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John Alan Gerlt

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Benjamin P E Warlick; Heidi J Imker; Jaya Sriram; F Robert Tabita; John Alan Gerlt
Mechanistic diversity in the RuBisCO superfamily: RuBisCO from Rhodospirillum rubrum is not promiscuous for reactions catalyzed by RuBisCO-like proteins.
Bijoy J Desai; Alexander A Fedorov; Elena V Fedorov; Steven C Almo; Tina L Amyes; Bogdana Goryanova; John Patrick Richard; B McKay Wood; John Alan Gerlt
Conformational changes in orotidine 5'-monophosphate decarboxylase: a structure-based explanation for how the 5'-phosphate group activates the enzyme.
Benjamin P Warlick; Steven C Almo; Jeffrey B Bonanno; Stephen K Burley; Tobias J Erb; Bradley S Evans; Heidi J Imker; Udupi A Ramagopal; J Michael Sauder; Jaya Sriram; Jonathan S Sweedler; F Robert Tabita; John Alan Gerlt
1-methylthio-D-xylulose 5-phosphate methylsulfurylase: a novel route to 1-deoxy-D-xylulose 5-phosphate in Rhodospirillum rubrum.

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2012: Benjamin P E Warlick; Heidi J Imker; Jaya Sriram; F Robert Tabita; John Alan Gerlt
Mechanistic diversity in the RuBisCO superfamily: RuBisCO from Rhodospirillum rubrum is not promiscuous for reactions catalyzed by RuBisCO-like proteins.
Biochemistry 2012;51(47):9470-9.
2012: Bijoy J Desai; Alexander A Fedorov; Elena V Fedorov; Steven C Almo; Tina L Amyes; Bogdana Goryanova; John Patrick Richard; B McKay Wood; John Alan Gerlt
Conformational changes in orotidine 5'-monophosphate decarboxylase: a structure-based explanation for how the 5'-phosphate group activates the enzyme.
Biochemistry 2012;51(43):8665-78.
2012: Benjamin P Warlick; Steven C Almo; Jeffrey B Bonanno; Stephen K Burley; Tobias J Erb; Bradley S Evans; Heidi J Imker; Udupi A Ramagopal; J Michael Sauder; Jaya Sriram; Jonathan S Sweedler; F Robert Tabita; John Alan Gerlt
1-methylthio-D-xylulose 5-phosphate methylsulfurylase: a novel route to 1-deoxy-D-xylulose 5-phosphate in Rhodospirillum rubrum.
Biochemistry 2012;51(42):8324-6.
2012: Wing-Yin Tsang; Freeman M Wong; B McKay Wood; Weiming Wu; Tina L Amyes; John Alan Gerlt; John Patrick Richard
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.
Journal of the American Chemical Society 2012;134(35):14580-94.
2012: Tina L Amyes; Bijoy J Desai; John Alan Gerlt; Lawrence M Goldman; Shonoi A Ming; B McKay Wood; John Patrick Richard
Orotidine 5'-monophosphate decarboxylase: transition state stabilization from remote protein-phosphodianion interactions.
Biochemistry 2012;51(23):4630-2.
2012: Tiit Lukk; Satish K Nair; Yury Patskovsky; Ayano Sakai; Ronald Seidel; Ling Song; Rafael Toro; Matthew W Vetting; Steven C Almo; Patricia C Babbitt; Shoshana D Brown; Alexander A Fedorov; Elena V Fedorov; John Alan Gerlt; Brandan S. Hillerich; Heidi J Imker; Chakrapani Kalyanaraman; Matthew P Jacobson
Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(11):4122-7.
2012: John Alan Gerlt; Patricia C Babbitt; Matthew P Jacobson; Steven C Almo
Divergent evolution in enolase superfamily: strategies for assigning functions.
The Journal of biological chemistry 2012;287(1):29-34.
2011: John Alan Gerlt; Heidi J Imker; Matthew P Jacobson; Wladek Minor; C Dale Poulter; Frank M Raushel; Andrej Sali; Brian K Shoichet; Karen N Allen; Steven C Almo; Richard N Armstrong; Patricia C Babbitt; John E Cronan; Debra Dunaway-Mariano; Jonathan V Sweedler
The Enzyme Function Initiative.
Biochemistry 2011;50(46):9950-62.
2011: Vanessa Iiams; Steven C Almo; Bijoy J Desai; Alexander A Fedorov; Elena V Fedorov; John Alan Gerlt
Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: importance of residues in the orotate binding site.
Biochemistry 2011;50(39):8497-507.
2011: Bogdana Goryanova; Tina L Amyes; John Alan Gerlt; John Patrick Richard
OMP decarboxylase: phosphodianion binding energy is used to stabilize a vinyl carbanion intermediate.
Journal of the American Chemical Society 2011;133(17):6545-8.
