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

    Title Crystal structure of putative oxidoreductase (YP_213212.1) from Bacteroides fragilis NCTC 9343 at 1.99 A resolution. To be published
    Site JCSG
    PDB Id 3eof Target Id 391632
    Molecular Characteristics
    Source Bacteroides fragilis nctc 9343
    Alias Ids TPS14641,YP_213212.1, 3.40.109.10, 85678 Molecular Weight 28392.12 Da.
    Residues 247 Isoelectric Point 5.26
    Sequence mmdtvknrrtirkyqqkditpdllndlletsfrastmggmqlysvvvtrdaekkeilspahfnqpmvke apvvltfcadfrrfckycqernavpgygnlmsflnaamdtllvaqtfctlaeeaglgicylgtttynpq miidalhlpelvfpittvtvgypaespkqvdrlpiegiiheesyhdytaedinrlyaykeslpenklfi eenqketlpqvftdvrytkkdnefmsenllkvlrrqgfmd
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.99 Rfree 0.224
    Matthews' coefficent 2.50 Rfactor 0.169
    Waters 368 Solvent Content 50.82

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    This protein is a putative oxidase belonging to Nitroreductase Pfam family PF00881. The protein is present as a dimer in the asymmetric unit of the unit cell of the crystal structure and packing analysis suggests that this dimer (green and cyan) is the relevant oligomeric form in solution. Endogenous cofactor FMN was found bound in the putative active site of the protein (red sticks) which is consistent with the possible function of the protein:

    Fig1_dimer.png

      

      

    Other proteins of significant sequence similarity with similar structure can be seen using FFAS. The top 5 hits with PDB accession ids 1f5v, 1bkj, 1zch, 2fre and 2b67 have very high similarity hits despite sequence identity of only ~25%.

      

    Comparing the dimer structure of this protein (green & cyan) with that of 1f5v (yellow, Ref1) reveals that the two dimers are similar in structure with the FMN bound at similar locations (FMN from 1f5v is in blue):

    Fig2_with1F5V.png

      

    References:

    Kobori T, Sasaki H, Lee WC, Zenno S, Saigo K, Murphy ME, Tanokura M.Structure and site-directed mutagenesis of a flavoprotein from Escherichia coli that reduces nitrocompounds: alteration of pyridine nucleotide binding by a single amino acid substitution. J Biol Chem. 2001 Jan 26;276(4):2816-23. Epub 2000 Oct 16.

     

    Ligand Summary

    Cofactor FMN was found bound to the protein. This is an endogenous ligand.

    Reviews

    References

     

    No references found.

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    Files (2)

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     Fig1_dimer.png
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    431.96 kB23:17, 2 Sep 2008debanuActions
     Fig2_with1F5V.png
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    572.15 kB23:55, 2 Sep 2008debanuActions
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