PDBsum entry 2nxw

Lyase

PDB id: 2nxw

Contents

Protein chains

537 a.a. *

Ligands

TPP ×2

GOL ×3

Metals

_MG ×2

_CL ×2

Waters ×1337

* Residue conservation analysis

PDB id:

2nxw

Name:

Lyase

Title:

Crystal structure of phenylpyruvate decarboxylase of azospirillum brasilense

Structure:

Phenyl-3-pyruvate decarboxylase. Chain: a, b. Synonym: phenyl-3-pyruvate decarboxylase. Engineered: yes

Source:

Azospirillum brasilense. Organism_taxid: 192. Gene: ipdc. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.50Å R-factor: 0.175 R-free: 0.196

Authors:

W.Versees,S.Spaepen,J.Vanderleyden,J.Steyaert

Key ref:

W.Versées et al. (2007). The crystal structure of phenylpyruvate decarboxylase from Azospirillum brasilense at 1.5 A resolution. Implications for its catalytic and regulatory mechanism. Febs J, 274, 2363-2375. PubMed id: 17403037

Date:

20-Nov-06 Release date: 29-May-07

Protein chains

P51852  (DCIP_AZOBR) -  Indole-3-pyruvate decarboxylase from Azospirillum brasilense

Seq: 545 a.a.

Struc: 537 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.4.1.1.74 - indolepyruvate decarboxylase.
• Reaction: indole-3-pyruvate + H⁺ = indole-3-acetaldehyde + CO2
• Cofactor: Mg(2+); Thiamine diphosphate

Mg(2+) Thiamine diphosphate (Bound ligand (Het Group name = TPP) corresponds exactly)

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

reference

Febs J 274:2363-2375 (2007)

PubMed id: 17403037

The crystal structure of phenylpyruvate decarboxylase from Azospirillum brasilense at 1.5 A resolution. Implications for its catalytic and regulatory mechanism.

W.Versées, S.Spaepen, J.Vanderleyden, J.Steyaert.

ABSTRACT

Phenylpyruvate decarboxylase (PPDC) of Azospirillum brasilense, involved in the biosynthesis of the plant hormone indole-3-acetic acid and the antimicrobial compound phenylacetic acid, is a thiamine diphosphate-dependent enzyme that catalyses the nonoxidative decarboxylation of indole- and phenylpyruvate. Analogous to yeast pyruvate decarboxylases, PPDC is subject to allosteric substrate activation, showing sigmoidal v versus [S] plots. The present paper reports the crystal structure of this enzyme determined at 1.5 A resolution. The subunit architecture of PPDC is characteristic for other members of the pyruvate oxidase family, with each subunit consisting of three domains with an open alpha/beta topology. An active site loop, bearing the catalytic residues His112 and His113, could not be modelled due to flexibility. The biological tetramer is best described as an asymmetric dimer of dimers. A cysteine residue that has been suggested as the site for regulatory substrate binding in yeast pyruvate decarboxylase is not conserved, requiring a different mechanism for allosteric substrate activation in PPDC. Only minor changes occur in the interactions with the cofactors, thiamine diphosphate and Mg2+, compared to pyruvate decarboxylase. A greater diversity is observed in the substrate binding pocket accounting for the difference in substrate specificity. Moreover, a catalytically important glutamate residue conserved in nearly all decarboxylases is replaced by a leucine in PPDC. The consequences of these differences in terms of the catalytic and regulatory mechanism of PPDC are discussed.