2010: Krisztina Toth; Tina L Amyes; Bryant M Wood; Kui Chan; John Alan Gerlt; John Patrick Richard
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.
Journal of the American Chemical Society 2010;132(20):7018-24.
2010: B McKay Wood; Tina L Amyes; Alexander A Fedorov; Elena V Fedorov; Andrew Shabila; Steven C Almo; John Patrick Richard; John Alan Gerlt
Conformational changes in orotidine 5'-monophosphate decarboxylase: "remote" residues that stabilize the active conformation.
Biochemistry 2010;49(17):3514-6.
2010: Shonoi A Barnett; Tina L Amyes; B McKay Wood; John Alan Gerlt; John Patrick Richard
Activation of R235A mutant orotidine 5'-monophosphate decarboxylase by the guanidinium cation: effective molarity of the cationic side chain of Arg-235.
Biochemistry 2010;49(5):824-6.
2009: John F Rakus; Chakrapani Kalyanaraman; Alexander A Fedorov; Elena V Fedorov; Fiona P Mills-Groninger; Rafael Toro; Jeffrey B Bonanno; Kevin Bain; J Michael Sauder; Stephen K Burley; Steven C Almo; Matthew P Jacobson; John Alan Gerlt
Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis .
Biochemistry 2009;48(48):11546-58.
2009: Krisztina Toth; Tina L Amyes; B McKay Wood; Kui K Chan; John Alan Gerlt; John Patrick Richard
An examination of the relationship between active site loop size and thermodynamic activation parameters for orotidine 5'-monophosphate decarboxylase from mesophilic and thermophilic organisms.
Biochemistry 2009;48(33):8006-13.
2009: John Alan Gerlt
Acetoacetate decarboxylase: hydrophobics, not electrostatics.
Nature chemical biology 2009;5(7):454-5.
2009: Kui K Chan; B McKay Wood; Alexander A Fedorov; Elena V Fedorov; Heidi J Imker; Tina L Amyes; John Patrick Richard; Steven C Almo; John Alan Gerlt
Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.
Biochemistry 2009;48(24):5518-31.
2009: B McKay Wood; Kui K Chan; Tina L Amyes; John Patrick Richard; John Alan Gerlt
Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: effect of solvent viscosity on kinetic constants.
Biochemistry 2009;48(24):5510-7.
2009: Ursula Pieper; Ranyee Chiang; Jennifer J Seffernick; Shoshana D Brown; Margaret E Glasner; Libusha Kelly; Narayanan Eswar; J Michael Sauder; Jeffrey B Bonanno; Subramanyam Swaminathan; Stephen K Burley; Xiaojing Zheng; Mark R Chance; Steven C Almo; John Alan Gerlt; Frank M Raushel; Matthew P Jacobson; Patricia C Babbitt; Andrej Sali
Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies.
Journal of structural and functional genomics 2009;10(2):107-25.
2009: Ayano Sakai; Alexander A Fedorov; Elena V Fedorov; Alexandra M Schnoes; Margaret E Glasner; Shoshana Brown; Marc E Rutter; Kevin Bain; Shawn Chang; Tarun Gheyi; J Michael Sauder; Stephen K Burley; Patricia C Babbitt; Steven C Almo; John Alan Gerlt
Evolution of enzymatic activities in the enolase superfamily: stereochemically distinct mechanisms in two families of cis,cis-muconate lactonizing enzymes.
Biochemistry 2009;48(7):1445-53.
2009: John Alan Gerlt; Patricia C Babbitt
Enzyme (re)design: lessons from natural evolution and computation.
Current opinion in chemical biology 2009;13(1):10-8.
2009: D S Froese; C Melissa Dobson; AP White; Xuchu Wu; D Padovani; Ruma Banerjee; T Haller; John Alan Gerlt; Michael Surette; Roy A Gravel
Sleeping beauty mutase (sbm) is expressed and interacts with ygfd in Escherichia coli.
Microbiological research 2009;164(1):1-8.
2008: Peter Karp; Gavin Sherlock; John Alan Gerlt; Ida Sim; Ian Paulsen; Patricia C Babbitt; Keith Laderoute; Lawrence Hunter; Paul Sternberg; John Wooley; Philip Bourne
Changes to NIH grant system may backfire.
Science (New York, N.Y.) 2008;322(5905):1187-8.
2008: Chakrapani Kalyanaraman; Heidi J Imker; Alexander A Fedorov; Elena V Fedorov; Margaret E Glasner; Patricia C Babbitt; Steven C Almo; John Alan Gerlt; Matthew P Jacobson
Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening.
Structure (London, England : 1993) 2008;16(11):1668-77.
2008: Heidi J Imker; Jaya Singh; Benjamin P Warlick; F Robert Tabita; John Alan Gerlt
Mechanistic diversity in the RuBisCO superfamily: a novel isomerization reaction catalyzed by the RuBisCO-like protein from Rhodospirillum rubrum.
