Vick, 2007, Biochemistry.

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

O. Fiehn, S. Copley, V. de Crécy-Lagard, 2016, ACS chemical biology.

Prediction of enzymatic pathways by integrative pathway mapping

Henry Lin, Andrej Sali, Matthew P Jacobson, 2018, eLife.

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

J. Gerlt, S. Almo, M. Jacobson, 2015, Journal of the American Chemical Society.

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

Eyal Akiva, Matthew P Jacobson, Suwen Zhao, 2014, eLife.

Epoxyqueuosine Reductase QueH in the Biosynthetic Pathway to tRNA Queuosine Is a Unique Metalloenzyme.

V. de Crécy-Lagard, J. Gerlt, A. Angerhofer, 2021, Biochemistry.

Mandelate pathway of Pseudomonas putida: sequence relationships involving mandelate racemase, (S)-mandelate dehydrogenase, and benzoylformate decarboxylase and expression of benzoylformate decarboxylase in Escherichia coli.

P. Babbitt, G. L. Kenyon, J. Gerlt, 1990, Biochemistry.

Functional assignment of multiple catabolic pathways for d-apiose

Steven C. Almo, Hua Huang, Matthew W. Vetting, 2018, Nature Chemical Biology.

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

J. Gerlt, S. Almo, M. Vetting, 2016, Acta crystallographica. Section F, Structural biology communications.

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

Ritesh Kumar, Patricia C. Babbitt, Steven C. Almo, 2016 .

Evolution of an enzyme active site: the structure of a new crystal form of muconate lactonizing enzyme compared with mandelate racemase and enolase.

P C Babbitt, G L Kenyon, G A Petsko, 1998, Proceedings of the National Academy of Sciences of the United States of America.

Divergent function in the crotonase superfamily: an anhydride intermediate in the reaction catalyzed by 3-hydroxyisobutyryl-CoA hydrolase.

J. Gerlt, B. Wong, 2003, Journal of the American Chemical Society.

Deletion of the omega-loop in the active site of staphylococcal nuclease. 2. Effects on protein structure and dynamics.

D. Torchia, J. Gerlt, D. Baldisseri, 1991, Biochemistry.

Deletion of the omega-loop in the active site of staphylococcal nuclease. 1. Effect on catalysis and stability.

J. Gerlt, L. Poole, S. Hale, 1991, Biochemistry.

Site-directed mutants of staphylococcal nuclease. Detection and localization by 1H NMR spectroscopy of conformational changes accompanying substitutions for glutamic acid-43.

J. Gerlt, P. H. Bolton, N. Stolowich, 1987, Biochemistry.

Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal structure of mandelate racemase at 2.5-A resolution: identification of the active site and possible catalytic residues.

G. Petsko, G. L. Kenyon, J. Gerlt, 1991, Biochemistry.

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

J. Gerlt, A. Fedorov, E. Fedorov, 2012, Biochemistry.

Oxygen chiral phosphodiesters. 2. Enzymic synthesis and configurational analysis of [.alpha.-18O]-2'-deoxyadenosine 5'-diphosphate

J. Gerlt, J. Coderre, 1980 .

3 Phosphate Ester Hydrolysis

J. Gerlt, 1992 .

OXYGEN CHIRAL PHOSPHODIESTERS. 2. ENZYMIC SYNTHESIS AND CONFIGURATIONAL ANALYSIS OF (α-18O)-2′-DEOXYADENOSINE 5′-DIPHOSPHATE

J. Gerlt, J. Coderre, 1981 .

Oxygen chiral phosphodiesters. 5. Stereochemical course of the hydrolysis of thymidine 3'-[(4-nitrophenyl)[17O,18O]phosphate] in water (oxygen-16) catalyzed by the exonuclease from bovine spleen

J. Gerlt, S. Mehdi, 1982 .

Mechanism of the reaction catalyzed by mandelate racemase: importance of electrophilic catalysis by glutamic acid 317.

G. Petsko, J. Clifton, G. L. Kenyon, 1995, Biochemistry.

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

John A Gerlt, J. Gerlt, 2017, Biochemistry.

Structural basis for substrate specificity in phosphate binding (beta/alpha)8-barrels: D-allulose 6-phosphate 3-epimerase from Escherichia coli K-12.

