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

Abstract

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.

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@article{Badger2005StructuralAO, title={Structural analysis of a set of proteins resulting from a bacterial genomics project.}, author={John Badger and J. Michael Sauder and Joanna Mary Adams and Stephen S Antonysamy and Kevin T Bain and Mark Bergseid and Sean G. Buchanan and Michelle D Buchanan and Yelena Batiyenko and Jon A. Christopher and Spencer Emtage and A. M. Eroshkina and Ingeborg K Feil and Eliana Badiale Furlong and Ketan S. Gajiwala and Xiu Lai Gao and Dongmei He and J{\"{o}rg Hendle and Andreas Huber and K Hoda and Peggy Kearins and Charles Kissinger and Beverley Laubert and Hal A. Lewis and J Lin and Kim Loomis and Don Lorimer and Gifford Louie and Mirjana Maleti{\'c} and Chris D. Marsh and Iakov E. Miller and Jos{\'e} Luis Molinari and H J Muller-Dieckmann and Janet Newman and Brian W. Noland and Barbra Pagarigan and Frances Park and Thomas S. Peat and Kai Post and Svetlana Radojicic and Andr{\'e}s Ramos and Rich Romero and Marc E Rutter and Wendy E. Sanderson and Kenneth D Schwinn and Jason W Tresser and J Winhoven and Thaiesha A Wright and Long Wu and Jijun Xu and Timothy J. R. Harris}, journal={Proteins}, year={2005}, volume={60 4}, pages={787-96} }