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The Open Protein Structure Annotation Network
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3gfa

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

    Title Crystal structure of putative nitroreductase in complex with FMN (YP_001089721.1) from CLOSTRIDIUM DIFFICILE 630 at 1.35 A resolution. To be published
    Site JCSG
    PDB Id 3gfa Target Id 391649
    Molecular Characteristics
    Source Clostridium difficile 630
    Alias Ids TPS14645,YP_001089721.1, 3.40.109.10, 85743 Molecular Weight 22361.45 Da.
    Residues 197 Isoelectric Point 6.76
    Sequence misdsiskrrsirkyknqsishetiekiieaginapssknrqpwrfvvitekekesmlkamskgiqnei ndngllpgsrqhiaganytveimkqapvtifilnilgkspleklspeerfyemanmqsigaaiqnmslt avelglgslwicdvyfayrelcewlntdsqlvaaislgypdeepsrrprlqlsdvtewr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.35 Rfree 0.157
    Matthews' coefficent 2.59 Rfactor 0.134
    Waters 349 Solvent Content 52.56

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3gfa
    1. Crystal structure of an eIF4G_like protein from Danio rerio
    E Bae, E Bitto, CA Bingman, JG McCoy - Proteins: Structure, , 2010 - Wiley Online Library
     

    Protein Summary

    Gene CD3205 translates into the YP_001089721 protein encoded by Clostridium difficile 630, a ubiquitous microbe found in both human and animal feces. The bacterium is especially prevalent  in in hospital environments. Under certain circumstances, this bacterium is pathogenic. The amino acid sequence for this target belongs to the Nitroreductase PF00881 Pfam Group.

    The 3gfa structure belongs to the alpha + beta class and reveals a FMN-dependent nitroreductase like fold, inside the SCOP NADH oxidase/flavin reductase family. Top DALI hits are with the nitroreducatse PDB:3e39 (Z=20), PDB:2i7h (Z=19), and PDB:1ywq (Z=19). Two additional JCSG targets that are structurally related to 3gfa include PDB:3eo8 (Z=21, topsan) and PDB:3eof  (Z=17, topsan). PDB ID 3eo8 shares several important features with 3gfa. First, both targets are from the same microcobe, Clostridium difficile 630. Second, both targets contain a tightly bound flavin mononucletide (FMN) cofactor. Third, both structures (3fga and 3eo8) show chloride anions bound at the active site near the FMN, and the presence of this negtaively-charged anion suggests a role for these two proteins in oxygen reduction.

    The x-ray crystal structure reported here, 3gfa, was determined by selenoMet-based multiwavelength anomalous dispersion at a resolution of 1.35 Angstroms. Shown below is a ribbon representation of the crystal structure of 3gfa. The polypeptide backbone is color-coded rainbow with the N-terminus in blue and the C-terminal region in red. An FMN prosthetic group is bound to the target (red sticks). The C-terminal extension of the monomer interacts with a beta-strand on a symmetry-related monomer.

     monomer.png

     

     

     

    Comparison with the structure of related proteins such as PDB ID 3eo8 and PDB ID 3eof suggest that the biologically significant oligomerization state of 3gfa is a dimer. Shown below it is a ribbon representation of the structure of the dimer with the individual monomers depicted in green and blue. The bound FMN cofactors are shown in red. The monomers are related by a two-fold non crystallographic dyad axis. The C-terminal end of each monomer contributes a beta strand to a symmetry-related monomer in the dimer to form a five-stranded beta sheet. In addition, each FMN cofactor interacts with residues from both monomers within the dimer.

    dimer.png

     

     

    A search of the Protein Data Bank for entries structurally-related to 3gfa was performed using the EBI Secondary Structure Match Server. The results are:

    Hit   Z-score   No. 
     SSE 
     RMSD 
     (Å) 
     Seq. 
     id 
     PDB 
     entry 
    Name
     1  10.0 12 1.19  33.1%  3e39 Crystal structure of putative nitroreductase in complex with fmn (yp_387283.1) from desulfovibrio desulfuricans g20 at 1.70 a resolution
      7.6 11 1.57  20.3%  2i7h Crystal structure of the nitroreductase-like family protein from bacillus cereus
      9.0 10 1.35  27.4%  2b67
     
    Crystal structure of the nitroreductase family protein from streptococcus pneumoniae tigr4
      7.8 10 1.77  27.4%  1ywq

    Crystal structure of a nitroreducta

     

    se family protein from bacillus cereus atcc 14579

      7.5 8 1.79  26.6%   3bm1  Crystal structure of a minimal nitroreductase ydja from escherichia coli k12 with and without fmn cofactor
     6  8.7 9 1.86  25.7%  3ek3  Crystal structure of nitroreductase with bound fmn (yp_211706.1) from bacteroides fragilis nctc 9343 at 1.70 a resolution
     7  8.1 9 1.57  25.9%  2fre
    The crystal structure of the oxidoreductase containing fmn
      8.1 9 1.80  21.3%  3bem Crystal structure of putative nitroreductase ydfn (2632848) from bacillus subtilis at 1.65 a resolution
     9  7.9 9 1.33  34.3%  3e10
    Crystal structure of putative nadh oxidase (np_348178.1) from clostridium acetobutylicum at 1.40 a resolution
     10  9.4 11 1.49  25.4%    1bkj  Nadph:fmn oxidoreductase from vibrio harveyi

     

    Shown below is a representation of the 3gfa residues defining the putative active site. The structure indicates that a chloride ion is adjacent to the FMN cofactor.  The structure also shows a methyl-pentane diol from the crystallization solutions bound nearby.

     

     

    MG0383AD_active_site.bmp

     

    Ligand Summary

    Reviews

    References

     

    No references found.

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