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The Open Protein Structure Annotation Network
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3qkx

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

    Title Crystal structure of a TetR-family transcriptional regulator (HI0893) from Haemophilus influenzae RD at 2.35 A resolution. To be published
    Site JCSG
    PDB Id 3qkx Target Id 399392
    Molecular Characteristics
    Source Haemophilus influenzae rd kw20
    Alias Ids TPS29724,NP_439054.1, _0088.001719_, 326454 Molecular Weight 22021.31 Da.
    Residues 187 Isoelectric Point 6.18
    Sequence mrqaktdlaeqifsatdrlmareglnqlsmlklakeanvaagtiylyfknkdelleqfahrvfsmfmat lekdfdetkpffeqyrqmwkniwyflqenptilsnlkqyeslpnfkdicknikncrwdlfchqaqkagl laelsedilfllslktainlasdakfidfdlkpeilesvierswraiqk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.35 Rfree 0.2484
    Matthews' coefficent 2.60 Rfactor 0.2227
    Waters 47 Solvent Content 52.71

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Target 399392 (JCSG target accession code MI0823AY, GenBank accession code NP_439054.1) is a 187-residue protein from Haemophilus influenzae rd, a Gram-negative bacterium which can cause human diseases such as bacteremia, pneumonia, and acute bacterial meningitis.

    Target 399392 is annotated as a transcriptional repressor, belonging to PFAM:PF00440.  This is a family of bacterial regulatory proteins which include the tetracycline resistance repressor (TetR) and other transcriptional regulators such as TetC and AcrR.  Many members of this family are repressors involved in controlling the susceptibility of the organism to hydrophobic antibiotics and detergents.

    The structure of 399392, which was solved by the Se-MAD method to a resolution of 2.35 Angstroms, adopts an all alpha-fold, with 12 alpha-helices (Figure 1).  Residues 1-82, which contain a helix-turn-helix motif, is classified as belonging to the homeodomain-like superfamily in the SCOP classification scheme, while residues 83-187 belong to the tetracycline repressor-like, C-terminal domain superfamily.

    Figure 1.  Structure of target 399392 monomer, gradiently colored from the N- (blue) to the C-terminus (red), adopts an all-alpha fold.

    MI0823AY-gradient.png

     

    Both crystallographic packing and PISA analyses suggest that the functional form of the protein is a dimer, which is consistent with the oligomeric state of other members in this Pfam (Figure 2).

    Figure 2.  Dimeric configuration of target 399392 (monomer A in orange, monomer B in blue).

    MI0823AY-dimer.png

     

    A structural alignment search with DALI (Table 1) resulted in matches with a number of transcriptional regulators including those from the TetR (PDB:3HEO), RutR ( PDB:3LOC), and YcdC (PDB:1PB6 ) families.  The closest structural match is with a transcriptional regulator from the TetR family ( PDB:3HEO ), with an r.m.s.d of 2.0 Angstroms over 174 C-alpha atoms and a sequence identity of 34%.

    Table 1.  Top structural neighbors of target 399392 as assessed by DALI.  Proteins that are color-highlighted are superimposed with target 399392 in Figure 3.

    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 3he0 19.3 2.0 174 186 34 TRANSCRIPTIONAL REGULATOR, TETR FAMILY
    2 2gen 16.4 2.7 174 188 15 PROBABLE TRANSCRIPTIONAL REGULATOR
    3 3loc 15.4 3.1 180 201 16 HTH-TYPE TRANSCRIPTIONAL REGULATOR RUTR
    4 1pb6 15.3 3.1 178 198 16 HYPOTHETICAL TRANSCRIPTIONAL REGULATOR YCDC
    5 1vi0 15.1 2.7 167 189 24 TRANSCRIPTIONAL REGULATOR
    6 3crj 14.9 3.3 172 189 17 TRANSCRIPTION REGULATOR
    7 3kz9 14.6 3.3 178 203 16 SMCR
    8 3col 14.6 3.3 168 180 20 PUTATIVE TRANSCRIPTION REGULATOR
    9 3him 14.4 3.4 178 190 14 PROBABLE TRANSCRIPTIONAL REGULATOR
    10 3ih4 14.2 3.6 174 202 17 TRANSCRIPTIONAL REGULATOR, TETR FAMILY

     

    Superposition of target 399392 with several of the top structural neighbors reveals overall similar folds and dimeric oligomeric states (Figure 3).

    Figure 3.  Superposition of target 399392 (yellow) with PDB id's 3he0 (blue) and 3loc (red).

    MI0823AY-superpose.png

     

    A sequence alignment of target 399392 and the top 10 sequence homologues derived from a PSI-BLAST search reveals that high residue conservation occurs predominantly in the N-terminal region, in the helix-turn-helix motif (Figure 4).  This is consistent with this region putatively being the DNA-binding region of the protein.

    Figure 4.  Residue conservation between target 399392 and its top 10 sequence homologues.  Residues in magenta are most conserved while those in cyan are least conserved.  Residues that are highly conserved are labeled.  ConSurf analysis was done only on monomer B.  Monomer A is shown in orange.  Orientation is the same as in Figures 2 and 3.

    MI0823AY-consurf.png

    Ligand Summary

    Reviews

    References

     

    No references found.

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