J Michael Sauder - Structural analysis of a set of proteins resulting from a bacterial genomics project

Version 1

      Publication Details (including relevant citation   information):

      Proteins (2005) 60: 787-796.

      Badger J, Sauder JM, Adams JM, Antonysamy S, Bain K, Bergseid MG,   Buchanan SG, Buchanan MD, Batiyenko Y, Christopher JA, Emtage S,   Eroshkina A, Feil I, Furlong EB, Gajiwala KS, Gao X, He D, Hendle   J, Huber A, Hoda K, Kearins P, Kissinger C, Laubert B, Lewis HA,   Lin J, Loomis K, Lorimer D, Louie G, Maletic M, Marsh CD, Miller   I, Molinari J, Muller-Dieckmann HJ, Newman JM, Noland BW,   Pagarigan B, Park F, Peat TS, Post KW, Radojicic S, Ramos A,   Romero R, Rutter ME, Sanderson WE, Schwinn KD, Tresser J,   Winhoven J, Wright TA, Wu L, Xu J, Harris TJ

      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.

      Address (URL): http://www.ncbi.nlm.nih.gov/pubmed/16021622