Structure of 3-isopropylmalate dehydrogenase in complex with NAD+: ligand-induced loop closing and mechanism for cofactor specificity.
Structure of 3-isopropylmalate dehydrogenase in complex with NAD+: ligand-induced loop closing and mechanism for cofactor specificity.
复制标题
DOI：
10.1016/s0969-2126(94)00104-9
复制
发表时间：
1994-11
期刊：
影响因子：
5.7
通讯作者：
James H. Hurley;Antony M. Dean
中科院分区：
文献类型：
--
作者：
James H. Hurley;Antony M. Dean
背景：亮氨酸生物合成酶3-异丙基苹果酸脱氢酶（IMDH）是一类独特的双功能脱羧酶。该家族的两个最著名的成员，IMDH和异柠檬酸脱氢酶（IDH），具有共同的结构框架和催化机制，但具有不同的底物和辅因子特异性。IMDH是NAD+依赖的，而IDHs发生在两个NAD+依赖和NADP+依赖的forms.ResultsWe有co-crystallizedThermus thermophilusIMDH与NAD+，并已确定在2.5 μ m分辨率的结构。NAD+以延伸构象结合。在没有辅因子的情况下与结构的比较表明，结合诱导形成二核苷酸结合位点的五个环中高达2.5 μ m的结构变化。NAD+的腺嘌呤和二磷酸部分通过也存在于NADP+-IDH复合物中的相互作用结合。与IDH中NADP+2′-磷酸相互作用的氨基酸在IMDH中被取代或缺失。腺苷核糖与Asp 278形成两个氢键，烟酰胺和烟酰胺核糖与Glu 87和Asp 78相互作用，所有独特的IMDH.ConclusionNAD+结合诱导IMDH的构象转变，导致中间的结构是最“开放”和“封闭”脱羧脱氢酶构象。通过Asp 278与NAD+腺苷的游离2-羟基之间的独特相互作用、Asp 278上的负电荷对2′-磷酸的存在的区分以及与NADP+的2 ′-磷酸缺乏潜在的有利相互作用，可以解释IMDH对NAD+与NADP+的生理特异性。
Background:The leucine biosynthetic enzyme 3–isopropylmalate dehydrogenase (IMDH) belongs to a unique class of bifunctional decarboxylating dehydrogenases. The two best–known members of this family, IMDH and isocitrate dehydrogenase (IDH), share a common structural framework and catalytic mechanism but have different substrate and cofactor specificities. IMDH is NAD+–dependent, while IDHs occur in both NAD+–dependent and NADP+–dependent forms.ResultsWe have co–crystallizedThermus thermophilusIMDH with NAD+and have determined the structure at 2.5 Å resolution. NAD+binds in an extended conformation. Comparisons with the structure in the absence of cofactor show that binding induces structural changes of up to 2.5 Å in the five loops which form the dinucleotide–binding site. The adenine and diphosphate moieties of NAD+are bound via interactions which are also present in the NADP+–IDH complex. Amino acids which interact with the NADP+2′–phosphate in IDH are substituted or absent in IMDH. The adenosine ribose forms two hydrogen bonds with Asp278, and the nicotinamide and nicotinamide ribose interact with Glu87 and Asp78, all unique to IMDH.ConclusionNAD+binding induces a conformational transition in IMDH, resulting in a structure that is intermediate between the most ‘open' and ‘closed' decarboxylating dehydrogenase conformations. Physiological specificity of IMDH for NAD+versus NADP+can be explained by the unique interaction between Asp278 and the free 2–hydroxyl of the NAD+adenosine, discrimination against the presence of the 2′–phosphate by the negative charge on Asp278, and the absence of potential favorable interactions with the 2′–phosphate of NADP+.