PDBsum entry 1vao

Flavoenzyme

PDB id: 1vao

Contents

Protein chains

550 a.a. *

Ligands

ACT ×2

FAD ×2

Metals

_CL ×2

Waters ×316

* Residue conservation analysis

PDB id:

1vao

Name:

Flavoenzyme

Title:

Structure of the octameric flavoenzyme vanillyl-alcohol oxidase

Structure:

Vanillyl-alcohol oxidase. Chain: a, b. Other_details: covalent bond between fad and his 422

Source:

Penicillium simplicissimum. Organism_taxid: 69488. Atcc: 90172. Organelle: peroxisomes. Cellular_location: intracellular. Other_details: fungus

Biol. unit:

Octamer (from PDB file)

Resolution:

2.50Å R-factor: 0.221 R-free: 0.290

Authors:

A.Mattevi

Key ref:

A.Mattevi et al. (1997). Crystal structures and inhibitor binding in the octameric flavoenzyme vanillyl-alcohol oxidase: the shape of the active-site cavity controls substrate specificity. Structure, 5, 907-920. PubMed id: 9261083

Date:

10-Apr-97 Release date: 15-Oct-97

Protein chains

P56216  (VAOX_PENSI) -  Vanillyl-alcohol oxidase from Penicillium simplicissimum

Seq: 560 a.a.

Struc: 550 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.3.38 - vanillyl-alcohol oxidase.
• Reaction: 4-hydroxy-3-methoxy-benzenemethanol + O2 = vanillin + 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

Structure 5:907-920 (1997)

PubMed id: 9261083

Crystal structures and inhibitor binding in the octameric flavoenzyme vanillyl-alcohol oxidase: the shape of the active-site cavity controls substrate specificity.

A.Mattevi, M.W.Fraaije, A.Mozzarelli, L.Olivi, A.Coda, W.J.van Berkel.

ABSTRACT

BACKGROUND: Lignin degradation leads to the formation of a broad spectrum of aromatic molecules that can be used by various fungal micro-organisms as their sole source of carbon. When grown on phenolic compounds, Penicillium simplicissimum induces the strong impression of a flavin-containing vanillyl-alcohol oxidase (VAO). The enzyme catalyses the oxidation of a vast array of substrates, ranging from aromatic amines to 4-alkyphenols. VAO is a member of a novel class of widely distributed oxidoreductases, which use flavin adenine dinucleotide (FAD) as a cofactor covalently bound to the protein. We have carried out the determination of the structure of VAO in order to shed light on the most interesting features of these novel oxidoreductases, such as the functional significance of covalent flavinylation and the mechanism of catalysis. RESULTS: The crystal structure of VAO has been determined in the native state and in complexes with four inhibitors. The enzyme is an octamer with 42 symmetry; the inhibitors bind in a hydrophobic, elongated cavity on the si side of the flavin molecule. Three residues, Tyr108, Tyr503 and Arg504 form an anion-binding subsite, which stabilises the phenolate form of the substrate. The structure of VAO complexed with the inhibitor 4-(1-heptenyl)phenol shows that the catalytic cavity is completely filled by the inhibitor, explaining why alkylphenols bearing aliphatic substituents longer than seven carbon atoms do not bind to the enzyme. CONCLUSIONS: The shape of the active-site cavity controls substrate specificity by providing a 'size exclusion mechanism'. Inside the cavity, the substrate aromatic ring is positioned at an angle of 18 degrees to the flavin ring. This arrangement is ideally suited for a hydride transfer reaction, which is further facilitated by substrate deprotonation. Burying the substrate beneath the protein surface is a recurrent strategy, common to many flavoenzymes that effect substrate oxidation or reduction via hydride transfer.