Biochemistry 2008;47(43):11171-3.
2008: John F Rakus; Alexander A Fedorov; Elena V Fedorov; Margaret E Glasner; BK Hubbard; Joseph D Delli; Patricia C Babbitt; Steven C Almo; John Alan Gerlt
Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase.
Biochemistry 2008;47(38):9944-54.
2008: Dean Rea; Rebecca Hovington; John F Rakus; John Alan Gerlt; Vilmos Fülöp; Timothy D H Bugg; David I Roper
Crystal structure and functional assignment of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12.
Biochemistry 2008;47(38):9955-65.
2008: Kui K Chan; Alexander A Fedorov; Elena V Fedorov; Steven C Almo; John Alan Gerlt
Structural basis for substrate specificity in phosphate binding (beta/alpha)8-barrels: D-allulose 6-phosphate 3-epimerase from Escherichia coli K-12.
Biochemistry 2008;47(36):9608-17.
2008: Shonoi A Barnett; Tina L Amyes; Bryant M Wood; John Alan Gerlt; John Patrick Richard
Dissecting the total transition state stabilization provided by amino acid side chains at orotidine 5'-monophosphate decarboxylase: a two-part substrate approach.
Biochemistry 2008;47(30):7785-7.
2008: Tina L Amyes; Bryant M Wood; Kui Chan; John Alan Gerlt; John Patrick Richard
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.
Journal of the American Chemical Society 2008;130(5):1574-5.
2007: Jacob E Vick; John Alan Gerlt
Evolutionary potential of (beta/alpha)8-barrels: stepwise evolution of a "new" reaction in the enolase superfamily.
Biochemistry 2007;46(50):14589-97.
2007: John F Rakus; Alexander A Fedorov; Elena V Fedorov; Margaret E Glasner; Jacob E Vick; Patricia C Babbitt; Steven C Almo; John Alan Gerlt
Evolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from Novosphingobium aromaticivorans.
Biochemistry 2007;46(45):12896-908.
2007: John Alan Gerlt
A Protein Structure (or Function ?) Initiative.
Structure (London, England : 1993) 2007;15(11):1353-6.
2007: Krisztina Toth; Tina L Amyes; Bryant M Wood; Kui Chan; John Alan Gerlt; John Patrick Richard
Product deuterium isotope effect for orotidine 5'-monophosphate decarboxylase: evidence for the existence of a short-lived carbanion intermediate.
Journal of the American Chemical Society 2007;129(43):12946-7.
2007: Wen Shan Yew; Alexander A Fedorov; Elena V Fedorov; Steven C Almo; John Alan Gerlt
Evolution of enzymatic activities in the enolase superfamily: L-talarate/galactarate dehydratase from Salmonella typhimurium LT2.
Biochemistry 2007;46(33):9564-77.
2007: Ling Song; Chakrapani Kalyanaraman; Alexander A Fedorov; Elena V Fedorov; Margaret E Glasner; Shoshana Brown; Heidi J Imker; Patricia C Babbitt; Steven C Almo; Matthew P Jacobson; John Alan Gerlt
Prediction and assignment of function for a divergent N-succinyl amino acid racemase.
Nature chemical biology 2007;3(8):486-91.
2007: John Alan Gerlt
Obituary: Frank H. Westheimer (1912-2007).
Nature 2007;447(7144):543.
2007: Heidi J Imker; Alexander A Fedorov; Elena V Fedorov; Steven C Almo; John Alan Gerlt
Mechanistic diversity in the RuBisCO superfamily: the "enolase" in the methionine salvage pathway in Geobacillus kaustophilus.
Biochemistry 2007;46(13):4077-89.
2007: Margaret E Glasner; John Alan Gerlt; Patricia C Babbitt
Mechanisms of protein evolution and their application to protein engineering.
Advances in enzymology and related areas of molecular biology 2007;75():193-239, xii-xiii.
2006: Wen Shan Yew; Alexander A Fedorov; Elena V Fedorov; Bryant McKay Wood; Steven C Almo; John Alan Gerlt
Evolution of enzymatic activities in the enolase superfamily: D-tartrate dehydratase from Bradyrhizobium japonicum.
Biochemistry 2006;45(49):14598-608.
2006: Wen Shan Yew; Alexander A Fedorov; Elena V Fedorov; John F Rakus; Richard W Pierce; Steven C Almo; John Alan Gerlt
Evolution of enzymatic activities in the enolase superfamily: L-fuconate dehydratase from Xanthomonas campestris.
Biochemistry 2006;45(49):14582-97.
2006: Margaret E Glasner; John Alan Gerlt; Patricia C Babbitt
Evolution of enzyme superfamilies.
Current opinion in chemical biology 2006;10(5):492-7.
2006: Margaret E Glasner; Nima Fayazmanesh; Ranyee A Chiang; Ayano Sakai; Matthew P Jacobson; John Alan Gerlt; Patricia C Babbitt
Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily.
