The Open Protein Structure Annotation Network
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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of uncharacterized protein BSU10800 (YP_054576.1) from Bacillus subtilis at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 2qe9 Target Id 374687
    Molecular Characteristics
    Source Bacillus subtilis subsp. subtilis str. 168
    Alias Ids TPS1632,YP_054576.1, PF05163, 432874 Molecular Weight 18810.59 Da.
    Residues 159 Isoelectric Point 5.96
    Sequence mmkffeynwqvrdqwftwchqltteellknrlggvenilytlfhiidveyswiraiqgkediavqfady qtlnkvkslsntfrteiidvlqthsdqikdelvsvpwetgvlytrdeilhhiiaheihhigqlsvware lklspvsasfigrtlkpihsy
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.90 Rfree 0.226
    Matthews' coefficent 2.09 Rfactor 0.185
    Waters 235 Solvent Content 41.06

    Ligand Information


    Google Scholar output for 2qe9
    1. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
    2. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
    3. The structure of DinB from Geobacillus stearothermophilus: a representative of a unique four-helix-bundle superfamily
    DR Cooper, K Grelewska, CY Kim - Section F: Structural , 2010 - scripts.iucr.org

    Protein Summary

    The yizA (BSU10800) gene from Bacillus subtilis encodes the YP_054576 protein, a homolog of the DNA damage-inducible (DinB) family (PF05163). Genome context analysis shows a functional linkage (score 0.7) based on co-ocurence with the Zn metalloprotease rasP (BSU16560).

    2qe9 is an all-alpha protein that adopts a DinB/YfiT-like putative metalloenzymes fold and shows strong similarity (DALI Z-scr=13-11) to other structures from the same family determined by structural genomics (PDB:2f22 (topsan), PDB:2hkv (topsan), PDB:2ou6 (topsan), PDB:2p1a topsan, PDB:2qnl (topsan), PDB:3di5 (topsan), PDB:3dka (topsan)). YfiT has been proposed to function as a metal-dependent hydrolase [1]. The 2qe9 structure shows a Ni metal per chain coordinated by the side chains of residues H44, H124 and H128.


    To do: compare metal coordination between DinB and YfiT. Phylogenetic analysis?

    Ligand Summary





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