The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of uncharacterized protein (YP_926603.1) from Shewanella amazonensis SB2B at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 2qvp Target Id 375152
    Molecular Characteristics
    Source Shewanella amazonensis sb2b
    Alias Ids TPS1650,YP_926603.1, 3.40.630.10, 92216 Molecular Weight 30062.33 Da.
    Residues 274 Isoelectric Point 5.66
    Sequence msrspfqtfvwrseifecqstdiqrfysllaieterlglgskilgqaghhplyllqspgqkaglpnlli sagfhgeesagpwgllhflsqldgelfkrvnlsvlplvnptgfakghrfnelgenpnrgffiengkakp gadtsaegrillehahllqvasrdgiltchedvlmtdtyvytfepsqapgrfshslrdalgqyfpiaad gdvdncpvrsgvifnhfdtsfesflvrsgarvgccsetpgqqpldqrilanaaamntfvnmlapels
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 3
    Resolution (Å) 2.00 Rfree 0.213
    Matthews' coefficent 2.52 Rfactor 0.161
    Waters 526 Solvent Content 51.14

    Ligand Information


    Google Scholar output for 2qvp

    Protein Summary

    The Sama_0725 (YP_926603.1) gene from Shewanella amazonensis encodes a protein that belongs to the succinylglutamate desuccinylase / aspartoacylase family (PF04952), one of the twelve families in the Peptidase_MH clan (MEROPS and PFAM). Its sequence conservation profile contains the motif H74-g75-e76-E77 probably involved in metal chelation. It is one of three closely related proteins from different Shewanella species solved by JCSG (3b2y from S. denitrificans and 3ieh from S. baltica). These three proteins form an outlier group which shares strong similarities with members of two other PFAM families from the same clan - PF10994 (DUF2817) and PF00246 (Zinc peptidase M14).  Based on gene co-ocurrence, STRING predicts a functional coupling with a putative O-methyl-transferase (Sama_1505, YP_927382) with a significance score of 0.74 and with an uncharacterized protein (Sama_1518) from PFAM family PF11143 (DUF2919) with a significance score of 0.74.


    SCOP classifies 2qvp in the alpha/beta class, phosphorylase/hydrolase-like fold, Zn-dependent exopeptidase superfamily, bacterial dinuclear Zn exopeptidase family (?). The most similar structure of a close homolog (65% seq. id.) from another species of Shewanella, 3b2y (Z=46), shows a metal ion (Ni) chelated by the side chain of conserved residues H75, E78 and two water molecules. Other DALI hits are with carboxypeptidase-A 3l2n (Z=23), and carboxypeptidase-B 2jew (Z=22). A significant hit (HHpred P-val=8e-29; FATCAT P-val=2e-7) is observed with 1m4l (Z=21), a metallocarboxypeptidase [Ref].

    Ligand Summary





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