Journal of molecular biology 2006;360(1):228-50.
2006: Ayano Sakai; Dao Feng Xiang; Chengfu Xu; Ling Song; Wen Shan Yew; Frank M Raushel; John Alan Gerlt
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.
Biochemistry 2006;45(14):4455-62.
2006: Julie Akana; Alexander A Fedorov; Elena V Fedorov; Walter R P Novak; Patricia C Babbitt; Steven C Almo; John Alan Gerlt
D-Ribulose 5-phosphate 3-epimerase: functional and structural relationships to members of the ribulose-phosphate binding (beta/alpha)8-barrel superfamily.
Biochemistry 2006;45(8):2493-503.
2006: Shoshana D Brown; John Alan Gerlt; Jennifer L Seffernick; Patricia C Babbitt
A gold standard set of mechanistically diverse enzyme superfamilies.
Genome biology 2006;7(1):R8.
2005: Jacob E Vick; Dawn M Z Schmidt; John Alan Gerlt
Evolutionary potential of (beta/alpha)8-barrels: in vitro enhancement of a "new" reaction in the enolase superfamily.
Biochemistry 2005;44(35):11722-9.
2005: Eric L Wise; Wen Shan Yew; Julie Akana; John Alan Gerlt; Ivan Rayment
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.
Biochemistry 2005;44(6):1816-23.
2005: Wen Shan Yew; Julie Akana; Eric L Wise; Ivan Rayment; John Alan Gerlt
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.
Biochemistry 2005;44(6):1807-15.
2005: John Alan Gerlt; Patricia C Babbitt; Ivan Rayment
Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity.
Archives of biochemistry and biophysics 2005;433(1):59-70.
2004: Eric L Wise; Julie Akana; John Alan Gerlt; Ivan Rayment
Structure of D-ribulose 5-phosphate 3-epimerase from Synechocystis to 1.6 A resolution.
Acta crystallographica. Section D, Biological crystallography 2004;60(Pt 9):1687-90.
2004: Vadim A Klenchin; Dawn M Z Schmidt; John Alan Gerlt; Ivan Rayment
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.
Biochemistry 2004;43(32):10370-8.
2004: Ellen D Eberhard; John Alan Gerlt
Evolution of function in the crotonase superfamily: the stereochemical course of the reaction catalyzed by 2-ketocyclohexanecarboxyl-CoA hydrolase.
Journal of the American Chemical Society 2004;126(23):7188-9.
2004: Eric L Wise; Wen Shan Yew; John Alan Gerlt; Ivan Rayment
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.
Biochemistry 2004;43(21):6438-46.
2004: Wen Shan Yew; Eric L Wise; Ivan Rayment; John Alan Gerlt
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.
Biochemistry 2004;43(21):6427-37.
2004: James B Thoden; Erika Taylor; James B Garrett; John Alan Gerlt; Hazel M Holden; Ivan Rayment
Evolution of enzymatic activity in the enolase superfamily: structural studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis.
Biochemistry 2004;43(19):5716-27.
2004: Brian J Wong; John Alan Gerlt
Evolution of function in the crotonase superfamily: (3S)-methylglutaconyl-CoA hydratase from Pseudomonas putida.
Biochemistry 2004;43(16):4646-54.
2004: Erika Taylor; James B Garrett; James B Thoden; Hazel M Holden; Ivan Rayment; John Alan Gerlt
Evolution of enzymatic activity in the enolase superfamily: functional studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis.
Biochemistry 2004;43(1):224-9.
2003: Vadim A Klenchin; Erika Taylor; John Alan Gerlt; Ivan Rayment
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.
Biochemistry 2003;42(49):14427-33.
2003: John Alan Gerlt
How to find "missing" genes.
Chemistry & biology 2003;10(12):1141-2.
2003: Hao Zhou; Dawn M Z Schmidt; John Alan Gerlt; Wilfred Adrianus van der Donk
Chemical and enzymatic synthesis of fluorinated-dehydroalanine-containing peptides.
Chembiochem : a European journal of chemical biology 2003;4(11):1206-15.
2003: Eric L Wise; Wen Shan Yew; John Alan Gerlt; Ivan Rayment
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.
Biochemistry 2003;42(42):12133-42.
2003: Brian J Wong; John Alan Gerlt
Divergent function in the crotonase superfamily: an anhydride intermediate in the reaction catalyzed by 3-hydroxyisobutyryl-CoA hydrolase.
Journal of the American Chemical Society 2003;125(40):12076-7.
2003: Dawn M Z Schmidt; Emily C Mundorff; Michael Dojka; Ericka Bermudez; Jon E Ness; Sridhar Govindarajan; Patricia C Babbitt; Jeremy Minshull; John Alan Gerlt
Evolutionary potential of (beta/alpha)8-barrels: functional promiscuity produced by single substitutions in the enolase superfamily.
