Structural analysis of a set of proteins resulting from a bacterial genomics project
Structural analysis of a set of proteins resulting from a bacterial genomics project
复制标题
DOI：
10.1002/prot.20541
复制
发表时间：
2005-09-01
影响因子：
2.9
通讯作者：
Harris, TJR
中科院分区：
文献类型：
--
作者：
Badger, J;Sauder, JM;Harris, TJR
Structural GenomiX（SGX）细菌基因组学项目的目标是在多种原核生物中保守的蛋白质，在已知结构的蛋白质数据库中没有明显的序列同源物。这项工作的结果是80个结构，涵盖60个独特的序列和49个不同的基因。实验阶段确定从蛋白质纳入硒-蛋氨酸进行了45个结构，其余的大部分解决了分子置换使用的实验阶段设置为搜索模型的成员。开发了一种自动化工具，将这些结构存款蛋白质数据库，沿着相关的X射线衍射数据（包括精确的实验相）和实验确认的序列。将SGX结构与自SGX靶序列表编制以来的3.5年内出现在蛋白质数据库中的结构进行BLAST比较，鉴定出由SGX结构代表的60个独特序列中的49个的同源物。这一结果表明，对于相对容易表达、纯化和结晶的细菌结构，基因空间的结构覆盖正在迅速进行。使用PDB-BLAST和组合扩展（CE）研究了SGX和PUB结构之间更远的序列-结构关系。与PDB中的所有折叠相比，只有一种结构SufD具有真正独特的拓扑结构。
The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X-ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence-structure relationships between the SGX and PUB structures were investigated using PDB-BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB.