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.

Free methionine-( R )-sulfoxide reductase from Escherichia coli reveals a new GAF domain function

“…4) has been determined (17). The proximity of the Mes sulfonic acid group to Cys-94 and the disulfide bond between Cys-84 and Cys-118 is reminiscent of the arrangement of active site residues in bMsrA and eMsrA (4,14).…”

YbeA is the m3Ψ methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA

“…Hunt, unpubl. ), TM0844 from Thermotoga maritima (PDB 1o6d) (Badger et al 2005), and SAV0024/SA0023 from Staphylococcus aureus (PDB 1vh0) (Badger et al 2005). The proteins display an unusual knotted structure.…”

Substrate specificity and properties of the Escherichia coli 16S rRNA methyltransferase, RsmE

“…Crystal structures of RsmE family proteins from Haemophilus influenzae (YggJ, PDB entry 1NXZ; Forouhar et al 2003), Bacillus subtilis (YqeU, PDB entry 1VHK; Badger et al 2005), Thermotoga maritima (Tm1380, PDB entry 1Z85; http://www.rcsb.org/pdb/), and Thermus thermophilus (Tt1573, PDB entry 1V6Z; Joint Center for Structural Genomics, http://www.rcsb.org/pdb/) have been determined, and indicated that RsmE forms dimers in the crystals. To determine the actual oligomeric state of the E. coli protein in solution, we analyzed purified His-RsmE by gel filtration chromatography on a Superose-6 column.…”