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 prokaryotic domain of unknown function (DUF849) with a TIM barrel fold (YP_164873.1) from Silicibacter pomeroyi DSS-3 at 1.45 A resolution. To be published
    Site JCSG
    PDB Id 3chv Target Id 374753
    Molecular Characteristics
    Source Silicibacter pomeroyi dss-3
    Alias Ids TPS1633,YP_164873.1, PF05853, 104654 Molecular Weight 30784.27 Da.
    Residues 283 Isoelectric Point 6.39
    Sequence mdtpankpciicvaitgsvptkadnpavpitvseqvestqeafeagaaiahchvrnddgtpssdpdrfa rlteglhthcpgmivqfstggrsgagqarggmlplkpdmaslsvgsnnfpsrvyenppdlvdwlaaqmr syrvtpeieafdlshilraidmhgrgllygklyvqfvmgvknampadrevfdfyvrmmrtrapqaewca agiganqltvnewaiaagghtrtglednirldrqtlapsnaalvrrsvelcdkyqrpvaswqqareilg lpaaarn
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.45 Rfree 0.158
    Matthews' coefficent 1.99 Rfactor 0.133
    Waters 372 Solvent Content 38.34

    Ligand Information


    Google Scholar output for 3chv
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
    2. Ligands in crystal structures that aid in functional characterization
    AE Speers, BF Cravatt - Acta Crystallographica Section F: Structural , 2010 - scripts.iucr.org
    3. 3-Keto-5-aminohexanoate Cleavage Enzyme
    M Bellinzoni, K Bastard, A Perret, A Zaparucha - Journal of Biological , 2011 - ASBMB

    Protein Summary

    Gene SPOA0042 from Silicibacter Pomeroyi  encodes the YP_164873 protein that belongs to the DUF849 group PF05853 (e-value: 6.2e-73). This family of prokaryotic proteins of unknown function is very large (>250 members), with mostly bacterial representatives and a few members in archea.  PF05853 overlaps with a COG family  COG3246: Uncharacterized conserved protein.  The first structure solved from this family was the 3-Keto-5-Aminohexanoate Cleavage Enzyme (YP_293392.1) from Ralstonia eutropha Jmp134, PDB code:3c6c .

    Pre-SCOP classifies 3chv in the TIM barrel fold, metallo-dependent hydrolase superfamily.  DALI top hits are with DUF849 proteins like 3fa5 (Z=50), 3e49 (Z=40) and 3e02 (Z=39). A close homolog to 3chv is 3c6c  (ffas score -96.700; structural superimposition using VAST: RMSD: 1.6 A,  30.3% sequence identity, with 264 Ca residues aligned; Z=38). The superimposition of these two proteins is shown in Figure 1.  Both JCSG proteins, 3chv and 3c6c are weakly similar to D-Ribulose 5-Phosphate 3-Epimerase (PDB ID: 1TQX; Z=15), with all three proteins sharing a conserved active site.

    Based on the results of calculations of surface interaction, the 3chv biomolecule should be a dimer in solution. 3chv chelates a Zn ion via the conserved side chains of residues H51, H53 and E233, plus three ordered water molecules.



    Figure 1:  The structure of 3chv protein (shown in magenta) is superimposed with the structure of 3-Keto-5-Aminohexanoate Cleavage Enzyme (PDB code:3c6c).  The superimposition was done by VAST.

    Ligand Summary






    No references found.

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