Crystal structure of diaminopelargonic acid synthase:: Evolutionary relationships between pyridoxal-5′-phosphate-dependent enzymes
Crystal structure of diaminopelargonic acid synthase:: Evolutionary relationships between pyridoxal-5′-phosphate-dependent enzymes
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DOI：
10.1006/jmbi.1999.2997
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发表时间：
1999-08-27
影响因子：
5.6
通讯作者：
Lindqvist, Y
中科院分区：
文献类型：
--
作者：
Käck, H;Sandmark, J;Lindqvist, Y
利用x射线晶体学在1.8埃分辨率下测定了生物素合成途径中依赖维生素b -6的酶二氨基藻酸合成酶的三维结构。利用汞离子衍生化晶体，采用多波长异常衍射技术解决了该结构。蛋白质模型的结晶x值为17.5%（无x值为22.6%）。每个酶亚基由两个结构域组成，一个大结构域（残基50-329）包含七股平行的β -片，由α -螺旋包围，一个小结构域包括残基1-49和330-429。两个亚基，由晶体中的非晶体二偶体连接，形成同型二聚体分子，其中包含两个相等的活性位点。吡哆醛-5'-磷酸结合在由一个亚基的结构域和第二个亚基的大结构域形成的裂缝中。辅因子通过与不变残基Lys274侧链的共价键固定在酶上。磷酸基团与主链氮原子和位于α -螺旋N端的Ser113侧链相互作用。吡啶氮与不变残基Asp245的侧链形成氢键。电子密度与金属离子（很可能是Na+）相对应，在酶表面的一个紧密转折中被发现。结构分析表明，二氨基膦酸合成酶属于维生素b -6依赖性转氨酶家族，其折叠与最初在天冬氨酸转氨酶中观察到的相同。对该家族酶的多重结构比对表明，它们至少形成6个不同的亚类。在多肽链的n端部分的折叠显著差异是这些亚类的标志之一。二氨基膦酸合成酶是转氨酶亚类III的成员。从全酶与底物7-酮-8-氨基壬二酸的非生产性配合物的结构中，确定了活性位点的位置和参与底物结合的残基。(C) 1999学术出版社。
The three-dimensional structure of diaminopelargonic acid synthase, a vitamin B-6-dependent enzyme in the pathway of the biosynthesis of biotin, has been determined to 1.8 Angstrom resolution by X-ray crystallography. The structure was solved by multi-wavelength anomalous diffraction techniques using a crystal derivatized with mercury ions. The protein model has been refined to a crystallographic X-value of 17.5% (X-free 22.6%). Each enzyme subunit consists of two domains, a large domain (residues 50-329) containing a seven-stranded predominantly parallel beta-sheet, surrounded by alpha-helices, and a small domain comprising residues 1-49 and 330-429. Two subunits, related by a non-crystallographic dyad in the crystals, form the homodimeric molecule, which contains two equal active sites. Pyridoxal-5'-phosphate is bound in a cleft formed by both domains of one subunit and the large domain of the second subunit. The cofactor is anchored to the enzyme by a covalent linkage to the sidechain of the invariant residue Lys274. The phosphate group interacts with main-chain nitrogen atoms and the side-chain of Ser113, located at the N terminus of an alpha-helix. The pyridine nitrogen forms a hydrogen bond to the side-chain of the invariant residue Asp245. Electron density corresponding to a metal ion, most likely Na+, was found in a tight turn at the surface of the enzyme. Structure analysis reveals that diaminopelargonic acid synthase belongs to the family of vitamin B-6-dependent aminotransferases with the same fold as originally observed in aspartate aminotransferase. A multiple structure alignment of enzymes in this family indicated that they form at least six different subclasses. Striking differences in the fold of the N-terminal part of the polypeptide chain are one of the hallmarks of these subclasses. Diaminopelargonic acid synthase is a member of the aminotransferase subclass III. From the structure of the non-productive complex of the holoenzyme with the substrate 7-keto-8-aminopelargonic acid the location of the active site and residues involved in substrate binding have been identified. (C) 1999 Academic Press.