D-甘油醛-3-磷酸脱氢酶：三维结构及进化意义
D-glyceraldehyde-3-phosphate dehydrogenase: three-dimensional structure and evolutionary significance.
作者信息
Buehner M, Ford G C, Moras D, Olsen K W, Rossman M G
出版信息
Proc Natl Acad Sci U S A. 1973 Nov;70(11):3052-4. doi: 10.1073/pnas.70.11.3052.
Abstract
A 3.0-A resolution electron density map of lobster glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) was computed. The essentially single isomorphous replacement map was very substantially improved by averaging subunits. NAD binds in an open conformation at sites close to subunit interfaces. The coenzyme binding portion of the enzyme has almost the same fold as the corresponding portion of lactate dehydrogenase (EC 1.1.1.27). The presence of this structure in the five enzymes, analyzed so far, that use nucleotide coenzymes might indicate a fundamental primordial structural element.
摘要
计算出了龙虾甘油醛-3-磷酸脱氢酶（EC 1.2.1.12）的3.0埃分辨率电子密度图。通过对亚基进行平均，基本的单对同晶置换图得到了显著改善。NAD以开放构象结合在靠近亚基界面的位点。该酶的辅酶结合部分与乳酸脱氢酶（EC 1.1.1.27）的相应部分具有几乎相同的折叠结构。在目前已分析的五种使用核苷酸辅酶的酶中都存在这种结构，这可能表明存在一个基本的原始结构元件。
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本文引用的文献
1
STRUCTURE OF GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE. STRUCTURE SYMMETRY WITHIN THE MOLECULE.3-磷酸甘油醛脱氢酶的结构。分子内的结构对称性。
Nature. 1964 Dec 5;204:918-20. doi: 10.1038/204918a0.
2
Glyceraldehyde 3-phosphate dehydrogenase: Amino acid sequence of enzyme from baker's yeast.3-磷酸甘油醛脱氢酶：来自面包酵母的酶的氨基酸序列。
FEBS Lett. 1972 May 1;22(2):185-189. doi: 10.1016/0014-5793(72)80040-1.
3
Glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus.嗜热脂肪芽孢杆菌的3-磷酸甘油醛脱氢酶
FEBS Lett. 1971 Mar 16;13(4):217-220. doi: 10.1016/0014-5793(71)80539-2.
4
Structure of lactate dehydrogenase at 2-8 A resolution.分辨率为2-8埃的乳酸脱氢酶结构。
Nature. 1970 Sep 12;227(5263):1098-103. doi: 10.1038/2271098a0.
5
Molecular symmetry of glyceraldehyde-3-phosphate dehydrogenase.
J Mol Biol. 1972 Feb 28;64(1):237-45. doi: 10.1016/0022-2836(72)90332-4.
6
Letter: Molecular symmetry axes and subunit interfaces in certain dehydrogenases.信件：某些脱氢酶中的分子对称轴和亚基界面
J Mol Biol. 1973 Jun 5;76(4):533-7. doi: 10.1016/0022-2836(73)90491-9.
7
Comparison of super-secondary structures in proteins.蛋白质中超级二级结构的比较。
J Mol Biol. 1973 May 15;76(2):241-56. doi: 10.1016/0022-2836(73)90388-4.
8
Low resolution structure of glyceraldehyde 3-phosphate dehydrogenase.
Nat New Biol. 1972 Nov 29;240(100):130-3. doi: 10.1038/newbio240130a0.
9
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