The Open Protein Structure Annotation Network
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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of Nitroreductase with Bound FMN (YP_211706.1) from Bacteroides fragilis NCTC 9343 at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 3ek3 Target Id 391613
    Molecular Characteristics
    Source Bacteroides fragilis nctc 9343
    Alias Ids TPS14636,YP_211706.1,, 85639 Molecular Weight 21005.85 Da.
    Residues 189 Isoelectric Point 6.08
    Sequence mktnevletikarrsvraydrkqipaddlnaileagayapsgmhyetwhftavcntvkleelnerikga faksddkhlrerghsetyccyyhaptlvivsnepkqwwagmdcacaienmflaatslgiascwinqlgt tcddpevrayltslgvpenhkvygcvalgykaegallkektvkagtitive
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.70 Rfree 0.183
    Matthews' coefficent 2.33 Rfactor 0.150
    Waters 206 Solvent Content 47.15

    Ligand Information


    Google Scholar output for 3ek3

    Protein Summary

    An obligate anaerobe, Bacteroides fragilis is usually a commensal organism, forming a large component of the normal human gut microbiota. However it is also an important opportunistic pathogen, with the potential to severly limit the success of gastro-intestinal surgery. YP_211706.1 from this medically-important organisim has been determined by MAD to a resolution of 1.7 Angstroms and refined to an (Rfree=18.3%)


     The Figure above shows a ribbon representation of the structure of YP_211706.1. The polypeptide ribbon is color-coded with the N-terminal end in blue and the C-terminal end in red. The x-ray structure shows the presence of a bound Flavin Mononucleotide (FMN) cofactor shown with red sticks. The FMN binds on one side of a beta sheet . The other side of the sheet is flanked by alpha-helices. From residue 167 to the C-terminal end, the polypeptide chain forms an extended beta strand. This extended beta stand interacts with a monomer related by crystallographic symmetry in the C222(1) crystal lattice of the protein crystal.



    The amino acid sequence of YP_211706.1 and the corresponding secondary structure topology.


    The PISA protein assembly prediction server indicates that the biologically significant oligomerization state in solution for  YP_211706.1 is the dimer.

    dimer_unl.pngShown to the left is a ribbon representation of the dimer with the indivifual monomers of the dimer shown in blue and green respectively. The extended beta-strand at the C-terminal end of each monomer interacts with the symmetry related monomer to form a five strand beta sheet.The FMN cofactor on each subunit is shown in red. Immediately adjacent to and stacked against the side of the FMN ring facing the solvent is crystallographic evidence for the binding of a biologically-relevant ligand. Extra electron density at this position was modeled as an unknown ligand (UNL) in the structure (grey dots).



    An InterPro scan reveals the sequence motif of  YP_211706.1 belongs to the nitroreductase family that uses FMN as a cofactor (PF00881). This family is involved in the reduction of nitrogen containing compounds. Members of this family utilise FMN as a cofactor and are often found to be homodimers. Possible characteristics include Oxygen-insensitive NAD(P)H nitroreductase (FMN-dependent nitroreductase) (Dihydropteridine reductase) and NADH dehydrogenase. A number of the proteins are described as oxidoreductases. They are primarily found in bacterial lineages though a number of eukaryotic homologs have been identified: Caenorhabditis elegans , Drosophila melanogaster , mouse and human . This protein is not found in photosynthetic eukaryotes. The sequences containing this entry in photosynthetic organisms are possible false positives.

      An EBI SSM search of the Protein Data Bank using the coordinates of YP_211706.1 as a search model shows several protein structures have been determined that are similar to the structure of YP_211706.1. The table below lists the structurally-similar proteins.

    RMSD (Angstroms)
    Sequence Identity (%)
    PDB ID
    Protein Name
    21.8 1vfr  The major NAD(p)h:fmn oxidoreductase from vibrio fischeri
     1.89  20.2 1ylu  The structure of e. Coli nitroreductase with bound acetate, crystal form 2
     1.99  21.3 1nec  Nitroreductase from enterobacter cloacae
     1.92  21.8 1v5y Binding of coumarins to NAD(p)h:fmn oxidoreductase
     1.91  21.8 1v5z  Binding of coumarins to NAD(p)h:fmn oxidoreductase
     2.03  24.6  2i7h TOPSAN page
     Crystal structure of the nitroreductase-like family protein from bacillus cereus
     2.48  27.9 3bm2  Crystal structure of a minimal nitroreductase ydja from escherichia coli k12 with and without fmn cofactor
     2.19  17.0  2ifa TOPSAN page
    Crystal structure of the putative nitroreductase (smu.260) in complex with fmn from streptococcus mutans, northeast structural genomics target smr5.
     2.07  28.2 3bm1  Crystal structure of a minimal nitroreductase ydja from escherichia coli k12 with and without fmn cofactor
     2.04  17.0 1ywq TOPSAN page
     Crystal structure of a nitroreductase family protein from bacillus cereus atcc 14579

    Ligand Summary

    Among the most significant feature revealed by the structure determination, is the presence of a bound FMN cofactor. Shown below is a diagram of the structure in dimer in the vicinity of the FMN binding site. Most of the close range interactions (hydrogen bonds-black dashes) form between FMN and one of the monomers in the dimer (green region in the Figure below). However,  sidechain and mainchain atoms from the symmetry related monomer (blue region in Figure below) are within Van der Waals contact distance. In addition, an MPD molecule (from the crystallization buffer) also is within hydrogen bonding contact distance from the phosphate moiety on the FMN cofactor.





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    Files (5)

    FileSizeDateAttached by 
    Dimer Biomol with FMN cofactor and UNL
    214.66 kB19:15, 17 Aug 2008haxelrodActions
    Protein Ligand Interactions at FMN binding site
    5.97 MB19:19, 17 Aug 2008haxelrodActions
    No description
    1779.84 kB02:35, 18 Aug 2008haxelrodActions
    monomer ribbon representation
    145.85 kB19:23, 17 Aug 2008haxelrodActions
    No description
    191.11 kB19:29, 17 Aug 2008haxelrodActions
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