John Alan Gerlt

1973 …2019
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Research Output 1973 2019

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2009

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

Pieper, U., Chiang, R., Seffernick, J. J., Brown, S. D., Glasner, M. E., Kelly, L., Eswar, N., Sauder, J. M., Bonanno, J. B., Swaminathan, S., Burley, S. K., Zheng, X., Chance, M. R., Almo, S. C., Gerlt, J. A., Raushel, F. M., Jacobson, M. P., Babbitt, P. C. & Sali, A., Apr 1 2009, In : Journal of Structural and Functional Genomics. 10, 2, p. 107-125 19 p.

Research output: Contribution to journalArticle

Amidohydrolases
Phosphopyruvate Hydratase
Genomics
mandelate racemase
Isomerases
2008

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

Rea, D., Hovington, R., Rakus, J. F., Gerlt, J. A., Fülöp, V., Bugg, T. D. H. & Roper, D. I., Sep 23 2008, In : Biochemistry. 47, 38, p. 9955-9965 11 p.

Research output: Contribution to journalArticle

Escherichia coli K12
Fructose-Bisphosphate Aldolase
Escherichia coli
Metal ions
Crystal structure

Discovery of a Dipeptide Epimerase Enzymatic Function Guided by Homology Modeling and Virtual Screening

Kalyanaraman, C., Imker, H. J., Fedorov, A. A., Fedorov, E. V., Glasner, M. E., Babbitt, P. C., Almo, S. C., Gerlt, J. A. & Jacobson, M. P., Nov 12 2008, In : Structure. 16, 11, p. 1668-1677 10 p.

Research output: Contribution to journalArticle

Racemases and Epimerases
Dipeptides
muconate cycloisomerase
Proteins
Phosphopyruvate Hydratase

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

Barnett, S. A., Amyes, T. L., Wood, B. M., Gerlt, J. A. & Richard, J. P., Jul 29 2008, In : Biochemistry. 47, 30, p. 7785-7787 3 p.

Research output: Contribution to journalArticle

Carboxy-Lyases
Phosphites
Stabilization
Amino Acids
Substrates

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

Rakus, J. F., Fedorov, A. A., Fedorov, E. V., Glasner, M. E., Hubbard, B. K., Delli, J. D., Babbitt, P. C., Almo, S. C. & Gerlt, J. A., Sep 23 2008, In : Biochemistry. 47, 38, p. 9944-9954 11 p.

Research output: Contribution to journalArticle

Hydro-Lyases
Phosphopyruvate Hydratase
Catalytic Domain
Salmonella typhimurium
Escherichia coli

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

Amyes, T. L., Wood, B. M., Chan, K., Gerlt, J. A. & Richard, J. P., Feb 6 2008, In : Journal of the American Chemical Society. 130, 5, p. 1574-1575 2 p.

Research output: Contribution to journalArticle

Uridine Monophosphate
Carboxy-Lyases
deuterium
Deuterium
Protons

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

Imker, H. J., Singh, J., Warlick, B. P., Tabita, F. R. & Gerlt, J. A., Oct 28 2008, In : Biochemistry. 47, 43, p. 11171-11173 3 p.

Research output: Contribution to journalArticle

Rhodospirillum rubrum
Oxygenases
Isomerization
Proton transfer
Sulfur

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

Chan, K. K., Fedorov, A. A., Fedorov, E. V., Almo, S. C. & Gerlt, J. A., Sep 9 2008, In : Biochemistry. 47, 36, p. 9608-9617 10 p.

Research output: Contribution to journalArticle

Racemases and Epimerases
Substrate Specificity
Escherichia coli
Phosphates
Substrates
2007

Evolutionary potential of (β/α)8-barrels: Stepwise evolution of a "new" reaction in the enolase superfamily

Vick, J. E. & Gerlt, J. A., Dec 18 2007, In : Biochemistry. 46, 50, p. 14589-14597 9 p.

Research output: Contribution to journalArticle

Phosphopyruvate Hydratase
Substitution reactions
Codon
Biochemistry
Substrate Specificity

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

Rakus, J. F., Fedorov, A. A., Fedorov, E. V., Glasner, M. E., Vick, J. E., Babbitt, P. C., Almo, S. C. & Gerlt, J. A., Nov 13 2007, In : Biochemistry. 46, 45, p. 12896-12908 13 p.

Research output: Contribution to journalArticle

Phosphopyruvate Hydratase
Dehydration
Catalysts
Acids
Anions

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

Wen, S. Y., Fedorov, A. A., Fedorov, E. V., Almo, S. C. & Gerlt, J. A., Aug 21 2007, In : Biochemistry. 46, 33, p. 9564-9577 14 p.

