来自多氯联苯降解菌的顺式联苯-2,3-二氢二醇-2,3-脱氢酶在2.0埃分辨率下的晶体结构。
Crystal structure of cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase from a PCB degrader at 2.0 A resolution.
作者信息
Hülsmeyer M, Hecht H J, Niefind K, Hofer B, Eltis L D, Timmis K N, Schomburg D
机构信息
National Institute for Biotechnological Research (GBF), Department of Structure Research, Braunschweig, Germany.
出版信息
Protein Sci. 1998 Jun;7(6):1286-93. doi: 10.1002/pro.5560070603.
Abstract
cis-Biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB) is involved in the aerobic biodegradation of polychlorinated biphenyls (PCBs). The crystal structure of the NAD+-enzyme complex was determined by molecular replacement and refined to an R-value of 17.9% at 2.0 A. As a member of the short-chain alcohol dehydrogenase/reductase (SDR) family, the overall protein fold and positioning of the catalytic triad in BphB are very similar to those observed in other SDR enzymes, although small differences occur in the cofactor binding site. Modeling studies indicate that the substrate is bound in a deep hydrophobic cleft close to the nicotinamide moiety of the NAD+ cofactor. These studies further suggest that Asn143 is a key determinant of substrate specificity. A two-step reaction mechanism is proposed for cis-dihydrodiol dehydrogenases.
摘要
顺式联苯-2,3-二氢二醇-2,3-脱氢酶（BphB）参与多氯联苯（PCBs）的需氧生物降解。通过分子置换确定了NAD⁺-酶复合物的晶体结构，并在2.0 Å分辨率下精修至R值为17.9%。作为短链醇脱氢酶/还原酶（SDR）家族的一员，BphB的整体蛋白质折叠和催化三联体的定位与其他SDR酶非常相似，尽管辅因子结合位点存在微小差异。建模研究表明，底物结合在靠近NAD⁺辅因子烟酰胺部分的深疏水裂缝中。这些研究进一步表明，Asn143是底物特异性的关键决定因素。提出了顺式二氢二醇脱氢酶的两步反应机制。
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本文引用的文献
1
NADP-dependent enzymes. I: Conserved stereochemistry of cofactor binding.依赖烟酰胺腺嘌呤二核苷酸磷酸（NADP）的酶。I：辅因子结合的保守立体化学
Proteins. 1997 May;28(1):10-28. doi: 10.1002/(sici)1097-0134(199705)28:1<10::aid-prot2>3.0.co;2-n.
2
Crystal structure of the ternary complex of mouse lung carbonyl reductase at 1.8 A resolution: the structural origin of coenzyme specificity in the short-chain dehydrogenase/reductase family.小鼠肺羰基还原酶三元复合物的晶体结构，分辨率为1.8埃：短链脱氢酶/还原酶家族中辅酶特异性的结构起源。
Structure. 1996 Jan 15;4(1):33-45. doi: 10.1016/s0969-2126(96)00007-x.
3
NAD-binding domains of dehydrogenases.脱氢酶的烟酰胺腺嘌呤二核苷酸结合结构域。
Curr Opin Struct Biol. 1995 Dec;5(6):775-83. doi: 10.1016/0959-440x(95)80010-7.
4
Crystal structures of the binary and ternary complexes of 7 alpha-hydroxysteroid dehydrogenase from Escherichia coli.来自大肠杆菌的7α-羟基类固醇脱氢酶二元和三元复合物的晶体结构。
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5
Crystal structures of the oxidized and reduced forms of UDP-galactose 4-epimerase isolated from Escherichia coli.从大肠杆菌中分离得到的UDP-半乳糖4-表异构酶氧化态和还原态的晶体结构。
Biochemistry. 1996 Feb 27;35(8):2557-66. doi: 10.1021/bi952715y.
6
Analysis of Pseudomonas gene products using lacIq/Ptrp-lac plasmids and transposons that confer conditional phenotypes.使用赋予条件表型的lacIq/Ptrp-lac质粒和转座子对假单胞菌基因产物进行分析。
Gene. 1993 Jan 15;123(1):17-24. doi: 10.1016/0378-1119(93)90533-9.
7
Protein superfamilies and domain superfolds.蛋白质超家族和结构域超折叠。
Nature. 1994 Dec 15;372(6507):631-4. doi: 10.1038/372631a0.
8
The refined three-dimensional structure of 3 alpha,20 beta-hydroxysteroid dehydrogenase and possible roles of the residues conserved in short-chain dehydrogenases.3α,20β-羟基类固醇脱氢酶的精细三维结构及短链脱氢酶中保守残基的可能作用。
Structure. 1994 Jul 15;2(7):629-40. doi: 10.1016/s0969-2126(00)00064-2.
9
Short-chain dehydrogenases/reductases (SDR).短链脱氢酶/还原酶（SDR）
Biochemistry. 1995 May 9;34(18):6003-13. doi: 10.1021/bi00018a001.
10
LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions.LIGPLOT：一个用于生成蛋白质-配体相互作用示意图的程序。
Protein Eng. 1995 Feb;8(2):127-34. doi: 10.1093/protein/8.2.127.
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