John Alan Gerlt

1973 …2019
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Research Output 1973 2019

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Article
2000

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

Benning, M. M., Haller, T., Gerlt, J. A. & Holden, H. M., Apr 25 2000, In : Biochemistry. 39, 16, p. 4630-4639 10 p.

Research output: Contribution to journalArticle

Methylmalonyl-CoA Decarboxylase
Enoyl-CoA Hydratase
Escherichia coli
Catalytic Domain
Sulfides
1999

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

Wieczorek, S. J., Kalivoda, K. A., Clifton, J. G., Ringe, D., Petsko, G. A. & Gerlt, J. A., May 12 1999, In : Journal of the American Chemical Society. 121, 18, p. 4540-4541 2 p.

Research output: Contribution to journalArticle

galactonate dehydratase
Phosphopyruvate Hydratase
Escherichia coli
Catalytic Domain
Catalysts

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

Palmer, D. R. J., Garrett, J. B., Sharma, V., Meganathan, R., Babbitt, P. C. & Gerlt, J. A., Apr 6 1999, In : Biochemistry. 38, 14, p. 4252-4258 7 p.

Research output: Contribution to journalArticle

Racemases and Epimerases
Acids
Enzymes
Proteins
Phosphopyruvate Hydratase
1998

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

Hasson, M. S., Schlichting, I., Moulai, J., Taylor, K., Barrett, W., Kenyon, G. L., Babbitt, P. C., Gerlt, J. A., Petsko, G. A. & Ringe, D., Sep 1 1998, In : Proceedings of the National Academy of Sciences of the United States of America. 95, 18, p. 10396-10401 6 p.

Research output: Contribution to journalArticle

mandelate racemase
Phosphopyruvate Hydratase
Catalytic Domain
Enzymes
Metals

Evolution of enzymatic activities in the enolase superfamily: Partitioning of reactive intermediates by (D)-glucarate dehydratase from Pseudomonas putida

Palmer, D. R. J., Hubbard, B. K. & Gerlt, J. A., Oct 13 1998, In : Biochemistry. 37, 41, p. 14350-14357 8 p.

Research output: Contribution to journalArticle

Pseudomonas putida
Phosphopyruvate Hydratase
Dehydration
mandelate racemase
Isotopes

Evolution of enzymatic activities in the enolase superfamily: Crystal structure of (D)-glucarate dehydratase from Pseudomonas putida

Gulick, A. M., Palmer, D. R. J., Babbitt, P. C., Gerlt, J. A. & Rayment, I., Oct 13 1998, In : Biochemistry. 37, 41, p. 14358-14368 11 p.

Research output: Contribution to journalArticle

mandelate racemase
Pseudomonas putida
Phosphopyruvate Hydratase
Crystal structure
R388

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

Hubbard, B. K., Koch, M., Palmer, D. R. J., Babbitt, P. C. & Gerlt, J. A., Oct 13 1998, In : Biochemistry. 37, 41, p. 14369-14375 7 p.

Research output: Contribution to journalArticle

Phosphopyruvate Hydratase
Escherichia coli
Genes
glycerate kinase
4 alpha-glucanotransferase

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

Gerlt, J. A. & Babbitt, P. C., Jan 1 1998, In : Current Opinion in Chemical Biology. 2, 5, p. 607-612 6 p.

Research output: Contribution to journalArticle

Catalysis
Catalyst activity
Catalytic Domain
Substrates
Enzymes

Structure and mechanism of benzoylformate decarboxylase, a thiamin dtthosphate-dependent enzyme

Kenvon, Q. L., Hasson, M. S., Muscate, A., McLeish, M. J., Harris, T. K., Babbitt, P. Ç., Gerlt, J. A., Petsko, G. A. & Rinye, D., 1998, In : FASEB Journal. 12, 8

Research output: Contribution to journalArticle

benzoylformate decarboxylase
Thiamine
Thiamine Pyrophosphate
R388
Enzymes

The crystal structure of benzoylformate decarboxylase at 1.6 Å Resolution: Diversity of catalytic residues in thiamin diphosphate-dependent enzymes

Hasson, M. S., Muscate, A., McLeish, M. J., Polovnikova, L. S., Gerlt, J. A., Kenyon, G. L., Petsko, G. A. & Ringe, D., Jul 14 1998, In : Biochemistry. 37, 28, p. 9918-9930 13 p.