Biochemistry 2003;42(28):8387-93.
2003: John Alan Gerlt; Frank M Raushel
Evolution of function in (beta/alpha)8-barrel enzymes.
Current opinion in chemical biology 2003;7(2):252-64.
2003: Michael McLeish; Malea Kneen; Kota N Gopalakrishna; Carolyn W Koo; Patricia C Babbitt; John Alan Gerlt; George L Kenyon
Identification and characterization of a mandelamide hydrolase and an NAD(P)+-dependent benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633.
Journal of bacteriology 2003;185(8):2451-6.
2002: John Alan Gerlt
"Fishing" for the functional proteome.
Nature biotechnology 2002;20(8):786-7.
2002: Eric L Wise; Wen Shan Yew; Patricia C Babbitt; John Alan Gerlt; Ivan Rayment
Homologous (beta/alpha)8-barrel enzymes that catalyze unrelated reactions: orotidine 5'-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase.
Biochemistry 2002;41(12):3861-9.
2002: Wen Shan Yew; John Alan Gerlt
Utilization of L-ascorbate by Escherichia coli K-12: assignments of functions to products of the yjf-sga and yia-sgb operons.
Journal of bacteriology 2002;184(1):302-6.
2001: Andrew Gulick; Dawn M Z Schmidt; John Alan Gerlt; Ivan Rayment
Evolution of enzymatic activities in the enolase superfamily: crystal structures of the L-Ala-D/L-Glu epimerases from Escherichia coli and Bacillus subtilis.
Biochemistry 2001;40(51):15716-24.
2001: Dawn M Z Schmidt; BK Hubbard; John Alan Gerlt
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.
Biochemistry 2001;40(51):15707-15.
2001: Andrew Gulick; BK Hubbard; John Alan Gerlt; Ivan Rayment
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.
Biochemistry 2001;40(34):10054-62.
2001: Erika Taylor; DR Palmer; John Alan Gerlt
The lesser "burden borne" by o-succinylbenzoate synthase: an "easy" reaction involving a carboxylate carbon acid.
Journal of the American Chemical Society 2001;123(24):5824-5.
2001: Hazel M Holden; Matthew M Benning; T Haller; John Alan Gerlt
The crotonase superfamily: divergently related enzymes that catalyze different reactions involving acyl coenzyme a thioesters.
Accounts of chemical research 2001;34(2):145-57.
2001: John Alan Gerlt; Patricia C Babbitt
Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies.
Annual review of biochemistry 2001;70():209-46.
2001: John Alan Gerlt; Patricia C Babbitt
Barrels in pieces?
Nature structural biology 2001;8(1):5-7.
2000: Thomas B Thompson; James B Garrett; Erika Taylor; R Meganathan; John Alan Gerlt; Ivan Rayment
Evolution of enzymatic activity in the enolase superfamily: structure of o-succinylbenzoate synthase from Escherichia coli in complex with Mg2+ and o-succinylbenzoate.
Biochemistry 2000;39(35):10662-76.
2000: Matthew M Benning; T Haller; John Alan Gerlt; Hazel M Holden
New reactions in the crotonase superfamily: structure of methylmalonyl CoA decarboxylase from Escherichia coli.
Biochemistry 2000;39(16):4630-9.
2000: T Haller; T Buckel; János Rétey; John Alan Gerlt
Discovering new enzymes and metabolic pathways: conversion of succinate to propionate by Escherichia coli.
Biochemistry 2000;39(16):4622-9.
2000: Andrew Gulick; BK Hubbard; John Alan Gerlt; Ivan Rayment
Evolution of enzymatic activities in the enolase superfamily: crystallographic and mutagenesis studies of the reaction catalyzed by D-glucarate dehydratase from Escherichia coli.
Biochemistry 2000;39(16):4590-602.
2000: John Alan Gerlt
New wine from old barrels.
Nature structural biology 2000;7(3):171-3.
2000: John Alan Gerlt; Patricia C Babbitt
Can sequence determine function?
Genome biology 2000;1(5):REVIEWS0005.
2000: Patricia C Babbitt; John Alan Gerlt
New functions from old scaffolds: how nature reengineers enzymes for new functions.
Advances in protein chemistry 2000;55():1-28.
1999: DR Palmer; James B Garrett; V Sharma; R Meganathan; Patricia C Babbitt; John Alan Gerlt
Unexpected divergence of enzyme function and sequence: "N-acylamino acid racemase" is o-succinylbenzoate synthase.
Biochemistry 1999;38(14):4252-8.
1998: BK Hubbard; M Koch; DR Palmer; Patricia C Babbitt; John Alan Gerlt
Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli.
Biochemistry 1998;37(41):14369-75.
1998: Andrew Gulick; DR Palmer; Patricia C Babbitt; John Alan Gerlt; Ivan Rayment
Evolution of enzymatic activities in the enolase superfamily: crystal structure of (D)-glucarate dehydratase from Pseudomonas putida.
