标题:
基于生物信息学对NAD(P)H辅酶氧化酶的结构识别The Structure Identifying of Coenzyme Oxidase NAD(P)H Based on Bioinformatics
作者:
王世珍, 王雅丽, 李红春, 李昊, 方柏山
关键字:
辅酶氧化酶, 生物信息学, 核心结构域, 构效关系, 活性位点Coenzyme Oxidase, Bioinformatics, Core Structure Domain, Structure-Activity Relationship, Active Site
期刊名称:
《Biophysics》, Vol.2 No.3, 2014-08-22
摘要:
辅酶再生是推动氧化还原酶大规模工业化应用的关键。辅酶氧化酶(NOX)是工业上用于NADH和NADPH再生的理想用酶。基于序列比对等生物信息学手段，分析NOX的氨基酸序列和蛋白质高级结构特点，为今后对辅酶氧化酶的识别和改造研究奠定基础。基于生物信息学的方法，利用ClustalX 2.0、PyMOL 1.0等相关软件，对来源于粪肠球菌(Enterococcus faecalis)，乳酸链球菌(Lactococcus lactis)，詹氏甲烷球菌(Methanocaldococcus jannaschii)，生殖支原体(Mycoplasma genitalium)，肺炎支原体(Mycoplasma pneumoniae)，化脓链球菌(Streptococcus pyogenes)中的辅酶氧化酶(已知型或推断型)进行序列比对、同源建模，分析其催化活性位点、活性位点的氨基酸残基保守性特点及反应机理，识别辅基及周围重点氨基酸残基。大量的比对分析结果表明，NOX的催化活性位点存在重点作用残基Cys42和辅基FAD，周围存在高度保守性残基His10，Leu40或Ser40和Gly43。研究结果可用于今后指导酶的筛选，在分子层面修饰和酶结构的改造。Coenzyme regeneration is the key to promote large-scale industrial application of oxidoreductase. Coenzyme oxidase (NOX) is an ideal candidate for industrial enzymes regeneration of NADH and NADPH. Based on sequence alignment tools and other bioinformatics methods, we analyze the amino acid sequence and high-level structural characteristics of NOX proteins, laying the foundation for future researches on the identification and transformation of coenzyme oxidase. Based on bioinformatics approaches, ClustalX 2.0, PyMOL 1.0 and other related software were used, and the nicotinamide coenzyme oxidase NOXs (the infer type or the known type) from Enterococcus faecalis, Lactococcus lactis, Methanocaldococcus jannaschii, Mycoplasma genitalium, Mycoplasma pneumoniae, Streptococcus pyogenes are compared for sequence alignment and homology modeling. The catalytically active sites, conservative characteristics of the active site amino acid residues and reaction mechanism were analyzed. Cofactors and important amino acid residues around them were identified. A lot of comparison analyses showed that NOX catalytic active sites presented important residues—Cys42 and cofactor FAD, and highly conserved residues—His10, Leu40 or Ser40 and Gly43 around them. The results can be used to guide future enzyme screening, modification and transformation of enzyme structure at the molecular level.