Research output: Contribution to journalArticle

Hydro-Lyases
Salmonella
Phosphopyruvate Hydratase
Salmonella typhimurium
Dehydration

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

Imker, H. J., Fedorov, A. A., Fedorov, E. V., Almo, S. C. & Gerlt, J. A., Apr 3 2007, In : Biochemistry. 46, 13, p. 4077-4089 13 p.

Research output: Contribution to journalArticle

Geobacillus
Salvaging
Oxygenases
Phosphopyruvate Hydratase
Methionine

Obituary: Frank H. Westheimer (1912-2007).

Gerlt, J. A., Jan 1 2007, In : Nature. 447, 7144, 1 p.

Research output: Contribution to journalArticle

20th Century History
Biochemistry
Enzymes

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

Song, L., Kalyanaraman, C., Fedorov, A. A., Fedorov, E. V., Glasner, M. E., Brown, S., Imker, H. J., Babbitt, P. C., Almo, S. C., Jacobson, M. P. & Gerlt, J. A., Jan 1 2007, In : Nature chemical biology. 3, 8, p. 486-491 6 p.

Research output: Contribution to journalArticle

Amino Acid Isomerases
Proteins
Ligands
Racemases and Epimerases
Protein Databases

Product deuterium isotope effect for orotidine 5′-monophosphate decarboxylase: Evidence for the existence of a short-lived carbanion intermediate

Toth, K., Amyes, T. L., Wood, B. M., Chan, K., Gerlt, J. A. & Richard, J. P., Oct 31 2007, In : Journal of the American Chemical Society. 129, 43, p. 12946-12947 2 p.

Research output: Contribution to journalArticle

Carboxy-Lyases
Deuterium
deuterium
Isotopes
Uridine Monophosphate
2006

A gold standard set of mechanistically diverse enzyme superfamilies

Brown, S. D., Gerlt, J. A., Seffernick, J. L. & Babbitt, P., Jan 31 2006, In : Genome biology. 7, 1, R8.

Research output: Contribution to journalArticle

gold
Cluster Analysis
enzyme
Enzymes
enzymes

D-ribulose 5-phosphate 3-epimerase: Functional and structural relationships to members of the ribulose-phosphate binding (β/α) 8-barrel superfamily

Akana, J., Fedorov, A. A., Fedorov, E., Novak, W. R. P., Babbitt, P. C., Almo, S. C. & Gerlt, J. A., Feb 28 2006, In : Biochemistry. 45, 8, p. 2493-2503 11 p.

Research output: Contribution to journalArticle

Carboxy-Lyases
Phosphates
Histidine
Catalytic Domain
Ions

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

Sakai, A., Xiang, D. F., Xu, C., Song, L., Yew, W. S., Raushel, F. M. & Gerlt, J. A., Apr 11 2006, In : Biochemistry. 45, 14, p. 4455-4462 8 p.

Research output: Contribution to journalArticle

Racemases and Epimerases
Phosphopyruvate Hydratase
Amino Acids
Acids
Enzymes

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

Yew, W. S., Fedorov, A. A., Fedorov, E. V., Wood, B. M. K., Almo, S. C. & Gerlt, J. A., Dec 12 2006, In : Biochemistry. 45, 49, p. 14598-14608 11 p.

Research output: Contribution to journalArticle

mandelate racemase
Bradyrhizobium
Phosphopyruvate Hydratase
Protons
Oxaloacetic Acid

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

Yew, W. S., Fedorov, A. A., Fedorov, E. V., Rakus, J. F., Pierce, R. W., Almo, S. C. & Gerlt, J. A., Dec 12 2006, In : Biochemistry. 45, 49, p. 14582-14597 16 p.

Research output: Contribution to journalArticle

Xanthomonas campestris
Phosphopyruvate Hydratase
mandelate racemase
Dehydration
Protons

Evolution of Structure and Function in the o-Succinylbenzoate Synthase/N-Acylamino Acid Racemase Family of the Enolase Superfamily

Glasner, M. E., Fayazmanesh, N., Chiang, R. A., Sakai, A., Jacobson, M. P., Gerlt, J. A. & Babbitt, P. C., Jun 30 2006, In : Journal of Molecular Biology. 360, 1, p. 228-250 23 p.

Research output: Contribution to journalArticle

Racemases and Epimerases
Phosphopyruvate Hydratase
Acids
Proteins
Protein Engineering
2005

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

Gerlt, J. A., Babbitt, P. C. & Rayment, I., Jan 1 2005, In : Archives of Biochemistry and Biophysics. 433, 1, p. 59-70 12 p.

