2NXW

Crystal structure of phenylpyruvate decarboxylase of Azospirillum brasilense

2NXW の概要

• エントリーDOI: 10.2210/pdb2nxw/pdb
• 分子名称: PHENYL-3-PYRUVATE DECARBOXYLASE, MAGNESIUM ION, CHLORIDE ION, ... (6 entities in total)
• 機能のキーワード: thiamine pyrophosphate, asymmetric dimer of dimers, open active site loops, lyase
• 由来する生物種: Azospirillum brasilense
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 121900.14

構造登録者

Versees, W.,Spaepen, S.,Vanderleyden, J.,Steyaert, J. (登録日: 2006-11-20, 公開日: 2007-05-29, 最終更新日: 2023-08-30)

主引用文献

Versees, W.,Spaepen, S.,Vanderleyden, J.,Steyaert, J.
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, 2007

PubMed 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.

PubMed: 17403037
DOI: 10.1111/j.1742-4658.2007.05771.x

実験手法

X-RAY DIFFRACTION (1.5 Å)