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The Open Protein Structure Annotation Network
PDB Keyword
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3nnr

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

    Title Crystal structure of a TetR-family transcriptional regulator (Maqu_3571) from MARINOBACTER AQUAEOLEI VT8 at 2.49 A resolution. To be published
    Site JCSG
    PDB Id 3nnr Target Id 403231
    Molecular Characteristics
    Source Marinobacter aquaeolei vt8
    Alias Ids TPS30652,YP_960827.1, _0018.007245_, 324464 Molecular Weight 26579.88 Da.
    Residues 227 Isoelectric Point 5.12
    Sequence mtmktrdkillsslelfndkgernittnhiaahlaispgnlyyhfrnksdiiyeifqeyeklvdyyldi pedrpitledmtfylesvfdglwsyrffhrdleylldsdprlrqdyreftnrclaainrifakladagi iqpqpedlrsamslnvwlvitnwmaflktahaaeepaslsltelkqgiyqvltlevpyltpeyrervla lrekyrptlpeaqgisgvea
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.49 Rfree 0.260
    Matthews' coefficent 2.77 Rfactor 0.230
    Waters 14 Solvent Content 55.57

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3nnr
    1. Blind prediction of quaternary structures of homo-oligomeric proteins from amino acid sequences based on templates
    M Morita, M Kakuta, K Shimizu, S Nakamura - 2012 - hoajonline.com
     

    Protein Summary

    This protein is annotated as a TetR family transcriptional regulator and a member of Pfam PF00440.

    Pfam update: I have built a family that avoids overlapping with the N-terminal TetR_N families. However, the sequences don't match our other TetR_C families although several members fall into families which are shown in InterPro to match G3DSA:1.10.357.10 TetR_C. There is a highly conserved Tryptophan at the very end of the model, otherwise there is not brilliant conservation. The alignment for the new family TetR_C_8, PF14278 can be seen at: https://pfamsvn.sanger.ac.uk/svn/pfam/trunk/Data/Families/PF14278

    It is present as a monomer in the asymmetric unit of the unit cell in the crystal structure. Sulfate (SO4, stick figure) from the crystallization solution has been modeled in the solvent structure. In addition, an Unidentified Ligand (UNL, red spheres) has been modeled at a putative functional site:

    Fig1revised.png

    Crystal packing analysis with PISA suggests that a dimer should be the significant oligomeric form in solution:

    Fig2.png

    The UNL (red spheres) has been modeled in this structure (cyan) based on comparison with the homolog structure with PDB id 3G1L (Ref1, yellow and blue):

    Fig3.png

     

    The sequence id between this target and the 3G1L is ~11% only but they are similar in structure. The 3G1L comes up as the 9th hit in FFAS (link above). All the other higher FFAS hits have < 20% seq id to this target. 

    However, the active site of 3G1L is more hydrophobic (comprised mainly of PHE and TRP residues, blue sticks) than for this target (two TYR residues, 1 HIS and 1 TRP, red sticks):

    Fig3revised.png

    References:

    1. Synthetic EthR inhibitors boost antituberculous activity of ethionamide.
    Willand N, Dirié B, Carette X, Bifani P, Singhal A, Desroses M, Leroux F, Willery E, Mathys V, Déprez-Poulain R, Delcroix G, Frénois F, Aumercier M, Locht C, Villeret V, Déprez B, Baulard AR.
    Nat Med. 2009 May;15(5):537-44. Epub 2009 May 3.

    Ligand Summary

     UNL (Unidentified Ligand) modeled at putative functional site by comparison with homolog structure with PDB id 3G1L.

    Reviews

    References

     

    No references found.

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