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

被引：209

作者：

Badger, J ^{[1
]}

Sauder, JM ^{[1
]}

Adams, JM ^{[1
]}

Antonysamy, S ^{[1
]}

Bain, K ^{[1
]}

Bergseid, MG ^{[1
]}

Buchanan, SG ^{[1
]}

Buchanan, MD ^{[1
]}

Batiyenko, Y ^{[1
]}

Christopher, JA ^{[1
]}

Emtage, S ^{[1
]}

Eroshkina, A ^{[1
]}

Feil, I ^{[1
]}

Furlong, EB ^{[1
]}

Gajiwala, KS ^{[1
]}

Gao, X ^{[1
]}

He, D ^{[1
]}

Hendle, J ^{[1
]}

Huber, A ^{[1
]}

Hoda, K ^{[1
]}

Kearins, P ^{[1
]}

Kissinger, C ^{[1
]}

Laubert, B ^{[1
]}

Lewis, HA ^{[1
]}

Lin, J ^{[1
]}

Loomis, K ^{[1
]}

Lorimer, D ^{[1
]}

Louie, G ^{[1
]}

Maletic, M ^{[1
]}

Marsh, CD ^{[1
]}

Miller, I ^{[1
]}

Molinari, J ^{[1
]}

Muller-Dieckmann, HJ ^{[1
]}

Newman, JM ^{[1
]}

Noland, BW ^{[1
]}

Pagarigan, B ^{[1
]}

Park, F ^{[1
]}

Peat, TS ^{[1
]}

Post, KW ^{[1
]}

Radojicic, S ^{[1
]}

Ramos, A ^{[1
]}

Romero, R ^{[1
]}

Rutter, ME ^{[1
]}

Sanderson, WE ^{[1
]}

Schwinn, KD ^{[1
]}

Tresser, J ^{[1
]}

Winhoven, J ^{[1
]}

Wright, TA ^{[1
]}

Wu, L ^{[1
]}

Xu, J ^{[1
]}

机构：

[1] Struct GenomiX Inc, San Diego, CA USA

来源：

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS | 2005年 / 60卷 / 04期

关键词：

x-ray crystallography; novel fold; protein knots; protein data bank;

D O I：

10.1002/prot.20541

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：

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.

引用

页码：787 / 796

页数：10

共 54 条

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