Research output: Contribution to journalArticle

benzoylformate decarboxylase
Thiamine Pyrophosphate
Crystal structure
Enzymes
R388
1997
galactonate dehydratase
Pseudomonas putida
Dehydration
Escherichia coli
Enzymes

Stereochemistry of the reaction catalyzed by galactonate dehydratase

Wieczorek, S. J., Mrachko, G. T. & Gerlt, J. A., 1997, In : FASEB Journal. 11, 9

Research output: Contribution to journalArticle

galactonate dehydratase
Stereochemistry
deuterium
Deuterium
stereochemistry

The enolase superfamily: Different reactions catalyzed by similar active sites

Gerlt, J. A. & Babbitt, P. C., 1997, In : FASEB Journal. 11, 9

Research output: Contribution to journalArticle

phosphopyruvate hydratase
Phosphopyruvate Hydratase
mandelate racemase
active sites
Functional groups
1996
Escherichia coli Proteins
Phosphates
Deoxyribose
Gas chromatography
Gas Chromatography-Mass Spectrometry

Enzyme-catalyzed enolization reactions: A theoretical study on the energetics of concerted and stepwise pathways

Sargent, A. L., Rollog, M. E., Almlöf, J. E., Gassman, P. G. & Gerlt, J. A., Dec 11 1996, In : Journal of Molecular Structure: THEOCHEM. 388, 1-3, p. 145-159 15 p.

Research output: Contribution to journalArticle

Proton transfer
Protons
enzymes
Potential energy surfaces
Theoretical Models
Pseudomonas putida
glucarate dehydratase

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

Highbarger, L. A., Gerlt, J. A. & Kenyon, G. L., Jan 9 1996, In : Biochemistry. 35, 1, p. 41-46 6 p.

Research output: Contribution to journalArticle

acetoacetate decarboxylase
Schiff Bases
Ammonium Compounds
Lysine
Catalytic Domain

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

Schafer, S. L., Barrett, W. C., Kallarakal, A. T., Mitra, B., Kozarich, J. W., Gerlt, J. A., Clifton, J. G., Petsko, G. A. & Kenyon, G. L., May 7 1996, In : Biochemistry. 35, 18, p. 5662-5669 8 p.

Research output: Contribution to journalArticle

mandelate racemase
Biochemistry
Acids
Catalysts
Catalytic Domain

The enolase superfamily: A general strategy for enzyme-catalyzed abstraction of the α-protons of carboxylic acids

Babbitt, P. C., Hasson, M. S., Wedekind, J. E., Palmer, D. R. J., Barrett, W. C., Reed, G. H., Rayment, I., Ringe, D., Kenyon, G. L. & Gerlt, J. A., Dec 24 1996, In : Biochemistry. 35, 51, p. 16489-16501 13 p.

Research output: Contribution to journalArticle

Phosphopyruvate Hydratase
Carboxylic Acids
Protons
Enzymes
galactonate dehydratase
1995

A functionally diverse enzyme superfamily than abstracts the α protons of carboxylic acids

Babbitt, P. C., Mrachko, G. T., Hasson, M. S., Huisman, G. W., Kolter, R., Ringe, D., Petsko, G. A., Kenyon, G. L. & Gerlt, J. A., Jan 1 1995, In : Science. 267, 5201, p. 1159-1161 3 p.

Research output: Contribution to journalArticle

mandelate racemase
galactonate dehydratase
Carboxylic Acids
Protons
Catalytic Domain

Mandelate Racemase: Structure-Function Studies of a Pseudosymmetric Enzyme

Kenyon, G. L., Gerlt, J. A., Petsko, G. A. & Kozarich, J. W., Jan 1 1995, In : Accounts of chemical research. 28, 4, p. 178-186 9 p.

