CRYSTAL-STRUCTURE OF A NAD-DEPENDENT D-GLYCERATE DEHYDROGENASE AT 2-CENTER-DOT-4-ANGSTROM RESOLUTION
CRYSTAL-STRUCTURE OF A NAD-DEPENDENT D-GLYCERATE DEHYDROGENASE AT 2-CENTER-DOT-4-ANGSTROM RESOLUTION
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DOI：
10.1016/0022-2836(94)90016-7
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发表时间：
1994-03-04
影响因子：
5.6
通讯作者：
BRICK, P
中科院分区：
文献类型：
--
作者：
GOLDBERG, JD;YOSHIDA, T;BRICK, P
甘油酸脱氢酶（GDH）催化NADH连接的羟基丙酮酸还原为甘油酸。GDH是NAD依赖性脱氢酶家族的成员，其特征在于对羟基酸底物的d-异构体具有特异性。本文用同晶置换法测定了甲腐丝微菌GDH脱辅基酶的晶体结构，并用限制性最小二乘法修正了其2.4 μ m的分辨率。在10.0和2.4 μ m分辨率之间的所有24，553个测量反射的晶体学R因子为19.4%。GDH分子是由分子量为38，000的亚基组成的对称二聚体，并且与另一种NAD依赖性酶甲酸脱氢酶具有显著的结构同源性。GDH亚基由两个结构相似的结构域组成，这两个结构域通过2重对称性彼此近似相关。这些结构域被形成推定的NAD和底物结合位点的深裂分开。其中一个结构域已被鉴定为NAD结合结构域，这是基于其与其他NAD依赖性内切酶的NAD结合结构域的紧密结构相似性。第二个结构域的拓扑结构与其他酶的各种催化结构域中发现的拓扑结构不同。GDH三元复合物的模型已经建立，其中推定的催化残基的基础上确定的d-异构体特异性脱氢酶之间的序列同源性。GDH和L-乳酸脱氢酶之间的结构比较表明这两种酶的活性位点残基和几何形状的收敛。所分析的反应在化学上是等价的，但立体专一性相反。一个假设，以解释这两种酶如何利用相同的辅酶立体化学和催化残基的类似的空间排列进行反应，进行相反的对映异构体。
d-Glycerate dehydrogenase (GDH) catalyzes the NADH-linked reduction of hydroxypyruvate tod-glycerate. GDH is a member of a family of NAD-dependent dehydrogenases that is characterized by a specificity for thed-isomer of the hydroxyacid substrate. The crystal structure of the apoenzyme form of GDH fromHyphomicrobium methylovorumhas been determined by the method of isomorphous replacement and refined at 2·4 Å resolution using a restrained least-squares method. The crystallographicR-factor is 19·4% for all 24,553 measured reflections between 10·0 and 2·4 Å resolution. The GDH molecule is a symmetrical dimer composed of subunits of molecular mass 38,000, and shares significant structural homology with another NAD-dependent enzyme, formate dehydrogenases The GDH subunit consists of two structurally similar domains that are approximately related to each other by 2-fold symmetry. The domains are separated by a deep cleft that forms the putative NAD and substrate binding sites. One of the domains has been identified as the NAD-binding domain based on its close structural similarity to the NAD-binding domains of other NAD-dependent dehydrogenases. The topology of the second domain is different from that found in the various catalytic domains of other dehydrogenases. A model of a ternary complex of GDH has been built in which putative catalytic residues are identified based on sequence homology between thed-isomer specific dehydrogenases. A structural comparison between GDH andl-lactate dehydrogenase indicates a convergence of active site residues and geometries for these two enzymes. The reactionscatalyzed are chemically equivalent but of opposing stereospecificity. A hypothesis is presented to explain how the two enzymes may exploit the same coenzyme stereochemistry and a similar spatial arrangement of catalytic residues to carry out reactions that proceed to opposite enantiomers.