A phylogenetic approach to target selection for structural genomics: solution structure of YciH

被引:38
作者
Cort, JR
Koonin, EV
Bash, PA
Kennedy, MA [1 ]
机构
[1] Pacific NW Natl Lab, Environm Mol Sci Lab, Richland, WA 99352 USA
[2] Natl Inst Hlth, Natl Ctr Biotechnol Informat, Natl Lib Med, Bethesda, MD 20894 USA
[3] Northwestern Univ, Dept Mol Pharmacol & Biol Chem, Chicago, IL 60611 USA
关键词
D O I
10.1093/nar/27.20.4018
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Structural genomics presents an enormous challenge with up to 100 000 protein targets in the human genome alone. At current rates of structure determination, judicious selection of targets is neccessary. Here, a phylogenetic approach to target selection is described which makes use of the National Center for Biotechnology Information database of Clusters of Orthologous Groups (COGS). The strategy is designed so that each new protein structure is likely to provide novel sequence-fold information. To demonstrate this approach, the NMR solution structure of YciH (COG0023), a putative translation initiation factor from Escherichia coli, has been determined and its fold classified. YciH is an ortholog of eIF-1/SUI1, an integral component of the translation initiation complex in eukaryotes, The structure consists of two antiparallel alpha-helices packed against the same side of a five-stranded beta-sheet. The first 31 residues of the 11.5 kDa protein are unstructured in solution. Comparative analysis indicates that the folded portion of YciH resembles a number of structures with the alpha-beta plait topology, though its sequence is not homologous to any of them. Thus, the phylogenetic approach to target selection described here was used successfully to identify a new homologous superfamily within this topology.
引用
收藏
页码:4018 / 4027
页数:10
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