The Open Protein Structure Annotation Network
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    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 394855
    Molecular Characteristics
    Source Marinobacter aquaeolei vt8
    Alias Ids TPS20309,YP_958225.1, PF04222 Molecular Weight 22265.25 Da.
    Residues 199 Isoelectric Point 4.94
    Sequence mnanqflkavsqlqgwrecafllalaersfpnyalfadavglktggkmrqlldlawdmlqkdvadaaip qllskletlcpnvdeydaygvypafdfcqlleqallnrlnpnkhrateasqlatrtvmdfvemsegegm denelvrvfehhpllkddklfqrdtvmalkkqrtpkeaflaelragaandgvsnlgisleg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.00 Rfree 0.196
    Matthews' coefficent 3.43 Rfactor 0.172
    Waters 121 Solvent Content 64.12

    Ligand Information


    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

    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 PDB:2q9r 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


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


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




    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




    No references found.

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    Files (3)

    FileSizeDateAttached by 
    domain with domain swapping
    137.56 kB22:39, 20 Oct 2008qxuActions
    comparison with pj04222c
    118.67 kB22:46, 20 Oct 2008qxuActions
    monomer of ps04222
    78.68 kB22:55, 20 Oct 2008qxuActions
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