3F6B

Crystal structure of benzoylformate decarboxylase in complex with the pyridyl inhibitor PAA

3F6B の概要

• エントリーDOI: 10.2210/pdb3f6b/pdb
• 関連するPDBエントリー: 3F6E
• 分子名称: Benzoylformate decarboxylase, MAGNESIUM ION, 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-2-[(1S,2E)-1-hydroxy-3-pyridin-3-ylprop-2-en-1-yl]-4-methyl-1,3-thiazol-3-ium, ... (4 entities in total)
• 機能のキーワード: thiamin adduct, aromatic hydrocarbons catabolism, calcium, decarboxylase, lyase, magnesium, mandelate pathway, metal-binding, thiamine pyrophosphate
• 由来する生物種: Pseudomonas putida
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 56626.00

構造登録者

Brandt, G.S.,McLeish, M.J.,Kenyon, G.L.,Petsko, G.A.,Ringe, D.,Jordan, F. (登録日: 2008-11-05, 公開日: 2008-12-09, 最終更新日: 2023-09-06)

主引用文献

Chakraborty, S.,Nemeria, N.S.,Balakrishnan, A.,Brandt, G.S.,Kneen, M.M.,Yep, A.,McLeish, M.J.,Kenyon, G.L.,Petsko, G.A.,Ringe, D.,Jordan, F.
Detection and time course of formation of major thiamin diphosphate-bound covalent intermediates derived from a chromophoric substrate analogue on benzoylformate decarboxylase.
Biochemistry, 48:981-994, 2009

PubMed Abstract: The mechanism of the enzyme benzoylformate decarboxylase (BFDC), which carries out a typical thiamin diphosphate (ThDP)-dependent nonoxidative decarboxylation reaction, was studied with the chromophoric alternate substrate (E)-2-oxo-4(pyridin-3-yl)-3-butenoic acid (3-PKB). Addition of 3-PKB resulted in the appearance of two transient intermediates formed consecutively, the first one to be formed a predecarboxylation ThDP-bound intermediate with lambda(max) at 477 nm, and the second one corresponding to the first postdecarboxylation intermediate the enamine with lambda(max) at 437 nm. The time course of formation/depletion of the PKB-ThDP covalent complex and of the enamine showed that decarboxylation was slower than formation of the PKB-ThDP covalent adduct. When the product of decarboxylation 3-(pyridin-3-yl)acrylaldehyde (PAA) was added to BFDC, again an absorbance with lambda(max) at 473 nm was formed, corresponding to the tetrahedral adduct of PAA with ThDP. Addition of well-formed crystals of BFDC to a solution of PAA resulted in a high resolution (1.34 A) structure of the BFDC-bound adduct of ThDP with PAA confirming the tetrahedral nature at the C2alpha atom, rather than of the enamine, and supporting the assignment of the lambda(max) at 473 nm to the PAA-ThDP adduct. The structure of the PAA-ThDP covalent complex is the first example of a product-ThDP adduct on BFDC. Similar studies with 3-PKB indicated that decarboxylation had taken place. Evidence was also obtained for the slow formation of the enamine intermediate when BFDC was incubated with benzaldehyde, the product of the decarboxylation reaction thus confirming its presence on the reaction pathway.

PubMed: 19140682
DOI: 10.1021/bi801810h

実験手法

X-RAY DIFFRACTION (1.34 Å)