5KLO

Crystal structure of thioacyl intermediate in 2-aminomuconate 6-semialdehyde dehydrogenase N169A

5KLO の概要

• エントリーDOI: 10.2210/pdb5klo/pdb
• 関連するPDBエントリー: 5KLK 5KLL 5KLM 5KLN
• 分子名称: 2-aminomuconate 6-semialdehyde dehydrogenase, (2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoic acid, SODIUM ION, ... (5 entities in total)
• 機能のキーワード: 2-aminomuconate 6-semialdehyde dehydrogenase, kynurenine pathway, oxidoreductase
• 由来する生物種: Pseudomonas fluorescens
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 227730.18

構造登録者

Yang, Y.,Davis, I.,Ha, U.,Wang, Y.,Shin, I.,Liu, A. (登録日: 2016-06-24, 公開日: 2016-11-09, 最終更新日: 2023-09-27)

主引用文献

Yang, Y.,Davis, I.,Ha, U.,Wang, Y.,Shin, I.,Liu, A.
A Pitcher-and-Catcher Mechanism Drives Endogenous Substrate Isomerization by a Dehydrogenase in Kynurenine Metabolism.
J.Biol.Chem., 291:26252-26261, 2016

PubMed Abstract: Aldehyde dehydrogenase typically performs oxidation of aldehydes to their corresponding carboxylic acid while reducing NAD(P) to NAD(P)H via covalent catalysis mediated by an active-site cysteine residue. One member of this superfamily, the enzyme 2-aminomuconate-6-semialdehyde dehydrogenase (AMSDH), is a component of the kynurenine pathway, which catabolizes tryptophan in mammals and certain bacteria. AMSDH catalyzes the NAD-dependent oxidation of 2-aminomuconate semialdehyde to 2-aminomuconate. We recently determined the first crystal structure of AMSDH and several catalytic cycle intermediates. A conserved asparagine in the oxyanion hole, Asn-169, is found to be H-bonded to substrate-derived intermediates in the active site of AMSDH during catalysis, including both the covalently bound thiohemiacetal and thioacyl intermediates. To better interrogate the significance of the hydrogen bond provided by Asn-169 to the reaction mechanism of AMSDH, we created Ala, Ser, Asp, and Gln mutants and studied them using biochemical, kinetic, crystallographic, and computational studies. The in crystallo chemical reaction of the primary substrate with the co-crystalized complex of the N169D mutant and NAD led to the successful trapping of a new catalytic intermediate that was not previously seen. The structural and computational data are consistent with a substrate imine/enol tautomer intermediate being formed prior to the formation of the covalent bond between the substrate and the active-site cysteine. Thus, AMSDH surprisingly includes an isomerization process within its known catalytic mechanism. These data establish a hidden intrinsic isomerization activity of the dehydrogenase and allow us to propose a pitcher-catcher type of catalytic mechanism for the isomerization.

PubMed: 27810899
DOI: 10.1074/jbc.M116.759712

実験手法

X-RAY DIFFRACTION (1.79 Å)