Research output: Contribution to journalArticle

Mechanism of the Reaction Catalyzed by Mandelate Racemase: Importance of Electrophilic Catalysis by Glutamic Acid 317

Mitra, B., Kallarakal, A. T., Kozarich, J. W., Gerlt, J. A., Clifton, J. G., Petsko, G. A. & Kenyon, G. L., Jan 1 1995, In : Biochemistry. 34, 9, p. 2777-2787 11 p.

Research output: Contribution to journalArticle

mandelate racemase
Catalysis
Glutamic Acid
Biochemistry
Acids

Mechanism of the Reaction Catalyzed by Mandelate Racemase: Structure and Mechanistic Properties of the K166R Mutant

Kallarakal, A. T., Mitra, B., Kozarich, J. W., Gerlt, J. A., Clifton, J. G., Petsko, G. A. & Kenyon, G. L., Jan 1 1995, In : Biochemistry. 34, 9, p. 2788-2797 10 p.

Research output: Contribution to journalArticle

mandelate racemase
Biochemistry
Protons
Deuterium
Substrates
1994

Protein engineering to study enzyme catalytic mechanisms

Gerlt, J. A., Jan 1 1994, In : Current Opinion in Structural Biology. 4, 4, p. 593-600 8 p.

Research output: Contribution to journalArticle

Protein Engineering
Catalytic Domain
Enzymes
Hydrogen Bonding
Catalysis

The Role of Lysine 166 in the Mechanism of Mandelate Racemase from Pseudomonas putida: Mechanistic and Crystallographic Evidence for Stereospecific Alkylation by (R)-α-Phenylglycidate

Landro, J. A., Gerlt, J. A., Kozarich, J. W., Koo, C. W., Shah, V. J., Kenyon, G. L., Neidhart, D. J., Fujita, S. & Petsko, G. A., Jan 1 1994, In : Biochemistry. 33, 3, p. 635-643 9 p.

Research output: Contribution to journalArticle

mandelate racemase
Pseudomonas putida
Alkylation
Lysine
Protons
1993
Protons
Carbon
Enzymes
enzyme
Acids

A Novel Structural Basis for Membrane Association of a Protein: Construction of a Chimeric Soluble Mutant of (S)-Mandelate Dehydrogenase from Pseudomonas putida

Mitra, B., Gerlt, J. A., Babbitt, P. C., Koo, C. W., Kenyon, G. L., Joseph, D. & Petsko, G. A., Jan 1 1993, In : Biochemistry. 32, 48, p. 12959-12967 9 p.

Research output: Contribution to journalArticle

Pseudomonas putida
Oxidoreductases
Membranes
Proteins
Membrane Proteins

Mechanism of the Reaction Catalyzed by Staphylococcal Nuclease: Identification of the Rate-Determining Step

Hale, S. P., Poole, L. B. & Gerlt, J. A., Jan 1 1993, In : Biochemistry. 32, 29, p. 7479-7487 9 p.

Research output: Contribution to journalArticle

Micrococcal Nuclease
Cats
Viscosity
Hydrolysis
Kinetic parameters

On the origin of enzymatic species

Petsko, G. A., Kenyon, G. L., Gerlt, J. A., Ringe, D. & Kozarich, J. W., Jan 1 1993, In : Trends in Biochemical Sciences. 18, 10, p. 372-376 5 p.

Research output: Contribution to journalArticle

Enzymes
Proteins

The structural enzymology of proton-transfer reactions

Petsko, G., Ringe, D., Allen, K., Lavie, A., Gerhart-Mueller, E., Clifton, J., Hasson, M., Fujita, S., Sugio, S., Xhang, X., Davenport, R., Lolis, E., Neidhart, D., Kenyon, G., Gerlt, J. A., Bash, P., Knowles, J. & Karplus, M., Jan 1 1993, In : Protein Engineering, Design and Selection. 6, 1 p.

Research output: Contribution to journalArticle

Proton transfer
Protons
Enzymes
Racemases and Epimerases
Isomerases
Protons
Carbon
Oxygen
Acids
Enzymes
1992

Mandelate racemase and class-related enzymes

Gerlt, J. A., Kenyon, G. L., Kozarich, J. W., Neidhart, D. J., Petsko, G. A. & Powers, V. M., Jan 1 1992, In : Current Opinion in Structural Biology. 2, 5, p. 736-742 7 p.

