3G18

Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum

Summary for 3G18

• Entry DOI: 10.2210/pdb3g18/pdb
• Related: 1DV7 3G1A 3G1D 3G1F 3G1H 3G1S 3G1V 3G1X 3G1Y 3G22 3G24
• Descriptor: Orotidine 5'-phosphate decarboxylase (2 entities in total)
• Functional Keywords: decarboxylase, pyrimidine biosynthesis, lyase
• Biological source: Methanothermobacter thermautotrophicus str. Delta H
• Total number of polymer chains: 2
• Total formula weight: 49769.39

Authors

Fedorov, A.A.,Fedorov, E.V.,Chan, K.K.,Gerlt, J.A.,Almo, S.C. (deposition date: 2009-01-29, 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 (1.6 Å)