Research output: Contribution to journalArticle

Phosphopyruvate Hydratase
Anions
Protons
Catalytic Domain
Ions

Evolutionary potential of (β/α)8-barrels: In vitro enhancement of a "new" reaction in the enolase superfamily

Vick, J. E., Schmidt, D. M. Z. & Gerlt, J. A., Sep 6 2005, In : Biochemistry. 44, 35, p. 11722-11729 8 p.

Research output: Contribution to journalArticle

Phosphopyruvate Hydratase
Substrates
Substitution reactions
Escherichia coli
Cats
Carboxy-Lyases
Phosphates
Catalytic Domain
Methylomonas
gulonic acid
Carboxy-Lyases
Phosphates
Biochemistry
Manuscripts
Formaldehyde
2004

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

Klenchin, V. A., Schmidt, D. M., Gerlt, J. A. & Rayment, I., Aug 17 2004, In : Biochemistry. 43, 32, p. 10370-10378 9 p.

Research output: Contribution to journalArticle

Racemases and Epimerases
Phosphopyruvate Hydratase
Bacilli
Substrate Specificity
Bacillus subtilis
Carboxy-Lyases
Protons
Catalytic Domain
Phosphates
Biochemistry
Carboxy-Lyases
Protons
Catalytic Domain
Phosphates
Substitution reactions

Evolution of Enzymatic Activity in the Enolase Superfamily: Functional Studies of the Promiscuous o-Succinylbenzoate Synthase from Amycolatopsis

Ringia, E. A. T., Garrett, J. B., Thoden, J. B., Holden, H. M., Rayment, I. & Gerlt, J. A., Jan 13 2004, In : Biochemistry. 43, 1, p. 224-229 6 p.

Research output: Contribution to journalArticle

Phosphopyruvate Hydratase
Racemases and Epimerases
Enantiomers
Acids
Hydrogen

Evolution of Enzymatic Activity in the Enolase Superfamily: Structural Studies of the Promiscuous o-Succinylbenzoate Synthase from Amycolatopsis

Thoden, J. B., Taylor Ringia, E. A., Garrett, J. B., Gerlt, J. A., Holden, H. M. & Rayment, I., May 18 2004, In : Biochemistry. 43, 19, p. 5716-5727 12 p.

Research output: Contribution to journalArticle

Phosphopyruvate Hydratase
Acids
Racemases and Epimerases
Biochemistry
Substrates
Enoyl-CoA Hydratase
Hydrolases
Coenzyme A
Coenzymes
substrate

Evolution of Function in the Crotonase Superfamily: (3S)-Methylglutaconyl-CoA Hydratase from Pseudomonas putida

Wong, B. J. & Gerlt, J. A., Apr 27 2004, In : Biochemistry. 43, 16, p. 4646-4654 9 p.

Research output: Contribution to journalArticle

methylglutaconyl-CoA hydratase
Enoyl-CoA Hydratase
Pseudomonas putida
Substrates
Coenzyme A

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

Wise, E. L., Akana, J., Gerlt, J. A. & Rayment, I., Sep 1 2004, In : Acta Crystallographica Section D: Biological Crystallography. 60, 9, p. 1687-1690 4 p.

Research output: Contribution to journalArticle

Synechocystis
Catalytic Domain
X Ray Crystallography
Cyanobacteria
Enzymes
2003

Chemical and Enzymatic Synthesis of Fluorinated-Dehydroalanine-Containing Peptides

Zhou, H., Schmidt, D. M. Z., Gerlt, J. A. & van der Donk, W. A., Nov 7 2003, In : ChemBioChem. 4, 11, p. 1206-1215 10 p.

Research output: Contribution to journalArticle

Racemases and Epimerases
Peptides
Dipeptides
Fluorides
Sulfoxides
3-hydroxyisobutyryl-CoA hydrolase
Enoyl-CoA Hydratase
Hydrolases
Anhydrides
anion

Evolutionary potential of (β/α)8-barrels: Functional promiscuity produced by single substitutions in the enolase superfamily

Schmidt, D. M. Z., Mundorff, E. C., Dojka, M., Bermudez, E., Ness, J. E., Govindarajan, S., Babbitt, P. C., Minshull, J. & Gerlt, J. A., Jul 22 2003, In : Biochemistry. 42, 28, p. 8387-8393 7 p.

Research output: Contribution to journalArticle

Phosphopyruvate Hydratase
Maximum likelihood estimation
Substitution reactions
Escherichia coli
Enzymes

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

Klenchin, V. A., Ringia, E. A. T., Gerlt, J. A. & Rayment, I., Dec 16 2003, In : Biochemistry. 42, 49, p. 14427-14433 7 p.

