Crystal structures of open and closed forms of D-serine deaminase from Salmonella typhimurium - implications on substrate specificity and catalysis
Crystal structures of open and closed forms of D-serine deaminase from Salmonella typhimurium - implications on substrate specificity and catalysis
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DOI：
10.1111/j.1742-4658.2011.08210.x
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发表时间：
2011-08-01
期刊：
影响因子：
5.4
通讯作者：
Murthy, Mattur Ramabhadrashastry Narasimha
中科院分区：
文献类型：
--
作者：
Bharath, Sakshibeedu Rajegowda;Bisht, Shveta;Murthy, Mattur Ramabhadrashastry Narasimha
由于d -氨基酸在细胞结构和功能中的重要作用，其代谢引起了相当大的兴趣。鼠伤寒沙门氏菌d -丝氨酸脱氨酶（StDSD）是一种依赖于吡哆醛5'磷酸（PLP）的酶，它催化d -丝氨酸降解为丙酮酸和氨。本文描述的d -丝氨酸脱氨酶的第一个晶体结构揭示了plp依赖性酶的典型折叠II型或色氨酸合成酶β亚基折叠。尽管全酶用于野生型StDSD （WtDSD）和硒代蛋氨酸标记StDSD （SeMetDSD）的结晶，但未观察到辅助因子的显著电子密度，表明该酶在结晶条件下对辅助因子的亲和力较低。有趣的是，在两种结构之间观察到意想不到的构象差异。WtDSD呈开放构象，而在异丝氨酸存在下结晶的SeMetDSD呈封闭构象，这表明该酶在与底物结合后可能发生构象变化，正如在其他Foldtype II plp依赖性酶中观察到的那样。电子密度与一个似是而非的钠离子相对应，在酶的关闭状态的活性位点附近发现，而不是在酶的开放状态。对活性位点和底物模型的研究表明，Thr166可能参与了从底物C α原子中提取质子的过程。除生理反应外，StDSD还催化a、b将d -苏氨酸、d -全素氨酸和l -丝氨酸消除为相应的α -酮酸和氨。StDSD的结构为理解与这些底物反应速率的差异提供了必要的分子框架。
Metabolism of D-amino acids is of considerable interest due to their key importance in cell structure and function. Salmonella typhimurium D-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 beta 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 C alpha atom of the substrate. Apart from the physiological reaction, StDSD catalyses a, b elimination of D-Thr, D-Allothr and L-Ser to the corresponding alpha-keto acids and ammonia. The structure of StDSD provides a molecular framework necessary for understanding differences in the rate of reaction with these substrates.