Nucleic Acids Research, Vol 27, Issue 20 4018-4027, Copyright © 1999 by Oxford University Press
JR Cort, EV Koonin, PA Bash and MA Kennedy
Structural genomics presents an enormous challenge with up to 100 000
protein targets in the human genome alone. At current rates of structure
deter-mination, judicious selection of targets is necessary. 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.
ARTICLES
A phylogenetic approach to target selection for structural genomics: solution structure of YciH
Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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