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The Open Protein Structure Annotation Network
PDB Keyword
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3djm

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

    Title Crystal structure of Protein of unknown function (DUF427) (YP_001042567.1) from RHODOBACTER SPHAEROIDES ATCC 17029 at 2.51 A resolution. To be published
    Site JCSG
    PDB Id 3djm Target Id 376596
    Molecular Characteristics
    Source Rhodobacter sphaeroides atcc 17029
    Alias Ids TPS6968,YP_001042567.1, PF04248, 86682 Molecular Weight 12668.74 Da.
    Residues 115 Isoelectric Point 5.15
    Sequence mqmnnhirlrkaegkwvirtdsavlgetlnaieltegsrdpviyfpredvamvmfdksekvtacplkge asyysivgasgtlkdaawsyespkegleaiagylafapdctkvgqy
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 5
    Resolution (Å) 2.51 Rfree 0.228
    Matthews' coefficent 3.06 Rfactor 0.212
    Waters 153 Solvent Content 59.81

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3djm
    1. Identification of CCR2_binding features in Cytl1 by a CCL2_like chemokine model
    A Tomczak, MT Pisabarro - Proteins: Structure, Function, and , 2011 - Wiley Online Library
     

    Protein Summary

    Gene Rsph17029_0682 from Rhodobacter sphaeroides atcc 17029 encodes the YP_001042567, a small all beta protein belonging to DUF427 group (PF04248). This family of proteins has a well defined active site consisting of residues: E36,V42,Y44,K67,W87,Y89. As a result, this protein is likely an enzyme.
     

    3djm has weak structural similarity (Dali Z-scr=5.5; rmsd 2.83A for 83 aligned Ca) to C-Terminal Regulatory Domain of the RNA 5'-Triphosphate Sensor of RIG-I (PDB id 2qfb). However, the electrostatic surface of 3djm is different from 2qfb. It also lacks the Zn binding site.


    Most of the sequences in PF04248 are single domain like 3djm. However, there are two sequences containing the adenylate/guanylate cyclase catalytic domain. This could give a good indication of possible substrates for this enzyme: substrate or product of cyclase (eg 3',5'-cyclic AMP or ATP) and possible function (eg, nucleotide transfer/degradation).


    Figure 1. monomer structure of 3djm


    Figure 2. electrostatic surface of 3djm



    Figure 3. 3djm contains a conserved active site on the protein surface

    Ligand Summary

    Reviews

    References

     

    No references found.

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