3GDL

Crystal structure of the orotidine 5'-monophosphate decarboxylase from Saccharomyces cerevisiae complexed with 6-azauridine 5'-monophosphate

Summary for 3GDL

• Entry DOI: 10.2210/pdb3gdl/pdb
• Related: 1DQW 3GDK 3GDM 3GDR 3GDT
• Descriptor: Orotidine 5'-phosphate decarboxylase, 6-AZA URIDINE 5'-MONOPHOSPHATE (3 entities in total)
• Functional Keywords: orotidine 5'-monophosphate decarboxylase, saccharomyces cerevisiae, 6-azauridine 5'-monophosphate, decarboxylase, lyase, phosphoprotein, pyrimidine biosynthesis, ubl conjugation
• Biological source: Saccharomyces cerevisiae (yeast)
• Total number of polymer chains: 2
• Total formula weight: 59209.40

Authors

Fedorov, A.A.,Fedorov, E.V.,Wood, B.M.,Gerlt, J.A.,Almo, S.C. (deposition date: 2009-02-24, release date: 2009-06-23, Last modification date: 2023-09-06)

Primary citation

Chan, K.K.,Wood, B.M.,Fedorov, A.A.,Fedorov, E.V.,Imker, H.J.,Amyes, T.L.,Richard, J.P.,Almo, S.C.,Gerlt, J.A.
Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.
Biochemistry, 48:5518-5531, 2009

PubMed Abstract: The reaction catalyzed by orotidine 5'-monophosphate decarboxylase (OMPDC) involves a stabilized anionic intermediate, although the structural basis for the rate acceleration (k(cat)/k(non), 7.1 x 10(16)) and proficiency [(k(cat)/K(M))/k(non), 4.8 x 10(22) M(-1)] is uncertain. That the OMPDCs from Methanothermobacter thermautotrophicus (MtOMPDC) and Saccharomyces cerevisiae (ScOMPDC) catalyze the exchange of H6 of the UMP product with solvent deuterium allows an estimate of a lower limit on the rate acceleration associated with stabilization of the intermediate and its flanking transition states (>or=10(10)). The origin of the "missing" contribution, or=10(10)), is of interest. Based on structures of liganded complexes, unfavorable electrostatic interactions between the substrate carboxylate group and a proximal Asp (Asp 70 in MtOMPDC and Asp 91 in ScOMPDC) have been proposed to contribute to the catalytic efficiency [Wu, N., Mo, Y., Gao, J., and Pai, E. F. (2000) Proc. Natl. Acad. Sci. U.S.A. 97, 2017-2022]. We investigated that hypothesis by structural and functional characterization of the D70N and D70G mutants of MtOMPDC and the D91N mutant of ScOMPDC. The substitutions for Asp 70 in MtOMPDC significantly decrease the value of k(cat) for decarboxylation of FOMP (a more reactive substrate analogue) but have little effect on the value of k(ex) for exchange of H6 of FUMP with solvent deuterium; the structures of wild-type MtOMPDC and its mutants are superimposable when complexed with 6-azaUMP. In contrast, the D91N mutant of ScOMPDC does not catalyze exchange of H6 of FUMP; the structures of wild-type ScOMPDC and its D91N mutant are not superimposable when complexed with 6-azaUMP, with differences in both the conformation of the active site loop and the orientation of the ligand vis a vis the active site residues. We propose that the differential effects of substitutions for Asp 70 of MtOMPDC on decarboxylation and exchange provide additional evidence for a carbanionic intermediate as well as the involvement of Asp 70 in substrate destabilization.

PubMed: 19435314
DOI: 10.1021/bi900623r

Experimental method

X-RAY DIFFRACTION (1.65 Å)