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 methyltransferase-like protein of unknown function (YP_167254.1) from Silicibacter pomeroyi DSS-3 at 1.80 A resolution. To be published
    Site JCSG
    PDB Id 3cvo Target Id 377915
    Molecular Characteristics
    Source Silicibacter pomeroyi dss-3
    Alias Ids TPS1699,YP_167254.1, 452591 Molecular Weight 22337.19 Da.
    Residues 201 Isoelectric Point 4.82
    Sequence mddqsgdqmrpeltmppaeaealrmayeeaevileygsggstvvaaelpgkhvtsvesdrawarmmkaw laanppaegtevnivwtdigptgdwghpvsdakwrsypdyplavwrtegfrhpdvvlvdgrfrvgcala tafsitrpvtllfddysqrrwqhqveeflgaplmigrlaafqvepqpippgslmqlirtmtsp
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 1.80 Rfree 0.194
    Matthews' coefficent 2.79 Rfactor 0.168
    Waters 496 Solvent Content 55.98

    Ligand Information


    Google Scholar output for 3cvo
    1. Getting a camel through the eye of a needle: the import of folded proteins by peroxisomes
    T Lanyon_Hogg, SL Warriner, A Baker - Biology of the Cell, 2010 - Wiley Online Library
    2. Structural insights into the recognition of peroxisomal targeting signal 1 by Trypanosoma brucei peroxin 5
    P Sampathkumar, C Roach, PAM Michels - Journal of molecular , 2008 - Elsevier
    3. Structural and Functional Discussion of the Tetra-Trico-Peptide Repeat, a Protein Interaction Module
    N Zeytuni, R Zarivach - Structure, 2012 - Elsevier

    Protein Summary

    Gene SPO2022 from Silicibacter pomeroyi dss-3 encodes a methyltransferase-like protein (YP_167254) of unknown function. Its gene is located in the conserved genomic neighborhood of SufB, SufC, SufD, and SufS (proteins involved in iron-sulfur cluster  assembly).

    SCOP classifies 3cvo inside the S-adenosyl-L-methionine-dependent methyltransferase superfamily. The Glycine-rich loop of 3cvo has a different conformation than the S-adenosylmethionine-binding loop found in SAM-dependent methyltransferases.

    Dali top hits (Z-scr=15) include the cathecol-O-methyltransferases PDB:3hvi, PDB:2zth and PDB:1jr4. SSM search shows that PDB:2gpy and PDB:2hnk are structurally similar to 3cvo (Dali Z-scr=13). The suggested biomolecule of 3cvo by interface calculation is a dimer (two dimers are shown below).

    The superposition of 3cvo with 2gpy shows that two structures are very similar except the N and C -terminal areas, as shown below (green: 3cvo5; cyan: 2gpy).

    Ligand Summary

    SO4, GOL from crystallization condition and EDO from cryo condition were found.





    No references found.

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