Biochemistry 1998;37(41):14358-68.
1998: DR Palmer; BK Hubbard; John Alan Gerlt
Evolution of enzymatic activities in the enolase superfamily: partitioning of reactive intermediates by (D)-glucarate dehydratase from Pseudomonas putida.
Biochemistry 1998;37(41):14350-7.
1998: W Wallace Cleland; Perry A Frey; John Alan Gerlt
The low barrier hydrogen bond in enzymatic catalysis.
The Journal of biological chemistry 1998;273(40):25529-32.
1998: John Alan Gerlt; Patricia C Babbitt
Mechanistically diverse enzyme superfamilies: the importance of chemistry in the evolution of catalysis.
Current opinion in chemical biology 1998;2(5):607-12.
1998: Miriam S Hasson; I Schlichting; J Moulai; K Taylor; William Barrett; G L Kenyon; Patricia C Babbitt; John Alan Gerlt; Gregory A Petsko; Dagmar Ringe
Evolution of an enzyme active site: the structure of a new crystal form of muconate lactonizing enzyme compared with mandelate racemase and enolase.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(18):10396-401.
1998: Miriam S Hasson; A Muscate; Michael McLeish; Lena S Polovnikova; John Alan Gerlt; George L Kenyon; Gregory A Petsko; Dagmar Ringe
The crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes.
Biochemistry 1998;37(28):9918-30.
1997: Patricia C Babbitt; John Alan Gerlt
Understanding enzyme superfamilies. Chemistry As the fundamental determinant in the evolution of new catalytic activities.
The Journal of biological chemistry 1997;272(49):30591-4.
1997: John Alan Gerlt; M M Kreevoy; W Wallace Cleland; P A Frey
Understanding enzymic catalysis: the importance of short, strong hydrogen bonds.
Chemistry & biology 1997;4(4):259-67.
1996: Patricia C Babbitt; Miriam S Hasson; J E Wedekind; DR Palmer; William Barrett; George H Reed; Ivan Rayment; Dagmar Ringe; G L Kenyon; John Alan Gerlt
The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids.
Biochemistry 1996;35(51):16489-501.
1996: S L Schafer; William Barrett; A T Kallarakal; Bharati Mitra; John W Kozarich; John Alan Gerlt; J G Clifton; Gregory A Petsko; G L Kenyon
Mechanism of the reaction catalyzed by mandelate racemase: structure and mechanistic properties of the D270N mutant.
Biochemistry 1996;35(18):5662-9.
1996: M Bhagwat; John Alan Gerlt
3'- and 5'-strand cleavage reactions catalyzed by the Fpg protein from Escherichia coli occur via successive beta- and delta-elimination mechanisms, respectively.
Biochemistry 1996;35(2):659-65.
1996: L A Highbarger; John Alan Gerlt; G L Kenyon
Mechanism of the reaction catalyzed by acetoacetate decarboxylase. Importance of lysine 116 in determining the pKa of active-site lysine 115.
Biochemistry 1996;35(1):41-6.
1995: A T Kallarakal; Bharati Mitra; John W Kozarich; John Alan Gerlt; J G Clifton; Gregory A Petsko; G L Kenyon
Mechanism of the reaction catalyzed by mandelate racemase: structure and mechanistic properties of the K166R mutant.
Biochemistry 1995;34(9):2788-97.
1995: Bharati Mitra; A T Kallarakal; John W Kozarich; John Alan Gerlt; J G Clifton; Gregory A Petsko; G L Kenyon
Mechanism of the reaction catalyzed by mandelate racemase: importance of electrophilic catalysis by glutamic acid 317.
Biochemistry 1995;34(9):2777-87.
1995: Patricia C Babbitt; G T Mrachko; Miriam S Hasson; G W Huisman; Roberto Kolter; Dagmar Ringe; Gregory A Petsko; G L Kenyon; John Alan Gerlt
A functionally diverse enzyme superfamily that abstracts the alpha protons of carboxylic acids.
Science (New York, N.Y.) 1995;267(5201):1159-61.
1994: J A Landro; John Alan Gerlt; John W Kozarich; C W Koo; V J Shah; G L Kenyon; D J Neidhart; S Fujita; Gregory A Petsko
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.
Biochemistry 1994;33(3):635-43.
1993: Bharati Mitra; John Alan Gerlt; Patricia C Babbitt; C W Koo; G L Kenyon; D Joseph; Gregory A Petsko
A novel structural basis for membrane association of a protein: construction of a chimeric soluble mutant of (S)-mandelate dehydrogenase from Pseudomonas putida.
Biochemistry 1993;32(48):12959-67.
1993: John Alan Gerlt; P G Gassman
Understanding the rates of certain enzyme-catalyzed reactions: proton abstraction from carbon acids, acyl-transfer reactions, and displacement reactions of phosphodiesters.
