Crystal structures of ligand-bound saccharopine dehydrogenase from Saccharomyces cerevisiae
Crystal structures of ligand-bound saccharopine dehydrogenase from Saccharomyces cerevisiae
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DOI：
10.1021/bi701428m
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发表时间：
2007-11-06
期刊：
影响因子：
2.9
通讯作者：
West, Ann H.
中科院分区：
文献类型：
--
作者：
Andi, Babak;Xu, Hengyu;West, Ann H.
在硫酸盐、单磷酸腺苷 (AMP) 和草酰甘氨酸 (OxGly) 存在的情况下，已确定糖碱脱氢酶（L-赖氨酸形成）(SDH) 的三种结构。在硫酸盐结合结构中，硫酸根离子结合在 SDH 的两个结构域之间的裂缝中，占据底物羧酸盐结合位点之一，并由于与脱辅基酶结构相比几乎 12 度的结构域旋转而导致酶的活性位点部分闭合。在第二种结构中，AMP 与 NAD(+) 辅因子预计结合的区域中的活性位点结合。所有 AMP 部分（腺嘌呤环、核糖和磷酸盐）均与酶的特定残基相互作用。在 OxGly 结合结构中，OxGly 的羧酸盐与精氨酸残基相互作用，代表底物（（x-酮戊二酸和糖苷）可能结合的方式。OxGly 的 a-酮基团与 Lys77 和 His96 相互作用，它们是酸碱催化的候选者。配体-酶相互作用分析、比较结构分析、动力学数据验证以及三元复合物模型的讨论本研究中提出。
Three structures of saccharopine dehydrogenase (L-lysine-forming) (SDH) have been determined in the presence of sulfate, adenosine monophosphate (AMP), and oxalylglycine (OxGly). In the sulfatebound structure, a sulfate ion binds in a cleft between the two domains of SDH, occupies one of the substrate carboxylate binding sites, and results in partial closure of the active site of the enzyme dueto a domain rotation of almost 12 degrees in comparison to the apoenzyme structure. In the second structure, AMP binds to the active site in an area where the NAD(+) cofactor is expected to bind. All of the AMP moieties (adenine ring, ribose, and phosphate) interact with specific residues of the enzyme. In the OxGly-bound structure, carboxylates of OxGly interact with arginine residues representative of the manner in which substrate ((x-ketoglutarate and saccharopine) may bind. The a-keto group of OxGly interacts with Lys77 and His96, which are candidates for acid-base catalysis. Analysis of ligand-enzyme interactions, comparative structural analysis, corroboration with kinetic data, and discussion of a ternary complex model are presented in this study.