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The Open Protein Structure Annotation Network
PDB Keyword
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3hoi

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

    Title Crystal structure of FMN-dependent nitroreductase BF3017 from Bacteroides fragilis NCTC 9343 (YP_212631.1) from Bacteroides fragilis NCTC 9343 at 1.55 A resolution. To be published
    Site JCSG
    PDB Id 3hoi Target Id 396586
    Molecular Characteristics
    Source Bacteroides fragilis nctc 9343
    Alias Ids TPS25947,YP_212631.1, 3.40.109.10, 326302 Molecular Weight 20820.78 Da.
    Residues 192 Isoelectric Point 9.52
    Sequence aertiqlpkpdmnragllmkalserhstreyaskalsntdlsdllwaanginrssegkrtapsamnrqd idiyvvlpqgtylydakghklnlisegdhrsavaggqafvnnapvslvlvsdlsklgdaksnhvqlmga mdagivsqnislfcsaarlatvprasmdlvrlkaalklkdtqmpmmnhpvgyfk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.55 Rfree 0.187
    Matthews' coefficent 2.39 Rfactor 0.161
    Waters 214 Solvent Content 48.44

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3hoi

    Protein Summary

    Pfam update: This protein is now in family PF00881.17 Nitroreductase along with other structures.

    Gene YP_212631.1 encodes a protein with 211 residues from Bacteroides fragilis nctc 9343. It has been annotated as a putative exported protein belonging to Nitroreductase Pfam family PF00881. Several JCSG targets including2r01, topsan_page, 3ek3, topsan_page, 3eof, topsan_page and 3gfa, topsan_page  belong to this family.

    The YP_212631.1 is present as a monomer in the asymmetric unit of the unit cell of the crystal structure (Fig. 1), and packing analysis suggests that the dimer with symmetry mate (cyan and light blue) is the relevant oligomeric form in solution. In the putative active site of the protein, a Cl ion  and a FMN (red sticks) are found. The FMN restraints dictionary was modified to allow bending of the isoalloxazine ring along the N5-N10 virtual azis resulting in an improved fit between the FMN coordinates and electron density. During QC round, Cl ion was replaced to UNL.

     monomer.png

    Fig.1. Crystal structure of YP_212631.1 in the asymmetric unit.

    dimer.png

    Fig. 2. Biomolecule of YP_212631.1.

     

    UNL.png

    Fig. 3. The surface representation of the YP_212621.1 shown putative active site. Final FMN (red stick) and UNL (balls) in the EDs (grey mesh) are shown. Although it didn't refine well, the EDs resemble either disordered Cl or acetate ions.

     

    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

     

    Unknown ligand (UNL), sulfate ions (SO4), citrate anion (FLC) and PEG fragement (PEG) were found.

    Reviews

    References

     

    No references found.

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