Biochemistry 1993;32(45):11943-52.
1993: Gregory A Petsko; G L Kenyon; John Alan Gerlt; Dagmar Ringe; John W Kozarich
On the origin of enzymatic species.
Trends in biochemical sciences 1993;18(10):372-6.
1993: S P Hale; L B Poole; John Alan Gerlt
Mechanism of the reaction catalyzed by staphylococcal nuclease: identification of the rate-determining step.
Biochemistry 1993;32(29):7479-87.
1991: J M Withka; J A Wilde; Philip H Bolton; A Mazumder; John Alan Gerlt
Characterization of conformational features of DNA heteroduplexes containing aldehydic abasic sites.
Biochemistry 1991;30(41):9931-40.
1991: J A Landro; A T Kallarakal; S C Ransom; John Alan Gerlt; John W Kozarich; D J Neidhart; G L Kenyon
Mechanism of the reaction catalyzed by mandelate racemase. 3. Asymmetry in reactions catalyzed by the H297N mutant.
Biochemistry 1991;30(38):9274-81.
1991: D J Neidhart; P L Howell; Gregory A Petsko; V M Powers; R S Li; G L Kenyon; John Alan Gerlt
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.
Biochemistry 1991;30(38):9264-73.
1991: V M Powers; C W Koo; G L Kenyon; John Alan Gerlt; John W Kozarich
Mechanism of the reaction catalyzed by mandelate racemase. 1. Chemical and kinetic evidence for a two-base mechanism.
Biochemistry 1991;30(38):9255-63.
1991: H L Ammon; S M Prasad; John Alan Gerlt
Structure of thialysine hydrochloride.
Acta crystallographica. Section C, Crystal structure communications 1991;47 ( Pt 7)():1476-8.
1991: D M Baldisseri; Dennis A Torchia; L B Poole; John Alan Gerlt
Deletion of the omega-loop in the active site of staphylococcal nuclease. 2. Effects on protein structure and dynamics.
Biochemistry 1991;30(15):3628-33.
1991: L B Poole; D A Loveys; S P Hale; John Alan Gerlt; S M Stanczyk; Philip H Bolton
Deletion of the omega-loop in the active site of staphylococcal nuclease. 1. Effect on catalysis and stability.
Biochemistry 1991;30(15):3621-7.
1991: A Mazumder; John Alan Gerlt; M J Absalon; JoAnne Stubbe; Richard P Cunningham; J Withka; Philip H Bolton
Stereochemical studies of the beta-elimination reactions at aldehydic abasic sites in DNA: endonuclease III from Escherichia coli, sodium hydroxide, and Lys-Trp-Lys.
Biochemistry 1991;30(4):1119-26.
1990: A Y Tsou; S C Ransom; John Alan Gerlt; D D Buechter; Patricia C Babbitt; G L Kenyon
Mandelate pathway of Pseudomonas putida: sequence relationships involving mandelate racemase, (S)-mandelate dehydrogenase, and benzoylformate decarboxylase and expression of benzoylformate decarboxylase in Escherichia coli.
Biochemistry 1990;29(42):9856-62.
1990: D J Neidhart; G L Kenyon; John Alan Gerlt; Gregory A Petsko
Mandelate racemase and muconate lactonizing enzyme are mechanistically distinct and structurally homologous.
Nature 1990;347(6294):692-4.
1990: T Pourmotabbed; M Dell'Acqua; John Alan Gerlt; S M Stanczyk; Philip H Bolton
Kinetic and conformational effects of lysine substitutions for arginines 35 and 87 in the active site of staphylococcal nuclease.
Biochemistry 1990;29(15):3677-83.
1990: D C Neidhart; P L Howell; Gregory A Petsko; John Alan Gerlt; John W Kozarich; V M Powers; G L Kenyon
Restructuring catalysis in the mandelate pathway.
Biochemical Society symposium 1990;57():135-41.
1989: E H Serpersu; D W Hibler; John Alan Gerlt; Albert S Mildvan
Kinetic and magnetic resonance studies of the glutamate-43 to serine mutant of staphylococcal nuclease.
Biochemistry 1989;28(4):1539-48.
1989: A Y Tsou; S C Ransom; John Alan Gerlt; V M Powers; G L Kenyon
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.
Biochemistry 1989;28(3):969-75.
1989: D W Hibler; L Harpold; M Dell'Acqua; T Pourmotabbed; John Alan Gerlt; J A Wilde; Philip H Bolton
Isotopic labeling with hydrogen-2 and carbon-13 to compare conformations of proteins and mutants generated by site-directed mutagenesis, I.
Methods in enzymology 1989;177():74-86.
