3R0Z

Crystal structure of apo D-serine deaminase from Salmonella typhimurium

3R0Z の概要

• エントリーDOI: 10.2210/pdb3r0z/pdb
• 関連するPDBエントリー: 3R0X
• 分子名称: D-serine dehydratase, SULFATE ION, 1,2-ETHANEDIOL, ... (4 entities in total)
• 機能のキーワード: foldtype 2 family of plp-dependent enzymes, alpha, beta elimination of d-serine, lyase
• 由来する生物種: Salmonella enterica subsp. enterica serovar Typhimurium
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 48899.20

構造登録者

Bharath, S.R.,Shveta, B.,Savithri, H.S.,Murthy, M.R.N. (登録日: 2011-03-09, 公開日: 2011-06-29, 最終更新日: 2024-03-20)

主引用文献

Bharath, S.R.,Bisht, S.,Savithri, H.S.,Murthy, M.R.N.
Crystal structures of open and closed forms of D-serine deaminase from Salmonella typhimurium - implications on substrate specificity and catalysis
Febs J., 2011

PubMed Abstract: Metabolism of D-amino acids is of considerable interest due to their key importance in cell structure and function. Salmonella typhimuriumd-serine deaminase (StDSD) is a pyridoxal 5' phosphate (PLP) dependent enzyme that catalyses degradation of D-Ser to pyruvate and ammonia. The first crystal structure of d-serine deaminase described here reveals a typical Foldtype II or tryptophan synthase β subunit fold of PLP-dependent enzymes. Although holoenzyme was used for crystallization of both wild-type StDSD (WtDSD) and selenomethionine labelled StDSD (SeMetDSD), significant electron density was not observed for the cofactor, indicating that the enzyme has a low affinity for the cofactor under crystallization conditions. Interestingly, unexpected conformational differences were observed between the two structures. The WtDSD was in an open conformation while SeMetDSD, crystallized in the presence of isoserine, was in a closed conformation suggesting that the enzyme is likely to undergo conformational changes upon binding of substrate as observed in other Foldtype II PLP-dependent enzymes. Electron density corresponding to a plausible sodium ion was found near the active site of the closed but not in the open state of the enzyme. Examination of the active site and substrate modelling suggests that Thr166 may be involved in abstraction of proton from the Cα atom of the substrate. Apart from the physiological reaction, StDSD catalyses α, β elimination of D-Thr, D-Allothr and L-Ser to the corresponding α-keto acids and ammonia. The structure of StDSD provides a molecular framework necessary for understanding differences in the rate of reaction with these substrates.

PubMed: 21668644
DOI: 10.1111/j.1742-4658.2011.08210.x

実験手法

X-RAY DIFFRACTION (2.4 Å)