PDBsum entry 1tt0

Oxidoreductase

PDB id: 1tt0

Contents

Protein chains

577 a.a. *

Ligands

ACT ×4

FAD ×4

12P ×20

Waters ×2496

* Residue conservation analysis

PDB id:

1tt0

Name:

Oxidoreductase

Title:

Crystal structure of pyranose 2-oxidase

Structure:

Pyranose oxidase. Chain: a, b, c, d. Synonym: pyranose-2-oxidase. Ec: 1.1.3.10

Source:

Trametes ochracea. Organism_taxid: 230624. Strain: mb49. Cellular_location: hyphal periplasmic space

Biol. unit:

Tetramer (from PQS)

Resolution:

1.80Å R-factor: 0.134 R-free: 0.171

Authors:

B.M.Hallberg,C.Leitner,D.Haltrich,C.Divne

Key ref:

B.M.Hallberg et al. (2004). Crystal structure of the 270 kDa homotetrameric lignin-degrading enzyme pyranose 2-oxidase. J Mol Biol, 341, 781-796. PubMed id: 15288786 DOI: 10.1016/j.jmb.2004.06.033

Date:

21-Jun-04 Release date: 21-Jun-05

Protein chains

Q7ZA32  (Q7ZA32_TRAOC) -  Pyranose 2-oxidase from Trametes ochracea

Seq: 623 a.a.

Struc: 577 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.3.10 - pyranose oxidase.
• Reaction: D-glucose + O2 = 2-dehydro-D-glucose + H2O2

D-glucose (Bound ligand (Het Group name = 12P) matches with 41.18% similarity) + O2 = 2-dehydro-D-glucose + 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

DOI no: 10.1016/j.jmb.2004.06.033

J Mol Biol 341:781-796 (2004)

PubMed id: 15288786

Crystal structure of the 270 kDa homotetrameric lignin-degrading enzyme pyranose 2-oxidase.

B.M.Hallberg, C.Leitner, D.Haltrich, C.Divne.

ABSTRACT

Pyranose 2-oxidase (P2Ox) is a 270 kDa homotetramer localized preferentially in the hyphal periplasmic space of lignocellulolytic fungi and has a proposed role in lignocellulose degradation to produce the essential co-substrate, hydrogen peroxide, for lignin peroxidases. P2Ox oxidizes D-glucose and other aldopyranoses regioselectively at C2 to the corresponding 2-keto sugars; however, for some substrates, the enzyme also displays specificity for oxidation at C3. The crystal structure of P2Ox from Trametes multicolor has been determined using single anomalous dispersion with mercury as anomalous scatterer. The model was refined at 1.8A resolution to R and Rfree values of 0.134 and 0.171, respectively. The overall fold of the P2Ox subunit resembles that of members of the glucose-methanol-choline family of long-chain oxidoreductases, featuring a flavin-binding Rossmann domain of class alpha/beta and a substrate-binding subdomain with a six-stranded central beta sheet and three alpha helices. The homotetramer buries a large internal cavity of roughly 15,000 A3, from which the four active sites are accessible. Four solvent channels lead from the surface into the cavity through which substrate must enter before accessing the active site. The present structure shows an acetate molecule bound in the active site with the carboxylate group positioned immediately below the flavin N5 atom, and with one carboxylate oxygen atom interacting with the catalytic residues His548 and Asn593. The entrance to the active site is blocked by a loop (residues 452 to 461) with excellent electron density but elevated temperature factors. We predict that this loop is dynamic and opens to allow substrate entry and exit. In silico docking of D-glucose in the P2Ox active site shows that with the active-site loop in the closed conformation, monosaccharides cannot be accommodated; however, after removing the loop from the model, a tentative set of protein-substrate interactions for beta-D-glucose have been outlined.

Selected figure(s)

Figure 5.
Figure 5. The active site in P2Ox. A, The binding of acetate in the P2Ox active site. Key residues that make up the active site are shown. The active-site loop (residues 452-456) that blocks the catalytic site from substrate access is highlighted in purple. Atom-coloring scheme: carbon, beige (protein), yellow (FAD), green (acetate); nitrogen, blue; oxygen, red. For clarity of the picture, water molecules were not included. B, Structural superposition of the oxidative site in P2Ox (violet) and DH[cdh][41.] (green). The least-squares comparison was made to optimize the overall superposition of the active sites. The FAD co-factor molecules, the catalytic His-Asn pairs (P2Ox residue numbering), and the ligands (P2Ox, acetate; DH[cdh], cellobionolactam) are included, as well as Phe454 in P2Ox, which assumes the approximate position of the non-reducing end glucosyl moiety in the DH[cdh]-cellobionolactam complex.

Figure 8.
Figure 8. Comparison of the active site in P2Ox with related GMC enzymes. The FAD co-factor and the catalytic residues are shown as stick models for P2Ox (violet), DH[cdh] (green), ChOx (yellow) and GOx (orange). The active sites were superimposed with respect to the flavin N5 atom. Residue numbering for the catalytic His-Asn is that for P2Ox (for details, see the text). The flavin ring in DH[cdh] is modified by hydroxylation at C6.[27.] FAD-HNL was not included in the comparison, since this enzyme is not an oxidoreductase.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 341, 781-796) copyright 2004.

Figures were selected by an automated process.