PDBsum entry 3gdk

Lyase

PDB id: 3gdk

Contents

Protein chains

260 a.a. *

Waters ×426

* Residue conservation analysis

PDB id:

3gdk

Name:

Lyase

Title:

Crystal structure of the orotidine 5'-monophosphate decarboxylase from saccharomyces cerevisiae

Structure:

Orotidine 5'-phosphate decarboxylase. Chain: a, b, c, d. Synonym: omp decarboxylase, ompdecase, ompdcase, uridine 5'- monophosphate synthase, ump synthase. Engineered: yes

Source:

Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Gene: ura3, yel021w. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.00Å R-factor: 0.249 R-free: 0.280

Authors:

A.A.Fedorov,E.V.Fedorov,B.M.Wood,J.A.Gerlt,S.C.Almo

Key ref:

K.K.Chan et al. (2009). Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization. Biochemistry, 48, 5518-5531. PubMed id: 19435314

Date:

24-Feb-09 Release date: 23-Jun-09

Protein chains

P03962  (PYRF_YEAST) -  Orotidine 5'-phosphate decarboxylase from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 267 a.a.

Struc: 260 a.a.

Enzyme reactions

• Enzyme class: E.C.4.1.1.23 - orotidine-5'-phosphate decarboxylase.
• Pathway: Pyrimidine Biosynthesis
• Reaction: orotidine 5'-phosphate + H⁺ = UMP + CO2

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Biochemistry 48:5518-5531 (2009)

PubMed id: 19435314

Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.

K.K.Chan, B.M.Wood, A.A.Fedorov, E.V.Fedorov, H.J.Imker, T.L.Amyes, J.P.Richard, S.C.Almo, J.A.Gerlt.

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(7) ( approximately 10(17) total - >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.