2YY7

Crystal structure of thermolabile L-threonine dehydrogenase from Flavobacterium frigidimaris KUC-1

2YY7 の概要

• エントリーDOI: 10.2210/pdb2yy7/pdb
• 分子名称: L-threonine dehydrogenase, 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... (6 entities in total)
• 機能のキーワード: l-threonine dehydrogenase, thermolabile, flavobacterium frigidimaris kuc-1, oxidoreductase
• 由来する生物種: Flavobacterium frigidimaris
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 74286.27

構造登録者

Yoneda, K.,Sakuraba, H.,Oikawa, T.,Muraoka, I.,Ohshima, T. (登録日: 2007-04-27, 公開日: 2008-04-29, 最終更新日: 2024-03-13)

主引用文献

Yoneda, K.,Sakuraba, H.,Muraoka, I.,Oikawa, T.,Ohshima, T.
Crystal structure of UDP-galactose 4-epimerase-like L-threonine dehydrogenase belonging to the intermediate short-chain dehydrogenase-reductase superfamily
Febs J., 277:5124-5132, 2010

PubMed Abstract: The crystal structure of a L-threonine dehydrogenase (L-ThrDH; EC 1.1.1.103) from the psychrophilic bacterium Flavobacterium frigidimaris KUC-1, which shows no sequence similarity to conventional L-ThrDHs, was determined in the presence of NAD and a substrate analog, glycerol. The asymmetric unit consisted of two subunits related by a two-fold rotation axis. Each monomer consisted of a Rossmann-fold domain and a carboxyl-terminal catalytic domain. The overall fold of F. frigidimaris L-ThrDH showed significant similarity to that of UDP-galactose 4-epimerase (GalE); however, structural comparison of the enzyme with E. coli and human GalEs showed clear topological differences in three loops (loop 1, loop 2 and the NAD-binding loop) around the substrate and NAD binding sites. In F. frigidimaris L-ThrDH, loops 1 and 2 insert toward the active site cavity, creating a barrier preventing the binding of UDP-glucose. Alternatively, loop 1 contributes to a unique substrate binding pocket in the F. frigidimaris enzyme. The NAD binding loop, which tightly holds the adenine ribose moiety of NAD in the Escherichia coli and human GalEs, is absent in F. frigidimaris L-ThrDH. Consequently, the cofactor binds to F. frigidimaris L-ThrDH in a reversible manner, unlike its binding to GalE. The substrate binding model suggests that the reaction proceeds through abstraction of the β-hydroxyl hydrogen of L-threonine via either a proton shuttle mechanism driven by Tyr143 and facilitated by Ser118 or direct proton transfer driven by Tyr143. The present structure provides a clear bench mark for distinguishing GalE-like L-ThrDHs from GalEs.

PubMed: 21078123
DOI: 10.1111/j.1742-4658.2010.07916.x

実験手法

X-RAY DIFFRACTION (2.061 Å)