Research output: Contribution to journalArticle

mandelate racemase
Racemases and Epimerases
Chemical Models
Enzymes
Catalysis

Phosphate Ester Hydrolysis

Gerlt, J. A., Jan 1 1992, In : Enzymes. 20, C, p. 95-139 45 p.

Research output: Contribution to journalArticle

Anions
Hydrolysis
Esters
Phosphates
Phosphorus
Protons
Carbon
Enzymes
enzyme
Acids
1991

Characterization of Conformational Features of DNA Heteroduplexes Containing Aldehydic Abasic Sites

Withka, J. M., Wilde, J. A., Bolton, P. H., Mazumder, A. & Gerlt, J. A., Oct 1 1991, In : Biochemistry. 30, 41, p. 9931-9940 10 p.

Research output: Contribution to journalArticle

Nucleic Acid Heteroduplexes
Base Pairing
DNA
Aldehydes
Deoxyribose

Deletion of the Ω-Loop in the Active Site of Staphylococcal Nuclease. 1. Effect on Catalysis and Stability

Poole, L. B., Deborah Loveys, A., Hale, S. P., Gerlt, J. A., Stanczyk, S. M. & Bolton, P. H., Apr 1 1991, In : Biochemistry. 30, 15, p. 3621-3627 7 p.

Research output: Contribution to journalArticle

Micrococcal Nuclease
Catalysis
Biochemistry
Hydrogen
Catalytic Domain

Deletion of the Ω-Loop in the Active Site of Staphylococcal Nuclease. 2. Effects on Protein Structure and Dynamics

Baldisseri, D. M., Torchia, D. A., Poole, L. B. & Gerlt, J. A., Apr 1 1991, In : Biochemistry. 30, 15, p. 3628-3633 6 p.

Research output: Contribution to journalArticle

Micrococcal Nuclease
Catalytic Domain
Enzymes
Chemical shift
Proteins

Mechanism of the Reaction Catalyzed by Mandelate Racemase. 1. Chemical and Kinetic Evidence for a Two-Base Mechanism

Powers, V. M., Koo, C. W., Kenyon, G. L., Gerlt, J. A. & Kozarich, J. W., Sep 1 1991, In : Biochemistry. 30, 38, p. 9255-9263 9 p.

Research output: Contribution to journalArticle

mandelate racemase
Hydrogen
Kinetics
Substrates
Diazomethane

Mechanism of the Reaction Catalyzed by Mandelate Racemase. 2. Crystal Structure of Mandelate Racemase at 2.5-Å Resolution: Identification of the Active Site and Possible Catalytic Residues

Neidhart, D. J., Howell, P. L., Petsko, G. A., Powers, V. M., Li, R., Kenyon, G. L. & Gerlt, J. A., Sep 1 1991, In : Biochemistry. 30, 38, p. 9264-9273 10 p.

Research output: Contribution to journalArticle

mandelate racemase
Catalytic Domain
Crystal structure
R388
Substrates

Mechanism of the Reaction Catalyzed by Mandelate Racemase. 3. Asymmetry in Reactions Catalyzed by the H297N Mutant

Landro, J. A., Kallarakal, A. T., Ransom, S. C., Gerlt, J. A., Kozarich, J. W., Neidhart, D. J. & Kenyon, G. L., Sep 1 1991, In : Biochemistry. 30, 38, p. 9274-9281 8 p.

Research output: Contribution to journalArticle

mandelate racemase
Protons
Enzymes
Mutagenesis
Biochemistry

Stereochemical Studies of the β-Elimination Reactions at Aldehydic Abasic Sites in DNA: Endonuclease III from Escherichia coli, Sodium Hydroxide, and Lys-Trp-Lys

Mazumder, A., Gerlt, J. A., Absalon, M. J., Stubbe, J. A., Cunningham, R. P., Withka, J. & Bolton, P. H., Jan 1 1991, In : Biochemistry. 30, 4, p. 1119-1126 8 p.

