.
The Open Protein Structure Annotation Network
PDB Keyword
.

3npi

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

    Title Crystal structure of a TetR family regulatory protein (DIP1788) from CORYNEBACTERIUM DIPHTHERIAE at 2.96 A resolution. To be published
    Site JCSG
    PDB Id 3npi Target Id 398877
    Molecular Characteristics
    Source Corynebacterium diphtheriae nctc 13129
    Alias Ids TPS29666,NP_940126.1, 328046 Molecular Weight 27612.66 Da.
    Residues 250 Isoelectric Point 4.86
    Sequence mnessthdsvaddptevstdtvldialslfselgfsdakleaiakksgmskrmihyhfgdkrglyiccl eeavrrlrptaeemylasavpvegvrtiveavfhryvqhpeavrmlqmenlhhygkvaeasplsdqsai tlqldrllmlgqdagafrpgisaqdvftliasiavfrinsrsttlnlygidmmngdntdgmrrmavdtv lafltsnlksadedsylsrpllstvtehvdeegsyevaadpfs
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.96 Rfree 0.2219
    Matthews' coefficent 2.64 Rfactor 0.2007
    Waters Solvent Content 53.34

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3npi

    Protein Summary

    Pfam Summary: This protein is now in family TetR_N, PF00440, which has other structures.

     

    The N-terminal domain of target ID 398877 (residues 22-67) is a member of the TetR_N bacterial regulatory proteins Pfam class (PF00440). This Pfam class is represented by 344 structures in the PDB. The sequence of the C-terminal domain does not correspond to currently annotated Pfam classes. The structure was determined by three-wavelength Se-MAD at a modest resolution of only ~3 Angstroms. Shown below is a ribbons representation of the structure of target ID 398877 with the N-terminal end in blue and the C-terminal end in red.

    monomer.png

     The structure consists of two domains. An N-terminal domain (residues 1-64) shows similarity to those proteins  belonging to the DNA/RNA-binding three-helical bundle SCOP fold  and Homeodomain-like Superfamily. A C-terminal domain (residues 69-195) shows a tetracyclin-repressor-like C-terminal domain-like SCOP fold  .

    The crystal structure suggests that a dimer is a significant oligomerization state. Shown below is a ribbons representation of the dimer with the individual monomer colored blue and yellow. Sulfate from the crystallization was modeled into the structures, and these are shown as red sticks.

    dimer.png

     

     

     

    PDB ID
    DALI Z-Score
    rmsd(Ang)
    Alignment Length
    total residues
    % sequence id
    Description
    1pb6 16.9 3.1 188 198 19 Hypothetical Transcriptional Regulator ycdC from E. coli.
    2qtq 15.3 3.5 186 198 21 Predicted DNA binding transcriptional regulator (YP_396351.1) from Novosphingobium aromativorans DSM 12444 at 1.85 Ang.
    2zcm 15.1 3.0 172 180 13 IcaR, a repressor of the TetR family implicated in biofilm formation in Staphylococcus epidermidis.(Pubmed 18208836)
     2d6y 14.6 2.6 176 186 17 Hypothetical transcriptional regulator SCO4008from Streptomyces coelicolor A3(2)
    3dew 14.5 4.0 180 192 21 Putative tetR family transcriptional regulator from Geobacter sulfurreducens PCA
    3geu 14.5 3.4 176 189 13 IcaR from Staphylococcus aureus, a member of the tetracycline repressor protein family.
    3bhq 14.1 3.3 178 202 16 TetR family transcriptional regulator (NP10565.1) from Mesorhizobium loti at 1.54 Angstrom.
    1t33 14.0 3.6 176 214 16 Putative transcriptional repressor (TetR/AcR family) from Salmonella typhimurium
    2eh3 13.8 2.8 159 171 15  aq_1058, a transcriptional regulator (TetR/AcR family) from Aquifex aeolicus VF5
    3crj 13.8 3.0 175 189 18  TetR transcriptional regulator from Haloaracula marismortui ATCC 43049
    2g3b 13.7 2.9 167 188 16 Putative TetR transcriptional regulator from Rhodococcus sp.

     

     

     

     

     

    M10823_consurf1.pngM10823_consurf2.png

     

     

     

     

     

     

     

     

     

     

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page
    • No tags
    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch