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

Pieper U, Chiang R, Seffernick JJ, Brown SD, Glasner ME, Kelly L, Eswar N, Sauder JM, Bonanno JB, Swaminathan S, Burley SK, Zheng X, Chance MR, Almo SC, Gerlt JA, Raushel FM, Jacobson MP, Babbitt PC, Sali A.

J Struct Funct Genomics. 2009 Apr;10(2):107-125. Epub 2009 Feb 14.

 

Evolution of Enzymatic Activities in the Enolase Superfamily: Stereochemically Distinct Mechanisms in Two Families of cis,cis-Muconate Lactonizing Enzymes.

Sakai A, Fedorov AA, Fedorov EV, Schnoes AM, Glasner ME, Brown S, Rutter ME, Bain K, Chang S, Gheyi T, Sauder JM, Burley SK, Babbitt PC, Almo SC, Gerlt JA.

Biochemistry. 2009 Mar 24;48(11):2569-70. No abstract available.

 

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

Sakai A, Fedorov AA, Fedorov EV, Schnoes AM, Glasner ME, Brown S, Rutter ME, Bain K, Chang S, Gheyi T, Sauder JM, Burley SK, Babbitt PC, Almo SC, Gerlt JA.

Biochemistry. 2009 Feb 24;48(7):1445-53.

 

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

Gerlt JA, Babbitt PC.

Curr Opin Chem Biol. 2009 Feb 21. [Epub ahead of print]

 

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

Froese DS, Dobson CM, White AP, Wu X, Padovani D, Banerjee R, Haller T, Gerlt JA, Surette MG, Gravel RA.

Microbiol Res. 2009;164(1):1-8. Epub 2008 Oct 23.

 

Changes to NIH grant system may backfire.

Karp PD, Sherlock G, Gerlt JA, Sim I, Paulsen I, Babbitt PC, Laderoute K, Hunter L, Sternberg P, Wooley J, Bourne PE.

Science. 2008 Nov 21;322(5905):1187-8. No abstract available.

 

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

Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP.

Structure. 2008 Nov 12;16(11):1668-77.

 

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

Imker HJ, Singh J, Warlick BP, Tabita FR, Gerlt JA.

Biochemistry. 2008 Oct 28;47(43):11171-3. Epub 2008 Oct 1.

 

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

Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Hubbard BK, Delli JD, Babbitt PC, Almo SC, Gerlt JA.

Biochemistry. 2008 Sep 23;47(38):9944-54. Epub 2008 Aug 29.

 

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

Rea D, Hovington R, Rakus JF, Gerlt JA, Fülöp V, Bugg TD, Roper DI.

Biochemistry. 2008 Sep 23;47(38):9955-65. Epub 2008 Aug 29.

 

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

Chan KK, Fedorov AA, Fedorov EV, Almo SC, Gerlt JA.

Biochemistry. 2008 Sep 9;47(36):9608-17. Epub 2008 Aug 14.

 

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

Barnett SA, Amyes TL, Wood BM, Gerlt JA, Richard JP.

Biochemistry. 2008 Jul 29;47(30):7785-7. Epub 2008 Jul 4.

 

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 TL, Wood BM, Chan K, Gerlt JA, Richard JP.

J Am Chem Soc. 2008 Feb 6;130(5):1574-5. Epub 2008 Jan 11. No abstract available.

 

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

Vick JE, Gerlt JA.

Biochemistry. 2007 Dec 18;46(50):14589-97. Epub 2007 Nov 20.

 

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

Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Vick JE, Babbitt PC, Almo SC, Gerlt JA.

Biochemistry. 2007 Nov 13;46(45):12896-908. Epub 2007 Oct 18.

 

A Protein Structure (or Function ?) Initiative.

Gerlt JA.

Structure. 2007 Nov;15(11):1353-6. No abstract available.

 

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

Toth K, Amyes TL, Wood BM, Chan K, Gerlt JA, Richard JP.

J Am Chem Soc. 2007 Oct 31;129(43):12946-7. Epub 2007 Oct 5. No abstract available.

 

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

Yew WS, Fedorov AA, Fedorov EV, Almo SC, Gerlt JA.

Biochemistry. 2007 Aug 21;46(33):9564-77. Epub 2007 Jul 25.

 

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

Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt PC, Almo SC, Jacobson MP, Gerlt JA.

Nat Chem Biol. 2007 Aug;3(8):486-91. Epub 2007 Jul 1.

 

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

Gerlt JA.

Nature. 2007 May 31;447(7144):543. No abstract available.

 

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

Imker HJ, Fedorov AA, Fedorov EV, Almo SC, Gerlt JA.

Biochemistry. 2007 Apr 3;46(13):4077-89. Epub 2007 Mar 13.

 

Mechanisms of protein evolution and their application to protein engineering.

Glasner ME, Gerlt JA, Babbitt PC.

Adv Enzymol Relat Areas Mol Biol. 2007;75:193-239, xii-xiii. Review.

