PDBsum entry: 2pry

Transferase

PDB id: 2pry

Contents

Protein chain

215 a.a. *

Metals

_MG

Waters ×100

* Residue conservation analysis

PDB id:

2pry

Name:

Transferase

Title:

Apo form of s. Cerevisiae orotate phosphoribosyltransferase

Structure:

Orotate phosphoribosyltransferase 1. Chain: a. Synonym: oprt 1, oprtase 1. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: ura5, pyr5. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.35Å R-factor: 0.239 R-free: 0.260

Authors:

L.Gonzalez-Segura,T.D.Hurley,R.W.Mcclard

Key ref:

L.González-Segura et al. (2007). Ternary complex formation and induced asymmetry in orotate phosphoribosyltransferase. Biochemistry, 46, 14075-14086. PubMed id: 18020427 DOI: 10.1021/bi701023z

Date:

04-May-07 Release date: 15-Jan-08

Protein chain

P13298  (PYRE_YEAST) -  Orotate phosphoribosyltransferase 1

Seq: 226 a.a.

Struc: 215 a.a.

Enzyme reactions

• Enzyme class: E.C.2.4.2.10 - Orotate phosphoribosyltransferase.
• Pathway: Pyrimidine Biosynthesis
• Reaction: Orotidine 5'-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (2 terms)
• Biological process: nucleoside metabolic process (4 terms)
• Biochemical function: protein binding (4 terms)

reference

DOI no: 10.1021/bi701023z

Biochemistry 46:14075-14086 (2007)

PubMed id: 18020427

Ternary complex formation and induced asymmetry in orotate phosphoribosyltransferase.

L.González-Segura, J.F.Witte, R.W.McClard, T.D.Hurley.

ABSTRACT

Orotate phosphoribosyltransferase (OPRTase, EC 2.4.2.10) catalyzes the Mg2+-dependent condensation of orotic acid (OA) with PRPP (5-alpha-d-phosphorylribose 1-diphosphate) to yield diphosphate (PPi) and the nucleotide OMP (orotidine 5'-monophosphate). We have determined the structures of three forms of Saccharomyces cerevisiae OPRTase representing different structural and enzymatic intermediates. The structures include the apoenzyme (2.35 A resolution); a ternary complex of enzyme, Mg2+-PRPP, and OA (1.74 A resolution); and the binary product complex of enzyme with OMP (1.89 A resolution). While the overall structure of the S. cerevisiae OPRTase is similar to that of the Salmonella typhimurium enzyme, as judged by comparison of the two apoenzymes, large conformational transitions occur proceeding from the apoenzyme structure to those of the substrate and product complexes. Comparison of these structures reveals a rotation of the upper hood domain onto the bound ligands by an average of 19.5 degrees in the OMP structure and an average of 24.6 degrees in the OA/Mg2+-PRPP ternary complex. As expected, the conserved loop, composed of residues 104-116, moves extensively and adopts a single stable conformation during the catalytic cycle in order to sequester the substrates from bulk solvent in the ternary complex. The OA and Mg2+-PRPP molecules bound in the ternary complex are oriented for proper attack of the N1 atom of OA onto the C1 atom of the ribose ring. This orientation of substrates, combined with the positioning of the flexible loop, provides a clear picture of a catalytically poised reaction complex for type I phosphoribosyltransferases. The structural asymmetry present in these structures, as well as that found in a recent structure of the S. typhimurium enzyme, combined with the closure of the flexible loop from one subunit into the active site of the opposing subunit in the ternary complex is consistent with the kinetic data [McClard, R. W., et al. (2006) Biochemistry 45, 5330-5342] that demonstrate induced nonequivalence and cooperativity of OPRTase.