1989: J A Wilde; Philip H Bolton; D W Hibler; L Harpold; T Pourmotabbed; M Dell'Acqua; John Alan Gerlt
Isotopic labeling with hydrogen-2 and carbon-13 to compare conformations of proteins and mutants generated by site-directed mutagenesis, II.
Methods in enzymology 1989;177():282-92.
1988: M M Holland; T K Leib; John Alan Gerlt
Isolation and characterization of a small catalytic domain released from the adenylate cyclase from Escherichia coli by digestion with trypsin.
The Journal of biological chemistry 1988;263(29):14661-8.
1988: D J Neidhart; V M Powers; G L Kenyon; A Y Tsou; S C Ransom; John Alan Gerlt; Gregory A Petsko
Preliminary x-ray data on crystals of mandelate racemase.
The Journal of biological chemistry 1988;263(19):9268-70.
1988: J A Wilde; Philip H Bolton; M Dell'Acqua; D W Hibler; T Pourmotabbed; John Alan Gerlt
Identification of residues involved in a conformational change accompanying substitutions for glutamate-43 in staphylococcal nuclease.
Biochemistry 1988;27(11):4127-32.
1988: S C Ransom; John Alan Gerlt; V M Powers; G L Kenyon
Cloning, DNA sequence analysis, and expression in Escherichia coli of the gene for mandelate racemase from Pseudomonas putida.
Biochemistry 1988;27(2):540-5.
1987: D W Hibler; N J Stolowich; M A Reynolds; John Alan Gerlt; J A Wilde; Philip H Bolton
Site-directed mutants of staphylococcal nuclease. Detection and localization by 1H NMR spectroscopy of conformational changes accompanying substitutions for glutamic acid-43.
Biochemistry 1987;26(19):6278-86.
1985: R O Calderon; N J Stolowich; John Alan Gerlt; Julian M Sturtevant
Thermal denaturation of staphylococcal nuclease.
Biochemistry 1985;24(22):6044-9.
1985: M Takahara; D W Hibler; P J Barr; John Alan Gerlt; M Inouye
The ompA signal peptide directed secretion of Staphylococcal nuclease A by Escherichia coli.
The Journal of biological chemistry 1985;260(5):2670-4.
1984: S Mehdi; John Alan Gerlt
Syntheses and configurational analyses of thymidine 4-nitrophenyl [17O,18O]phosphates and the stereochemical course of a reaction catalyzed by bovine pancreatic deoxyribonuclease I.
Biochemistry 1984;23(21):4844-52.
1983: T K Leib; John Alan Gerlt
Evidence for a small catalytic domain in the adenylate cyclase from Salmonella typhimurium.
The Journal of biological chemistry 1983;258(21):12982-7.
1983: John Alan Gerlt; J A Coderre; S Mehdi
Oxygen chiral phosphate esters.
Advances in enzymology and related areas of molecular biology 1983;55():291-380.
1981: S Mehdi; John Alan Gerlt
Stereochemical course of the hydrolysis of thymidine 5'-(4-nitrophenyl [17O,18O]phosphate) in H216O catalyzed by the phosphodiesterase from snake venom.
The Journal of biological chemistry 1981;256(23):12164-6.
1980: John Alan Gerlt; J A Coderre; M S Wolin
Mechanism of the adenylate cyclase reaction. Stereochemistry of the reaction catalyzed by the enzyme from Brevibacterium liquefaciens.
The Journal of biological chemistry 1980;255(2):331-4.
1979: John Alan Gerlt; W H Wan
Stereochemistry of the hydrolysis of the endo isomer of uridine 2',3'-cyclic phosphorothioate catalyzed by the nonspecific phosphohydrolase from Enterobacter aerogenes.
Biochemistry 1979;18(21):4630-8.
1975: John Alan Gerlt; F H Westheimer; Julian M Sturtevant
The enthalpies of hydrolysis of acyclic, monocyclic, and glycoside cyclic phosphate diesters.
The Journal of biological chemistry 1975;250(13):5059-67.
1975: John Alan Gerlt; Glenn Joseph Robert Whitman
Purification and properties of a phosphohydrolase from Enterobacter aerogenes.
The Journal of biological chemistry 1975;250(13):5053-8.
1973: John Alan Gerlt; K W Rabinowitz; C P Dunne; W A Wood
The mechanism of action of 5'-adenylic acid-activated threonine dehydrase. V. Relation between ligand-induced allosteric activation and the protomeroligomer interconversion.
The Journal of biological chemistry 1973;248(23):8200-6.
1973: C P Dunne; John Alan Gerlt; K W Rabinowitz; W A Wood
The mechanism of action of 5'-adenylic acid-activated threonine dehydrase. IV. Characterization of kinetic effect of adenosine monophosphate.
The Journal of biological chemistry 1973;248(23):8189-99.
1973: John Alan Gerlt; F H Westheimer
Letter: A phosphodiesterase from Enterobacter aerogenes.
Journal of the American Chemical Society 1973;95(24):8166-8.