J. Gerlt, A. Fedorov, E. Fedorov, 2008, Biochemistry.

Barrels in pieces?

P. Babbitt, J. Gerlt, 2001, Nature Structural Biology.

Evolution of enzymatic activity in the enolase superfamily: structure of o-succinylbenzoate synthase from Escherichia coli in complex with Mg2+ and o-succinylbenzoate.

I. Rayment, J. Gerlt, E. Taylor, 2000, Biochemistry.

New functions from old scaffolds: how nature reengineers enzymes for new functions.

P C Babbitt, P. Babbitt, J. Gerlt, 2000, Advances in protein chemistry.

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

H. Nothaft, C. Szymanski, J. Gerlt, 2020, Communications Biology.

Crystal and molecular structure of 5-ethoxytrimethylenephosphoric acid

J. Gerlt, R. D. Adams, D. Chodosh, 1980 .

Theoretical calculations of hydrolysis energies of "high-energy" molecules. 3. Theoretical calculations on the geometric destabilization of 3',5'- and 2',3'-cyclic nucleotides

P. Weiner, G. L. Kenyon, J. Gerlt, 1980 .

Conformational properties of 5-alkoxy and 5-alkyl substituted trimethylene phosphates in solution

J. Gerlt, N. Gutterson, J. Sokolow, 1980 .

Evolution of function in the crotonase superfamily: the stereochemical course of the reaction catalyzed by 2-ketocyclohexanecarboxyl-CoA hydrolase.

J. Gerlt, E. Eberhard, 2004, Journal of the American Chemical Society.

A RubisCO like protein links SAM metabolism with isoprenoid biosynthesis

Heidi J. Imker, Jonathan V. Sweedler, Tobias J. Erb, 2012, Nature chemical biology.

New reactions in the crotonase superfamily: structure of methylmalonyl CoA decarboxylase from Escherichia coli.

H M Holden, J. Gerlt, H. Holden, 2000, Biochemistry.

Identification and Characterization of a Mandelamide Hydrolase and an NAD(P)+-Dependent Benzaldehyde Dehydrogenase from Pseudomonas putida ATCC 12633

P. Babbitt, G. L. Kenyon, J. Gerlt, 2003, Journal of bacteriology.

Isotopic labeling with hydrogen-2 and carbon-13 to compare conformations of proteins and mutants generated by site-directed mutagenesis, II.

J. Gerlt, P. H. Bolton, T. Pourmotabbed, 1989, Methods in enzymology.

Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: enhancing the promiscuous D-arabino-hex-3-ulose 6-phosphate synthase reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase.

I. Rayment, J. Gerlt, E. Wise, 2005, Biochemistry.

Characterization of conformational features of DNA heteroduplexes containing aldehydic abasic sites.

J. Gerlt, P. H. Bolton, J. Withka, 1991, Biochemistry.

Evolutionary potential of (beta/alpha)8-barrels: functional promiscuity produced by single substitutions in the enolase superfamily.

Jeremy Minshull, Patricia C Babbitt, Emily C Mundorff, 2003, Biochemistry.

Understanding the rates of certain enzyme-catalyzed reactions: proton abstraction from carbon acids, acyl-transfer reactions, and displacement reactions of phosphodiesters.

P. G. Gassman, J. Gerlt, 1993, Biochemistry.

Evolution of enzymatic activities in the enolase superfamily: N-succinylamino acid racemase and a new pathway for the irreversible conversion of D- to L-amino acids.

J. Gerlt, F. Raushel, A. Sakai, 2006, Biochemistry.

Evolutionary Potential of (β/α)8-Barrels: In Vitro Enhancement of a “New” Reaction in the Enolase Superfamily†

John Alan Gerlt, J. Gerlt, J. E. Vick, 2005 .

Oxygen-17 NMR spectral properties of simple phosphate esters and adenine nucleotides

J. Gerlt, P. Demou, S. Mehdi, 1982 .

Stereochemical course of the hydrolysis of thymidine 5'-(4-nitrophenyl [17O,18O]phosphate) in H216O catalyzed by the phosphodiesterase from snake venom.

J. Gerlt, S. Mehdi, 1981, The Journal of biological chemistry.

Mechanism of the adenylate cyclase reaction. Stereochemistry of the reaction catalyzed by the enzyme from Brevibacterium liquefaciens.

