PDBsum entry 2rgo

Oxidoreductase

PDB id: 2rgo

Contents

Protein chains

557 a.a. *

530 a.a. *

Ligands

FAD ×2

Waters ×232

* Residue conservation analysis

PDB id:

2rgo

Name:

Oxidoreductase

Title:

Structure of alpha-glycerophosphate oxidase from streptococcus sp.: A template for the mitochondrial alpha-glycerophosphate dehydrogenase

Structure:

Alpha-glycerophosphate oxidase. Chain: a, b. Synonym: fad dependent oxidoreductase. Engineered: yes

Source:

Streptococcus sp.. Organism_taxid: 1306. Gene: glpo. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.40Å R-factor: 0.238 R-free: 0.247

Authors:

T.Colussi,W.Boles,T.C.Mallett,P.A.Karplus,A.Claiborne

Key ref:

T.Colussi et al. (2008). Structure of alpha-glycerophosphate oxidase from Streptococcus sp.: a template for the mitochondrial alpha-glycerophosphate dehydrogenase. Biochemistry, 47, 965-977. PubMed id: 18154320

Date:

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

Protein chain

D0VWP7  (D0VWP7_STRSP) -  Alpha-glycerophosphate oxidase from Streptococcus sp

Seq: 607 a.a.

Struc: 557 a.a.

Protein chain

D0VWP7  (D0VWP7_STRSP) -  Alpha-glycerophosphate oxidase from Streptococcus sp

Seq: 607 a.a.

Struc: 530 a.a.

Enzyme reactions

• Enzyme class: Chains A, B: E.C.1.1.3.21 - glycerol-3-phosphate oxidase.
• Reaction: sn-glycerol 3-phosphate + O2 = dihydroxyacetone phosphate + H2O2
• Cofactor: FAD

FAD (Bound ligand (Het Group name = FAD) corresponds exactly)

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

reference

Biochemistry 47:965-977 (2008)

PubMed id: 18154320

Structure of alpha-glycerophosphate oxidase from Streptococcus sp.: a template for the mitochondrial alpha-glycerophosphate dehydrogenase.

T.Colussi, D.Parsonage, W.Boles, T.Matsuoka, T.C.Mallett, P.A.Karplus, A.Claiborne.

ABSTRACT

The FAD-dependent alpha-glycerophosphate oxidase (GlpO) from Enterococcus casseliflavus and Streptococcus sp. was originally studied as a soluble flavoprotein oxidase; surprisingly, the GlpO sequence is 30-43% identical to those of the alpha-glycerophosphate dehydrogenases (GlpDs) from mitochondrial and bacterial sources. The structure of a deletion mutant of Streptococcus sp. GlpO (GlpODelta, lacking a 50-residue insert that includes a flexible surface region) has been determined using multiwavelength anomalous dispersion data and refined at 2.3 A resolution. Using the GlpODelta structure as a search model, we have also determined the intact GlpO structure, as refined at 2.4 A resolution. The first two domains of the GlpO fold are most closely related to those of the flavoprotein glycine oxidase, where they function in FAD binding and substrate binding, respectively; the GlpO C-terminal domain consists of two helix bundles and is not closely related to any known structure. The flexible surface region in intact GlpO corresponds to a segment of missing electron density that links the substrate-binding domain to a betabetaalpha element of the FAD-binding domain. In accordance with earlier biochemical studies (stabilizations of the covalent FAD-N5-sulfite adduct and p-quinonoid form of 8-mercapto-FAD), Ile430-N, Thr431-N, and Thr431-OG are hydrogen bonded to FAD-O2alpha in GlpODelta, stabilizing the negative charge in these two modified flavins and facilitating transfer of a hydride to FAD-N5 (from Glp) as well. Active-site overlays with the glycine oxidase-N-acetylglycine and d-amino acid oxidase-d-alanine complexes demonstrate that Arg346 of GlpODelta is structurally equivalent to Arg302 and Arg285, respectively; in both cases, these residues interact directly with the amino acid substrate or inhibitor carboxylate. The structural and functional divergence between GlpO and the bacterial and mitochondrial GlpDs is also discussed.