Research output: Contribution to journalArticle

lysyl-tryptophyl-alpha-lysine
Sodium Hydroxide
Deoxyribonuclease I
Escherichia coli
Protons

Structure of thialysine hydrochloride.

Ammon, H. L., Prasad, S. M. & Gerlt, J. A., Jan 1 1991, In : Acta crystallographica. Section C, Crystal structure communications. 47 ( Pt 7), p. 1476-1478 3 p.

Research output: Contribution to journalArticle

Ions
Propionates
Ammonium Compounds
Cations
Chlorides
1990

Kinetic and Conformational Effects of Lysine Substitutions for Arginines 35 and 87 in the Active Site of Staphylococcal Nuclease

Pourmotabbed, T., Dell’Acqua, M., Gerlt, J. A., Stanczyk, S. M. & Bolton, P. H., Apr 1 1990, In : Biochemistry. 29, 15, p. 3677-3683 7 p.

Research output: Contribution to journalArticle

Micrococcal Nuclease
Lysine
Arginine
Catalytic Domain
Substitution reactions

Mandelate Pathway of Pseudomonas putida: Sequence Relationships Involving Mandelate Racemase, (S)-Mandelate Dehydrogenase, and Benzoylformate Decarboxylase and Expression of Benzoylformate Decarboxylase in Escherichia coli

Tsou, A. Y., Ransom, S. C., Gerlt, J. A., Buechter, D. D., Babbitt, P. C. & Kenyon, G. L., Oct 1 1990, In : Biochemistry. 29, 42, p. 9856-9862 7 p.

Research output: Contribution to journalArticle

benzoylformate decarboxylase
mandelate racemase
Pseudomonas putida
Escherichia coli
Genes

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

Neidhart, D. J., Kenyon, G. L., Gerlt, J. A. & Petsko, G. A., Jan 1 1990, In : Nature. 347, 6294, p. 692-694 3 p.

Research output: Contribution to journalArticle

mandelate racemase
Racemases and Epimerases
Enzymes
Metabolic Networks and Pathways
Pseudomonas

Restructuring catalysis in the mandelate pathway

Neidhart, D. C., Howell, P. L., Petsko, G. A., Gerlt, J. A., Kozarich, J. W., Powers, V. M. & Kenyon, G. L., 1990, In : Biochemical Society Symposia. 57, p. 135-141 7 p.

Research output: Contribution to journalArticle

Mandelic Acids
Racemases and Epimerases
Isomerases
Protein Conformation
Molecular Structure
1989

Characterization of the Equilibrating Forms of the Aldehydic Abasic Site in Duplex DNA by 17O NMR

Wilde, J. A., Bolton, P. H., Mazumder, A., Manoharan, M. & Gerlt, J. A., Mar 1 1989, In : Journal of the American Chemical Society. 111, 5, p. 1894-1896 3 p.

Research output: Contribution to journalArticle

DNA
Nuclear magnetic resonance

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

Hibler, D. W., Harpold, L., Dell'Acqua, M., Pourmotabbed, T., Gerlt, J. A., Wilde, J. A. & Bolton, P. H., Jan 1 1989, In : Methods in enzymology. 177, C, p. 74-86 13 p.

Research output: Contribution to journalArticle

Mutagenesis
Protein Conformation
Mutant Proteins
Site-Directed Mutagenesis
Labeling

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

Wilde, J. A., Bolton, P. H., Hibler, D. W., Harpold, L., Pourmotabbed, T., Dell'Acqua, M. & Gerlt, J. A., Jan 1 1989, In : Methods in enzymology. 177, C, p. 282-292 11 p.

Research output: Contribution to journalArticle

Mutagenesis
Protein Conformation
Mutant Proteins
Site-Directed Mutagenesis
Labeling

Kinetic and Magnetic Resonance Studies of the Glutamate-43 to Serine Mutant of Staphylococcal Nuclease

Serpersu, E. H., Hibler, D. W., Gerlt, J. A. & Mildvan, A. S., Jan 1 1989, In : Biochemistry. 28, 4, p. 1539-1548 10 p.

Research output: Contribution to journalArticle

Micrococcal Nuclease
Magnetic resonance
Serine
Glutamic Acid
Magnetic Resonance Spectroscopy