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The Open Protein Structure Annotation Network
PDB Keyword
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3r4k

    Title Crystal structure of a putative ICLR transcriptional regulator (TM1040_3717) from SILICIBACTER SP. TM1040 at 2.46 A resolution. To be published
    Site JCSG
    PDB Id 3r4k Target Id 398828
    Molecular Characteristics
    Source Silicibacter sp. tm1040
    Alias Ids TPS30571,YP_611946.1, _0011.004359_, _0034.004179_, 325291 Molecular Weight 27528.77 Da.
    Residues 259 Isoelectric Point 6.09
    Sequence mgtvskaltlltyfnhgrleiglsdltrlsgmnkatvyrlmselqeagfveqvegarsyrlgpqvlrla alreasvpilsasrrvlrelsedtgetthlsllqgeqlaslshayssrnatkvmmedaevltfhgtasg lavlaysepsfvdavlaapltartpqtqtdpaairaeiaevrrtglaqsiggfeaevhshavpifgpdr avlgalavaaptsrmtpdqkrtippalraaglslteriggacppefptdiaa
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 2.46 Rfree 0.2312
    Matthews' coefficent 2.66 Rfactor 0.1901
    Waters 289 Solvent Content 53.72

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

     The protein YP_611946.1 is annotated as transcriptional regulator, IclR family. YP_611946.1 belongs to PFAM PF09339 HTH_IclR and PFAM PF01614 IclR. This N-terminal domain (residues 3-53) is the IclR helix-turn-helix domain, while the C-terminal domain (residues 129-241) is the Bacterial transcriptional regulator domain.

     

    The two domain monomer structure is shown below.

    MI15778A_mon.png

    Fig.1. Monomer structure in rainbow representation.

    The N-terminal domain is the dimerization domain as well as the DNA binding domain. The dimerization is mediated mostly by the helix linking the N- and C-terminal domains. This helix is not part of the helix-turn-helix motif. Thus the protein should be able to  dimerize and bind DNA simultaneously.

     

    MI15778A_dim.png

    Fig.2. The protein dimerizes using the N-terminal domain.

    The oligomeric state of the protein could be a dimer of dimers, shown below.

    MI15778A_tetra.png

    Fig.3. The crystallographic structure is a tetramer. However, a dimer is more functionally relevant, since a dimer can bind DNA. A tetramer can not bind to the same DNA using all the four HTH domain.

     

    The connection between the N-terminal and C-terminal domains is flexible. Indeed there are two conformations of the monomers in the crystal structure. This is shown by superposing all monomers together.

    aligned.png

    Fig 4. Two monomers (Chains A,D) point their N-terminal domain opposite to that of the other monomers (chains B,C).

     

    There are many structural homologs of this protein.

    Top 10 DALI Structural Homologs
    N PDB Z-score RMSD LALI NRES %ID Description
    1 2g7u 25.6 2.2 174 250 24 Transcriptional Regulator
    2 1mkm 25.6 1.6 169 247 21 Iclr Transcriptional Regulator
    3 2ia2 25.5 2.1 172 247 23 Putative Transcriptional Regulator
    4 2o9a 25.4 1.8 170 179 22 Acetate Operon Repressor
    5 2o99 25.3 1.8 170 179 22 Acetate Operon Repressor
    6 1td5 25.3 1.7 170 178 22 Acetate Operon Repressor
    7 1tf1 25.0 1.7 169 184 18 Negative Regulator of Allantoin and Glyoxylate
    8 2xro 24.4 2.5 238 240 26 Hth-type Transcriptional Regulator Ttgv
    9 2xrn 24.2 7.5 191 241 26 Hth-type Transcriptional Regulator Ttgv
    10 1ysq 23.8 1.9 171 181 21 Hth-type Transcriptional Regulator Yiaj

     

     

    A superposition of closest homologs are shown below.

    MI15778A_1mkm_2g7u.png

    Fig 5. YP_611946.1(green), 1mkm (cyan),  2g7u (magenta)

    Ligand Summary

    Reviews

    References

     

    No references found.

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