We want to understand the structural origins of functional diversity in the (beta/alpha)8 barrel fold, the most commonly observed fold in enzymes. We have identified a group of homologous (beta/alpha)8-barrel fold enzymes that catalyze reactions with unrelated substrates and mechanisms in different metabolic pathways. Orotidine 5'-phosphate decarboxylase (OMPDC) is the best characterized member of this """"""""suprafamily."""""""" We propose to determine structure/function relationships for other members of the OMPDC suprafamily so that we can understand the structural strategies for using a homologous scaffold to catalyze unrelated reactions. These studies significantly expand the scope of functional diversity beyond those found in mechanistically diverse enzyme superfamilies, e.g., the enolase and crotonase superfamilies, in which homologous enzymes catalyze different reactions that share a common partial reaction. The four Specific Aims integrate mechanistic and structural studies: the mechanistic studies will be performed in Dr. Gerlt's laboratory at Illinois (P.I.); the structural studies will be performed in Dr. Rayment's laboratory at Wisconsin (Co-P.I.): 1) Structure/function relationships will be established for 3-keto-L-gulonate 6-phosphate decarboxylase that catalyzes Mg2+-dependent decarboxylation of beta-ketoacids via an enediolate intermediate. 2) Structure/function relationships will be established for D-arabino-hex-3-ulose 6-phosphate synthase that catalyzes Mg2+-dependent aldol condensation via an enediolate intermediate. 3) Structure/function relationships will be established for D-ribulose 5-phosphate 3-epimerase that catalyzes divalent metal-independent 1,1-proton transfer via an enediolate intermediate. 4) A structural blueprint for functional diversity in the ((beta/alpha)8-barrel fold will be tested.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM065155-02
Application #
6701354
Study Section
Physical Biochemistry Study Section (PB)
Program Officer
Jones, Warren
Project Start
2003-02-01
Project End
2007-01-31
Budget Start
2004-02-01
Budget End
2005-01-31
Support Year
2
Fiscal Year
2004
Total Cost
$345,012
Indirect Cost
Name
University of Illinois Urbana-Champaign
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
041544081
City
Champaign
State
IL
Country
United States
Zip Code
61820
Goryanova, Bogdana; Goldman, Lawrence M; Ming, Shonoi et al. (2015) Rate and Equilibrium Constants for an Enzyme Conformational Change during Catalysis by Orotidine 5'-Monophosphate Decarboxylase. Biochemistry 54:4555-64
Goldman, Lawrence M; Amyes, Tina L; Goryanova, Bogdana et al. (2014) Enzyme architecture: deconstruction of the enzyme-activating phosphodianion interactions of orotidine 5'-monophosphate decarboxylase. J Am Chem Soc 136:10156-65
Desai, Bijoy J; Goto, Yuki; Cembran, Alessandro et al. (2014) Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution. Proc Natl Acad Sci U S A 111:15066-71
Kellett, Whitney F; Brunk, Elizabeth; Desai, Bijoy J et al. (2013) Computational, structural, and kinetic evidence that Vibrio vulnificus FrsA is not a cofactor-independent pyruvate decarboxylase. Biochemistry 52:1842-4
Goryanova, Bogdana; Goldman, Lawrence M; Amyes, Tina L et al. (2013) Role of a guanidinium cation-phosphodianion pair in stabilizing the vinyl carbanion intermediate of orotidine 5'-phosphate decarboxylase-catalyzed reactions. Biochemistry 52:7500-11
Erb, Tobias J; Evans, Bradley S; Cho, Kyuil et al. (2012) A RubisCO-like protein links SAM metabolism with isoprenoid biosynthesis. Nat Chem Biol 8:926-32
Tsang, Wing-Yin; Wood, B McKay; Wong, Freeman M et al. (2012) 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. J Am Chem Soc 134:14580-94
Desai, Bijoy J; Wood, B McKay; Fedorov, Alexander A et al. (2012) Conformational changes in orotidine 5'-monophosphate decarboxylase: a structure-based explanation for how the 5'-phosphate group activates the enzyme. Biochemistry 51:8665-78
Warlick, Benjamin P E; Imker, Heidi J; Sriram, Jaya et al. (2012) Mechanistic diversity in the RuBisCO superfamily: RuBisCO from Rhodospirillum rubrum is not promiscuous for reactions catalyzed by RuBisCO-like proteins. Biochemistry 51:9470-9
Warlick, Benjamin P; Evans, Bradley S; Erb, Tobias J et al. (2012) 1-methylthio-D-xylulose 5-phosphate methylsulfurylase: a novel route to 1-deoxy-D-xylulose 5-phosphate in Rhodospirillum rubrum. Biochemistry 51:8324-6

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