J. Gerlt, J. Coderre, M. Wolin, 1980, The Journal of biological chemistry.

Discovery of a Novel l-Lyxonate Degradation Pathway in Pseudomonas aeruginosa PAO1

J. Gerlt, S. Almo, S. Swaminathan, 2014, Biochemistry.

Evolution of Enzymatic Activities in the Enolase Superfamily: Galactarate Dehydratase III from Agrobacterium tumefaciens C58

Steven C. Almo, Matthew P. Jacobson, Chakrapani Kalyanaraman, 2014, Biochemistry.

Galactaro δ-Lactone Isomerase: Lactone Isomerization by a Member of the Amidohydrolase Superfamily

J. Gerlt, S. Almo, M. Vetting, 2014, Biochemistry.

Evolution of enzymatic activities in the enolase superfamily: L-talarate/galactarate dehydratase from Salmonella typhimurium LT2.

Steven C Almo, John A Gerlt, Wen Shan Yew, 2007, Biochemistry.

Enzymatic and Structural Characterization of rTSγ Provides Insights into the Function of rTSβ

Wyatt W. Yue, J. Gerlt, W. Yue, 2014, Biochemistry.

Insights Into the Function of Rtsbeta.

J. Gerlt, W. Yue, D. S. Froese, 2014 .

Evolution of function in ( b / a ) 8-barrel enzymes

John A Gerlt, J. Gerlt, F. Raushel, 2003 .

Tools and strategies for discovering novel enzymes and metabolic pathways

J. Gerlt, 2016 .

Evolution of enzymatic activity in the enolase superfamily: functional studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis.

Ivan Rayment, John A Gerlt, I. Rayment, 2004, Biochemistry.

Cloning, DNA sequence analysis, and expression in Escherichia coli of the gene for mandelate racemase from Pseudomonas putida.

G. L. Kenyon, J. Gerlt, S. Ransom, 1988, Biochemistry.

Homologous (β/α)8-Barrel enzymes that catalyze unrelated reactions: Orotidine 5'-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase

P. Babbitt, I. Rayment, J. Gerlt, 2002 .

Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase.

Patricia C Babbitt, Steven C Almo, John A Gerlt, 2008, Biochemistry.

Thermal denaturation of staphylococcal nuclease.

J. Gerlt, J. Sturtevant, N. Stolowich, 1985, Biochemistry.

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.

J. Gerlt, Weiming Wu, J. Richard, 2012, Journal of the American Chemical Society.

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

J. Gerlt, J. Richard, T. L. Amyes, 2010, Biochemistry.

Dissecting the total transition state stabilization provided by amino acid side chains at orotidine 5'-monophosphate decarboxylase: a two-part substrate approach.

J. Gerlt, J. Richard, T. L. Amyes, 2008, Biochemistry.

Product deuterium isotope effect for orotidine 5'-monophosphate decarboxylase: evidence for the existence of a short-lived carbanion intermediate.

J. Gerlt, J. Richard, T. L. Amyes, 2007, Journal of the American Chemical Society.

Evolution of function in (beta/alpha)8-barrel enzymes.

J. Gerlt, F. Raushel, 2003, Current opinion in chemical biology.

Structural evidence for a 1,2-enediolate intermediate in the reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase, a member of the orotidine 5'-monophosphate decarboxylase suprafamily.

I. Rayment, J. Gerlt, E. Wise, 2003, Biochemistry.

Evolutionary potential of (beta/alpha)8-barrels: in vitro enhancement of a "new" reaction in the enolase superfamily.

John A Gerlt, J. Gerlt, J. E. Vick, 2005, Biochemistry.

The Need for Manuscripts To Include Database Identifiers for Proteins.

John Alan Gerlt, J. Gerlt, 2018, Biochemistry.

Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies

Stephen K. Burley, Narayanan Eswar, Ursula Pieper, 2009, Journal of Structural and Functional Genomics.

EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools.

J. Gerlt, Nils Oberg, Rémi Zallot, 2023, Journal of molecular biology.

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

Shoshana D. Brown, P. Babbitt, J. Gerlt, 2013, Nature.

Prediction of enzymatic pathways by integrative pathway mapping

Matthew J. O’Meara, Daniel Russel, A. Sali, 2018, eLife.

Prediction and Biochemical Demonstration of a Catabolic Pathway for the Osmoprotectant Proline Betaine

J. Gerlt, S. Almo, M. Jacobson, 2014, mBio.

Mechanism of the reaction catalyzed by staphylococcal nuclease: identification of the rate-determining step.

J. Gerlt, L. Poole, S. Hale, 1993, Biochemistry.

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

Hua Huang, Matthew W Vetting, Steven C Almo, 2015, Journal of the American Chemical Society.

Evolution of function in the crotonase superfamily: (3S)-methylglutaconyl-CoA hydratase from Pseudomonas putida.

J. Gerlt, B. Wong, 2004, Biochemistry.

**1**5N AND **1**7O NMR STUDIES OF THE PROTON BINDING SITES IN IMIDODIPHOSPHATE, TETRAETHYL IMIDODIPHOSPHATE, AND ADENYLYL IMIDODIPHOSPHATE.

N. Oppenheimer, G. L. Kenyon, J. Gerlt, 1983 .

Nitrogen-15 and oxygen-17 NMR studies of the proton binding sites in imidodiphosphate, tetraethyl imidodiphosphate, and adenylyl imidodiphosphate

N. Oppenheimer, G. L. Kenyon, J. Gerlt, 1984 .

Protein engineering to study enzyme catalytic mechanisms

J. Gerlt, 1994 .

17O NMR Spectral Properties of Pyrophosphate, Simple Phosphonates, and Thiophosphate and Phosphonate Analogues of ATP

G. L. Kenyon, J. Gerlt, P. Demou, 1983 .

OXYGEN-17 NMR SPECTRAL PROPERTIES OF PYROPHOSPHATE, SIMPLE PHOSPHONATES, AND THIOPHOSPHATE AND PHOSPHONATE ANALOGUES OF ATP

G. L. Kenyon, J. Gerlt, P. Demou, 1984 .

“Fishing” for the functional proteome

J. Gerlt, 2002, Nature Biotechnology.

The mechanism of action of 5'-adenylic acid-activated threonine dehydrase. IV. Characterization of kinetic effect of adenosine monophosphate.

J. Gerlt, W. Wood, C. Dunne, 1973, The Journal of biological chemistry.

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

J. Gerlt, A. Fedorov, S. Almo, 2013, Biochemistry.

Mechanistic diversity in the RuBisCO superfamily: a novel isomerization reaction catalyzed by the RuBisCO-like protein from Rhodospirillum rubrum.

Heidi J. Imker, J. Gerlt, F. Tabita, 2008, Biochemistry.

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

Heidi J. Imker, J. Gerlt, K. Whalen, 2015, Biochimica et biophysica acta.

The Enzyme Function Initiative.

Heidi J. Imker, A. Sali, P. Babbitt, 2011, Biochemistry.

Sleeping beauty mutase (sbm) is expressed and interacts with ygfd in Escherichia coli.

M. Surette, J. Gerlt, D. S. Froese, 2009, Microbiological research.

Discovery of Function in the Enolase Superfamily

S. Martinis, J. Gerlt, T. Lukk, 2009 .

Evolution of enzymatic activity in the enolase superfamily: structural studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis.

I. Rayment, J. Gerlt, J. Thoden, 2004, Biochemistry.

No Job Name

I. Rayment, J. Gerlt, J. Thoden, 2022 .

Evolution of enzymatic activity in the enolase superfamily: structural and mutagenic studies of the mechanism of the reaction catalyzed by o-succinylbenzoate synthase from Escherichia coli.

I. Rayment, J. Gerlt, V. A. Klenchin, 2003, Biochemistry.

Mechanism of the reaction catalyzed by mandelate racemase. 3. Asymmetry in reactions catalyzed by the H297N mutant.

G. L. Kenyon, J. Gerlt, S. Ransom, 1991, Biochemistry.

Mechanism of the reaction catalyzed by mandelate racemase. 1. Chemical and kinetic evidence for a two-base mechanism.

G L Kenyon, G. L. Kenyon, J. Gerlt, 1991, Biochemistry.

Enthalpy of hydrolysis of simple phosphate diesters

J. Gerlt, J. Sturtevant, F. Westheimer, 1973 .

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

Heidi J. Imker, J. Gerlt, F. Tabita, 2012, Biochemistry.

A Protein Structure (or Function ?) Initiative.

J. Gerlt, 2007, Structure.