John Alan Gerlt

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2009

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

Sakai, A., Fedorov, A. A., Fedorov, E. V., Schnoes, A. M., Glasner, M. E., Brown, S., Rutter, M. E., Bain, K., Chang, S., Gheyi, T., Sauder, J. M., Burley, S. K., Babbitt, P. C., Almo, S. C. & Gerlt, J. A., Feb 24 2009, In : Biochemistry. 48, 7, p. 1445-1453 9 p.

Research output: Contribution to journalArticle

Mechanism of the orotidine 5′-monophosphate decarboxylase-catalyzed reaction: Evidence for substrate destabilization

Chan, K. K., Wood, B. M. K., Fedorov, A. A., Fedorov, E. V., Imker, H. J., Amyes, T. L., Richard, J. P., Almo, S. C. & Gerlt, J. A., Jun 23 2009, In : Biochemistry. 48, 24, p. 5518-5531 14 p.

Research output: Contribution to journalArticle

Mechanism of the orotidine 5′-monophosphate decarboxylase-catalyzed reaction: Effect of solvent viscosity on kinetic constants

Wood, B. M. K., Chan, K. K., Amyes, T. L., Richard, J. P. & Gerlt, J. A., Jun 23 2009, In : Biochemistry. 48, 24, p. 5510-5517 8 p.

Research output: Contribution to journalArticle

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

Froese, D. S., Dobson, C. M., White, A. P., Wu, X., Padovani, D., Banerjee, R., Haller, T., Gerlt, J. A., Surette, M. G. & Gravel, R. A., Jan 1 2009, In : Microbiological Research. 164, 1, p. 1-8 8 p.

Research output: Contribution to journalArticle

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

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

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

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

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

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

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

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

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

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

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

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

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

Gerlt, J. A., May 31 2007, In : Nature. 447, 7144, 1 p.

Research output: Contribution to journalArticle

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., Aug 2007, In : Nature chemical biology. 3, 8, p. 486-491 6 p.

Research output: Contribution to journalArticle

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

2001

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

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

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

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

2000

Can sequence determine function?

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

Research output: Contribution to journalArticle