Research output: Contribution to journalArticle

Phosphopyruvate Hydratase
Dehydration
Escherichia coli
Catalytic Domain
Vitamin K 2

Identification and characterization of a mandelamide hydrolase and an NAD(P) + -dependent benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633

McLeish, M. J., Kneen, M. M., Gopalakrishna, K. N., Koo, C. W., Babbitt, P. C., Gerlt, J. A. & Kenyon, G. L., Apr 1 2003, In : Journal of bacteriology. 185, 8, p. 2451-2456 6 p.

Research output: Contribution to journalArticle

Pseudomonas putida
Hydrolases
NAD
Oxidoreductases
Genes
Carboxy-Lyases
Phosphates
Ions
Oxygen
Catalytic Domain
2002

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

Wise, E., Wen, S. Y., Babbitt, P. C., Gerlt, J. A. & Rayment, I., Mar 26 2002, In : Biochemistry. 41, 12, p. 3861-3869 9 p.

Research output: Contribution to journalArticle

Carboxy-Lyases
Phosphates
Enzymes
Decarboxylation
Anions

Utilization of L-ascorbate by Escherichia coli K-12: Assignments of functions to products of the yjf-sga and yia-sgb operons

Wen Shan Yew, S. Y. & Gerlt, J. A., Jan 4 2002, In : Journal of bacteriology. 184, 1, p. 302-306 5 p.

Research output: Contribution to journalArticle

Operon
Escherichia coli
Carboxy-Lyases
Phosphates
Racemases and Epimerases
2001

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

Schmidt, D. M. Z., Hubbard, B. K. & Gerlt, J. A., Dec 25 2001, In : Biochemistry. 40, 51, p. 15707-15715 9 p.

Research output: Contribution to journalArticle

Racemases and Epimerases
Phosphopyruvate Hydratase
Bacilli
Bacillus subtilis
Escherichia coli

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

Gulick, A. M., Hubbard, B. K., Gerlt, J. A. & Rayment, I., Aug 28 2001, In : Biochemistry. 40, 34, p. 10054-10062 9 p.

Research output: Contribution to journalArticle

Phosphopyruvate Hydratase
Escherichia coli
Protons
Catalytic Domain
Catalysts

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

Gulick, A. M., Schmidt, D. M. Z., Gerlt, J. A. & Rayment, I., Dec 25 2001, In : Biochemistry. 40, 51, p. 15716-15724 9 p.

Research output: Contribution to journalArticle

Racemases and Epimerases
Phosphopyruvate Hydratase
Bacilli
Bacillus subtilis
Escherichia coli

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

Holden, H. M., Benning, M. M., Haller, T. & Gerlt, J. A., Mar 3 2001, In : Accounts of chemical research. 34, 2, p. 145-157 13 p.

Research output: Contribution to journalArticle

Enoyl-CoA Hydratase
Coenzymes
Acyl Coenzyme A
Enzymes
Carbon
2000

Can sequence determine function?

Gerlt, J. A. & Babbitt, P. C., Dec 1 2000, In : Genome biology. 1, 5

Research output: Contribution to journalArticle

Molecular Sequence Annotation
divergent evolution
genome
Genome
Databases

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

Haller, T., Buckel, T., Rétey, J. & Gerlt, J. A., Apr 25 2000, In : Biochemistry. 39, 16, p. 4622-4629 8 p.

Research output: Contribution to journalArticle

Enoyl-CoA Hydratase
Propionates
Succinic Acid
Methylmalonyl-CoA Mutase
Methylmalonyl-CoA Decarboxylase

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

Gulick, A. M., Hubbard, B. K., Gerlt, J. A. & Rayment, I., Apr 25 2000, In : Biochemistry. 39, 16, p. 4590-4602 13 p.

Research output: Contribution to journalArticle

mandelate racemase
Mutagenesis
Phosphopyruvate Hydratase
Escherichia coli
Dehydration

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

Thompson, T. B., Garrett, J. B., Taylor, E. A., Meganathan, R., Gerlt, J. A. & Rayment, I., Sep 5 2000, In : Biochemistry. 39, 35, p. 10662-10676 15 p.

Research output: Contribution to journalArticle

Phosphopyruvate Hydratase
Escherichia coli
Catalytic Domain
Biochemistry
Molecules

New functions from old scaffolds: How nature reengineers enzymes for new functions

Babbit, P. C. & Gerlt, J. A., Jan 1 2000, In : Advances in Protein Chemistry. 55, p. 1-28 28 p.

Research output: Contribution to journalArticle

Molecular Sequence Data
Chemical Models
Protein Engineering
Amino Acid Sequence Homology
Amino Acid Sequence