Publications from 2009

Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis.
Rakus JF, Kalyanaraman C, Fedorov AA, Fedorov EV, Mills-Groninger FP, Toro R, Bonanno J, Bain K, Sauder JM, Burley SK, Almo SC, Jacobson MP, Gerlt JA.
Biochemistry. 2009 Dec 8;48(48):11546-58. Pubmed

An examination of the relationship between active site loop size and thermodynamic activation parameters for orotidine 5'-monophosphate decarboxylase from mesophilic and thermophilic organisms.
Toth K, Amyes TL, Wood BM, Chan KK, Gerlt JA, Richard JP.
Biochemistry. 2009 Aug 25;48(33):8006-13. Pubmed

Acetoacetate decarboxylase: hydrophobics, not electrostatics.
Gerlt JA.
Nat Chem Biol. 2009 Jul;5(7):454-5. No abstract available. Pubmed

Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.
Chan KK, Wood BM, Fedorov AA, Fedorov EV, Imker HJ, Amyes TL, Richard JP, Almo SC, Gerlt JA.
Biochemistry. 2009 Jun 23;48(24):5518-31. Pubmed

Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: effect of solvent viscosity on kinetic constants.
Wood BM, Chan KK, Amyes TL, Richard JP, Gerlt JA.
Biochemistry. 2009 Jun 23;48(24):5510-7. Pubmed

Enzyme (re)design: lessons from natural evolution and computation.
Gerlt JA, Babbitt PC.
Curr Opin Chem Biol. 2009 Feb;13(1):10-8. Epub 2009 Feb 23. Review. Pubmed

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. Pubmed

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):107-25. Epub 2009 Feb 14. Pubmed

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. Pubmed