Bioinformatics study of the 3-hydroxy-3-methylglotaryl-coenzyme A reductase (HMGR) gene in Gramineae
Bioinformatics study of the 3-hydroxy-3-methylglotaryl-coenzyme A reductase (HMGR) gene in Gramineae
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DOI：
10.1007/s11033-012-1761-2
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发表时间：
2012-09-01
影响因子：
2.8
通讯作者：
Nemat-Zadeh, Ghorbanali
中科院分区：
文献类型：
--
作者：
Darabi, Maryam;Masoudi-Nejad, Ali;Nemat-Zadeh, Ghorbanali
异戊二烯类化合物是由二甲基烯丙基二磷酸酯和异戊烯基二磷酸(IPP)两个重要单元合成的。植物使用两种不同的方法来形成IPP，即胞质和胞质方法。3-羟基-3-甲基戊二酰辅酶A还原酶(HMGR，EC 1.1.1.34)催化HMG-CoA转化为甲羟戊酸，这是植物类异戊二烯生物合成的胞液途径的第一阶段。本研究对来自禾本科和人、小鼠、果蝇三种动物样品的50个HMGR蛋白序列进行了比对和分析，以预测其分子质量、等电点、信号肽、跨膜和保守结构域、二级结构和空间结构等性质。序列比对分析表明，植物和动物之间有很高的同源性。通过HMGR的结构建模，检测到L结构域、N结构域和S结构域三个催化区域。用PROCHECK算法进一步验证了水稻HMGR(登录号：NP_001063541)的三级结构模型，发现90.3%的氨基酸残基位于Ramachandran图中最有利的区域，表明模拟的三维结构是可靠的。系统发育分析表明，禾本科植物与其他生物之间存在一定的亲缘关系。根据这些结果，HMGRs应该起源于共同的祖先。
Isoprenoids or terpenoids are synthesized by two important units' including dimethylallyl diphosphate and isopentenyl diphosphate (IPP). Plants use two different methods for formation of IPP, which is a cytosolic and a plastidial method. The 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR, EC 1.1.1.34) catalyzes the conversion of HMG-CoA to mevalonate, which is the first stage in the cytosolic pathway for biosynthesis of isoprenoid in plants. In this study, a total of fifty HMGR protein sequences from Gramineae and three animal samples including human, mouse and fruit fly were aligned and analyzed by computational tools to predict the protein properties, such as molecular mass, pI, signal peptide, transmembrane and conserved domains, secondary and spatial structures. Sequence comparison analysis revealed that there is high identity between plants and animals. Three catalytic regions including L domain, N domain and S domain were detected by structural modeling of HMGR. The tertiary structure model of Oryza sativa HMGR (Accession Number: NP_001063541) was further checked by PROCHECK algorithm, and showed that 90.3 % of the amino acid residues were located in the most favored regions in Ramachandran plot, indicating that the simulated three-dimensional structure was reliable. Phylogenetic analysis indicated that there is a relationship among species of Gramineae and other organisms. According to these results, HMGRs should be derived from a common ancestor.