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The Open Protein Structure Annotation Network
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3nqo

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

    Title Crystal structure of a MarR family transcriptional regulator (CD1569) from Clostridium difficile 630 at 2.20 A resolution. To be published
    Site JCSG
    PDB Id 3nqo Target Id 399389
    Molecular Characteristics
    Source Clostridium difficile 630
    Alias Ids TPS29720,YP_001088069.1, _0054.001598_, 430107 Molecular Weight 21995.95 Da.
    Residues 188 Isoelectric Point 5.39
    Sequence mdysnelkelflmnqtyatlftltnkiqiegdkyfgiltsrqymtilsilhlpeeettlnniarkmgts kqninrlvanlekngyvdvipsphdkrainvkvtdlgkkvmvtcsrtginfmadvfheftkdeletlws llkkmyrfngeeqdgfeedanfmeyeeidkiksealeefakrrnrvnknd
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.20 Rfree 0.237
    Matthews' coefficent 2.15 Rfactor 0.197
    Waters 63 Solvent Content 42.68

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3nqo

    Protein Summary

    Target 399389 (JCSG target accession code MI11708B, GenBank accession code YP_001088069.1) is a 188-residue protein from Clostridium difficile strain 630.  C. difficile is a Gram-positive anaerobic bacterium which is ubiquitous in nature (including the human intestine in 2-5% of the population), with strain 630 being one which is virulant and multi-drug resistant.

    Target 399389 is annotated as a MarR (Multiple antibiotic resistance Regulator) family transcriptional regulator, belonging to Pfam PF01047.  This is a family of bacterial regulatory proteins which controls the transcription of the mar (multiple antibiotic resistance) operon.  The Mar proteins regulate the efflux and influx of various phenolic compounds, and, if left unregulated by MarR, are responsible for conferring to bacteria resistance to multiple antibiotics, organic solvents, disinfectants, oxidative stress agents, etc.  Proper functioning of the MarR regulatory protein is essential, therefore, to the prevention of such resistance.

    The structure of target 399389 was solved by the Se-SAD method to a resolution of 2.20 Angstroms and reveals a mostly helical alpha/beta fold, with the core of this fold belonging to "winged-helix" DNA-binding domain superfamily in the SCOP classification scheme (Figure 1).

    Figure 1.  Structure of target 399389 monomer, gradiently colored from the N- (blue) to the C-terminus (red).

    MI11708B-gradient.png

     

    Crystal packing and PISA analyses suggests that target 399389 forms a dimer, which is consistent with many other members of the MarR family (Figure 2).

    Figure 2.  Target 399389 is most likely a dimer.  Monomers A and B are colored orange and blue, respectively.  (a) and (b) are orthogonal views.

    (a)                                                                                        (b)

    MI11708B-oligomer.png     MI11708B-oligomer2.png

     

    A DALI structural neighbor search yields top matches that are all transcriptional regulators (Table 1).  The top three structural neighbors are the transcriptional regulators BldR from Sulfolobus solfataricus (PDB id 3f3x), one from Rhodococcus jostii (PDB id 3fm5), and SlyA from Salmonella typhimurium (PDB id 3deu).

    Table 1. Top structural neighbors of target 399389 as assessed by DALI.  Structural neighbors that are color-highlighted are superimposed with target 399389 in Figure 3.

    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 3f3x 14.4 2.3 135 139 18 TRANSCRIPTIONAL REGULATOR, MARR FAMILY, PUTATIVE [Ref]
    2 3fm5 14.2 2.6 136 140 17 TRANSCRIPTIONAL REGULATOR
    3 3deu 14.0 2.2 129 132 18 TRANSCRIPTIONAL REGULATOR SLYA
    4 2nnn 14.0 2.1 132 133 19 PROBABLE TRANSCRIPTIONAL REGULATOR
    5 3e6m 13.8 3.1 143 149 20 MARR FAMILY TRANSCRIPTIONAL REGULATOR
    6 3bro 13.7 2.8 138 140 16 TRANSCRIPTIONAL REGULATOR
    7 3bpx 13.7 2.2 134 138 19 TRANSCRIPTIONAL REGULATOR [Ref]
    8 2yr2 13.6 3.3 137 142 16 146AA LONG HYPOTHETICAL TRANSCRIPTIONAL
    9 1z9c 13.6 2.3 135 137 15 DNA (29-MER) [Ref]
    10 1lnw 13.5 2.3 134 140 19 MULTIDRUG RESISTANCE OPERON REPRESSOR [Ref]

     

    A superposition of the top three structural neighbors from the DALI search with target 399389 reveals that the folds are very similar, with the main difference being that target 399389 contains an additional alpha-helix at the C-terminus (Figure 3).

    Figure 3.  Superposition of target 399389 (yellow) with top 3 DALI matches: PDB id's 3f3x (blue), 3fm5 (red), and 3deu (green).

    MI11708B-superpose.png

     

    If target 399389 were indeed shown to be a MarR transcriptional repressor, helix 4 of the winged-helix motif would most likely act as the recognition helix and bind to the DNA major groove.

    Ligand Summary

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