 

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

Yew WS, Fedorov AA, Fedorov EV, Wood BM, Almo SC, Gerlt JA.

Biochemistry. 2006 Dec 12;45(49):14598-608.

 

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

Yew WS, Fedorov AA, Fedorov EV, Rakus JF, Pierce RW, Almo SC, Gerlt JA.

Biochemistry. 2006 Dec 12;45(49):14582-97.

 

Evolution of enzyme superfamilies.

Glasner ME, Gerlt JA, Babbitt PC.

Curr Opin Chem Biol. 2006 Oct;10(5):492-7. Epub 2006 Aug 28. Review.

 

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

Glasner ME, Fayazmanesh N, Chiang RA, Sakai A, Jacobson MP, Gerlt JA, Babbitt PC.

J Mol Biol. 2006 Jun 30;360(1):228-50. Epub 2006 May 11.

 

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 DF, Xu C, Song L, Yew WS, Raushel FM, Gerlt JA.

Biochemistry. 2006 Apr 11;45(14):4455-62.

 

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

Akana J, Fedorov AA, Fedorov E, Novak WR, Babbitt PC, Almo SC, Gerlt JA.

Biochemistry. 2006 Feb 28;45(8):2493-503.

 

A gold standard set of mechanistically diverse enzyme superfamilies.

Brown SD, Gerlt JA, Seffernick JL, Babbitt PC.

Genome Biol. 2006;7(1):R8. Epub 2006 Jan 31.

 

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

Vick JE, Schmidt DM, Gerlt JA.

Biochemistry. 2005 Sep 6;44(35):11722-9.

 

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.

Wise EL, Yew WS, Akana J, Gerlt JA, Rayment I.

Biochemistry. 2005 Feb 15;44(6):1816-23.

 

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.

Yew WS, Akana J, Wise EL, Rayment I, Gerlt JA.

Biochemistry. 2005 Feb 15;44(6):1807-15.

 

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

Gerlt JA, Babbitt PC, Rayment I.

Arch Biochem Biophys. 2005 Jan 1;433(1):59-70. Review.

 

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

Wise EL, Akana J, Gerlt JA, Rayment I.

Acta Crystallogr D Biol Crystallogr. 2004 Sep;60(Pt 9):1687-90. Epub 2004 Aug 26.

 

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 VA, Schmidt DM, Gerlt JA, Rayment I.

Biochemistry. 2004 Aug 17;43(32):10370-8.

 

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

Eberhard ED, Gerlt JA.

J Am Chem Soc. 2004 Jun 16;126(23):7188-9.

 

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.

Wise EL, Yew WS, Gerlt JA, Rayment I.

Biochemistry. 2004 Jun 1;43(21):6438-46.

 

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.

Yew WS, Wise EL, Rayment I, Gerlt JA.

Biochemistry. 2004 Jun 1;43(21):6427-37.

 

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

Thoden JB, Taylor Ringia EA, Garrett JB, Gerlt JA, Holden HM, Rayment I.

Biochemistry. 2004 May 18;43(19):5716-27.

 

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

Wong BJ, Gerlt JA.

Biochemistry. 2004 Apr 27;43(16):4646-54.

 

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

Taylor Ringia EA, Garrett JB, Thoden JB, Holden HM, Rayment I, Gerlt JA.

Biochemistry. 2004 Jan 13;43(1):224-9.

 

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 VA, Taylor Ringia EA, Gerlt JA, Rayment I.

Biochemistry. 2003 Dec 16;42(49):14427-33.

 

How to find "missing" genes.

Gerlt JA.

Chem Biol. 2003 Dec;10(12):1141-2.

 

Chemical and enzymatic synthesis of fluorinated-dehydroalanine-containing peptides.

Zhou H, Schmidt DM, Gerlt JA, van der Donk WA.

Chembiochem. 2003 Nov 7;4(11):1206-15.

 

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.

Wise EL, Yew WS, Gerlt JA, Rayment I.

Biochemistry. 2003 Oct 28;42(42):12133-42.

 

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

Wong BJ, Gerlt JA.

J Am Chem Soc. 2003 Oct 8;125(40):12076-7. Erratum in: J Am Chem Soc. 2004 Feb 18;126(6):1921.

 

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

Schmidt DM, Mundorff EC, Dojka M, Bermudez E, Ness JE, Govindarajan S, Babbitt PC, Minshull J, Gerlt JA.

Biochemistry. 2003 Jul 22;42(28):8387-93.

 

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

Gerlt JA, Raushel FM.

Curr Opin Chem Biol. 2003 Apr;7(2):252-64. Review.

 

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

McLeish MJ, Kneen MM, Gopalakrishna KN, Koo CW, Babbitt PC, Gerlt JA, Kenyon GL.

J Bacteriol. 2003 Apr;185(8):2451-6.

 

"Fishing" for the functional proteome.

Gerlt JA.

Nat Biotechnol. 2002 Aug;20(8):786-7. No abstract available.