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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of DJ-1 like Protein (YP_001094981.1) from Shewanella loihica PV-4 at 1.76 A resolution. To be published
    Site JCSG
    PDB Id 3bhn Target Id 377869
    Molecular Characteristics
    Source Shewanella sp. pv-4
    Alias Ids TPS1696,YP_001094981.1, 383195 Molecular Weight 23724.88 Da.
    Residues 217 Isoelectric Point 4.75
    Sequence mykvgivlfddftdvdfflmndllgrtsdswtvrilgtkpehhsqlgmtvktdghvsevkeqdvvlits gyrgipaalqdenfmsalkldpsrqligsicagsfvlhelgllkgkklttnpdakavlqgmggdvqdlp lviegniataggclsllylvgwlaerlfdsvkrkqiqnqlipagqmeifetlisetiqsaesayeyrsa cesdaeslvv
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.76 Rfree 0.190
    Matthews' coefficent 2.51 Rfactor 0.162
    Waters 204 Solvent Content 51.05

    Ligand Information


    Google Scholar output for 3bhn
    1. Dissection of the dimerization modes in the DJ-1 superfamily
    HJ Jung, S Kim, YJ Kim, MK Kim, SG Kang, JH Lee - Molecules and , 2012 - Springer

    Protein Summary

    Shew_2856 gene from from Shewanella loihica PV-4 translates into the YP_001094981 protein that belongs to the DJ-1/PfpI family (PF01965). The CDD (Conserved Domain Database) indicates sequence similarity to GATase1_PfpI_2, Type 1 glutamine amidotransferase (GATase1)-like domain, GATase1_AraC_ArgR_like, A subgroup of AraC transcriptional regulators, DJ-1_PfpI, DJ-1/PfpI family, and transcriptional activator FtrA. PSI-BLAST produces hits to ThiJ/PfpI domain proteins, Putative intracellular protease/amidase, AraC-family transcriptional regulator, DJ-1/PfpI family protein and 4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme from different organisms with sequence identities ranging from 84% (6e-85) to 32% (e=0.009) but no structures are available for any of these sequences.

    pre-SCOP classifies 3bhn in the alpha/beta class, class I amidotransferase-like superfamily, DJ-1/PfpI-like family. DALI top hits are with DJ-1/PfpI protein 3ewn (Z=22), DJ-1 protein 1pdw (Z=21), and the RNA binding protein regulatory subunit 1p5f (Z=21).

    3 DALI significant hits using 3bhn (green) as query, are with 1PS4 (pink; Z=20), 1G2I (gold; Z=19), 2FEX (firebrick; Z=17).

    The predicted catalytic triad from 1G2I.pdb [Ref], which is the structure of an intracellular protease from Pyrococcus horikoshii (expected to be hexameric in solution) includes the residues Cys-100, His-101 and Glu-474 from another subunit. This triad is not strictly conserved in 1PS4 where it shows a Cys-100 followed by Ala-101. In 3bhn too, it is Cys-100, Ala-101.

    Ligand Summary





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