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The Open Protein Structure Annotation Network
PDB Keyword
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3f7c

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

    Title Crystal structure of protein of unknown function (DUF416) (YP_958225.1) from MARINOBACTER AQUAEOLEI VT8 at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 3f7c Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS20309,YP_958225.1, PF04222
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 3.43 Rfactor 0.172
    Waters
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    Solvent Content 64.12

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3f7c
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     

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    Protein Summary

    Gene Maqu_0942 from Marinobacter aquaeolei vt8 encodes the protein YP_958225 whose sequence belongs to the DUF416 group. 3f7c is structurally similar to a previous solved JCSG structure

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    topsan (Dali Zscr=20, 1.72A for 153 aligned Ca atoms, 24% seq id). Both proteins are representatives of DUF416 ( PF04222). The structure contains three mutations (K168Y,K169Y and Q170Y). Interestingly, the dimer of 3f7c differs from that of 2q9r. The last helix in 3f7c is swapped between the dimer. It is quite possible that the point mutations (at the connection loop before the last helix) have induced such structural changes.

    STRING genome context analysis provides a 0.87 scored hit with the deoxycytidine triphosphate deaminase gene (Maqu_0941). Sequence neighbor analysis indicated that YP_958225 is downstream of a Sensor histidine kinase/response regulator (Maqu_1708 with a 0.7 score), suggesting this protein is probably a part of a two-component signal transduction system. There seems to be no DNA binding motif in it, however, YP_958225 may bind a small molecule as a component of a transcription regulator system.

     

    Figure 1. Monomer of 3f7c

    ps04222-mono.png

    Figure 2. Comparison between 3f7c (red & green) and  2q9r (blue and cyan)

    ps04222-2q9r.png

    Figure 3. Dimer of 3f7c5, the mutations K168Y,K169Y,Q170Y are shown in sticks

    dimer.png

     

    References:

    Steegborn, C., Danot, O., Huber, R., Clausen, T. Crystal structure of transcription factor MalT domain III: a novel helix repeat fold implicated in regulated oligomerization. Structure v9 pp.1051-1060 , 2001

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page

    Files (3)

    FileSizeDateAttached by 
     dimer.png
    domain with domain swapping
    137.56 kB22:39, 20 Oct 2008qxuActions
     ps04222-2q9r.png
    comparison with pj04222c
    118.67 kB22:46, 20 Oct 2008qxuActions
     ps04222-mono.png
    monomer of ps04222
    78.68 kB22:55, 20 Oct 2008qxuActions
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