Structural analysis of a set of proteins resulting from a bacterial genomics project

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 ge...

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Published in:	Proteins, structure, function, and bioinformatics Vol. 60; no. 4; pp. 787 - 796
Main Authors:	Badger, J., Sauder, J.M., Adams, J.M., Antonysamy, S., Bain, K., Bergseid, M.G., Buchanan, S.G., Buchanan, M.D., Batiyenko, Y., Christopher, J.A., Emtage, S., Eroshkina, A., Feil, I., Furlong, E.B., Gajiwala, K.S., Gao, X., He, D., Hendle, J., Huber, A., Hoda, K., Kearins, P., Kissinger, C., Laubert, B., Lewis, H.A., Lin, J., Loomis, K., Lorimer, D., Louie, G., Maletic, M., Marsh, C.D., Miller, I., Molinari, J., Muller-Dieckmann, H.J., Newman, J.M., Noland, B.W., Pagarigan, B., Park, F., Peat, T.S., Post, K.W., Radojicic, S., Ramos, A., Romero, R., Rutter, M.E., Sanderson, W.E., Schwinn, K.D., Tresser, J., Winhoven, J., Wright, T.A., Wu, L., Xu, J., Harris, T.J.R.
Format:	Journal Article
Language:	English
Published:	Hoboken Wiley Subscription Services, Inc., A Wiley Company 01-09-2005
Subjects:	Databases, Protein Enzymes - chemistry Enzymes - genetics Escherichia coli - genetics Escherichia coli Proteins - chemistry Escherichia coli Proteins - genetics Genome, Bacterial Genomics Models, Molecular novel fold Protein Conformation Protein Data Bank protein knots Regression Analysis X-ray crystallography X-Ray Diffraction
Online Access:	Get full text
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Summary:	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 PDB 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. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Bibliography:	ark:/67375/WNG-5C5X887C-9 Structural GenomiX, Inc. istex:E31D82B367CAC29BDDD6EAAF473750AD63859B0B U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences - No. W-31-109-Eng-38 ArticleID:PROT20541 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0887-3585 1097-0134
DOI:	10.1002/prot.20541