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The Open Protein Structure Annotation Network
PDB Keyword
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3ihu

    Title Crystal structure of DNA binding protein (YP_298823.1) from Ralstonia eutropha JMP134 at 1.92 A resolution. To be published
    Site JCSG
    PDB Id 3ihu Target Id 383474
    Molecular Characteristics
    Source Ralstonia eutropha jmp134
    Alias Ids TPS7420,YP_298823.1, 92895 Molecular Weight 24059.00 Da.
    Residues 221 Isoelectric Point 8.30
    Sequence mpidtptdaspadgsasdtvffgimsglelgtfvpgqrlvetdlvahfgvgrnsvrealqrlaaegivd lqrhrgavirrlslqetldvldvaermtgllaraatrgsgnqpqvqalrasvqalvaaekaqdgetfsn arrhfyrtllemgdnrelrrlfptihmpivhaqhrlaslrqmrlddyrriatavlagepdaaeaagaah vknvrgaildrqpa
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.92 Rfree 0.237
    Matthews' coefficent 2.23 Rfactor 0.199
    Waters 202 Solvent Content 44.93

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3ihu
    1. The mll6786 gene encodes a repressor protein controlling the degradation pathway for vitamin B6 in Mesorhizobium loti
    T Nagase, AN Mugo, HN Chu - FEMS Microbiology , 2012 - Wiley Online Library
     

    Protein Summary

    The protein YP_298823.1 is annotated as regulatory protein GntR, HTH. YP_298823.1 belongs to PFAM   PF00392 GntR(residues 31-78) and  PF07729 FCD residues (88-210). The FCD domain is the C-terminal ligand binding domain of many members of the GntR family which are bacterial regulatory proteins.

    The monomer structure is shown below.

    FM9641B_monomer.png

    The PFAM assignment of the domains (GNTR-magenta and FCD-orange) are shown below.

    FM9641B_domains.png

    There are several structural homologs of this protein.

    DALI Structural Homologs
    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 2hs5 18.5 3.4 201 207 21 PUTATIVE TRANSCRIPTIONAL REGULATOR GNTR
    2 3dbw 16.5 3.6 196 209 15 TRANSCRIPTIONAL REGULATOR, GNTR FAMILY
    3 3fms 16.0 3.3 192 209 16 TRANSCRIPTIONAL REGULATOR, GNTR FAMILY
    4 3c7j 13.6 5.3 136 227 15 TRANSCRIPTIONAL REGULATOR, GNTR FAMILY
    5 2di3 12.9 3.8 146 230 12 BACTERIAL REGULATORY PROTEINS, GNTR FAMILY
    6 1h9g 11.3 4.4 152 223 11 FATTY ACID METABOLISM REGULATOR PROTEIN
    7 1hw2 11.1 4.3 156 222 12 FATTY ACID METABOLISM REGULATOR PROTEIN
    8 1e2x 11.1 4.0 152 222 13 FATTY ACID METABOLISM REGULATOR PROTEIN
    9 1hw1 10.9 3.8 151 226 15 FATTY ACID METABOLISM REGULATOR PROTEIN
    10 3edp 10.5 3.0 74 223 18 LIN2111 PROTEIN

     

    A structural alignment of these proteins indicates that GNTR domain moves relative to the FCD domain.

     

    The alignment below shows that these proteins have the same relative orientation of the two domains as compared to the YP_298823.1. These proteins belong to the GNTR family.

    FM9641B_all2.png

    YP_298823.1 (green), 2hs5 (lightgrey), 3fms (lime), 3dbw (orange)

     

    However, other homologs show domain motion, as shown below.

    FM9641B_all1.png


    YP_298823.1 (green), 1e2x (cyan), 1h9g (lightmagenta), 1hw1 (yellow), 2di3 (salmon), 3c7j (slate)

     

    Ligand Summary

    Reviews

    References

     

    No references found.

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