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The Open Protein Structure Annotation Network
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3gbh

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

    Title Crystal structure of putative NAD(P)H:FMN oxidoreductase (NP_765521.1) from Staphylococcus epidermidis ATCC 12228 at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 3gbh Target Id 391352
    Molecular Characteristics
    Source Staphylococcus epidermidis atcc 12228
    Alias Ids TPS24307,NP_765521.1, 3.40.109.10, 323977 Molecular Weight 24220.37 Da.
    Residues 212 Isoelectric Point 4.91
    Sequence mqkltrindfnevlnsrksvkvfdenykipreemdeiitkatkapssvnmqpwriavvqsdemkekvke sfgfnsrqlttssamliifgdlqnyekaeqiygdaveqqlmtedikaqlldwilpyyknlsregmkdiv nidsslmamqlmltakahgydtnpiggfdkeniadiigydsdryvpvlaiaigkkaqdahdsvrlpidd vrefl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 2.00 Rfree 0.185
    Matthews' coefficent 2.16 Rfactor 0.146
    Waters 561 Solvent Content 43.13

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    The gene SE1966 (refseq accessin number NP_765521.1) belongs to the Nitroreductase, PF00881, Pfam A group. This Pfam group is represented by 71 structures in the Protein Data Bank.

    The structure of NP_765521.1  is a member of the Nitroreductase-like family from Staphylococcus epidermidids strain ATCC 12228 . This strain is a non-biofilm-forming, non-infection associated strain used for detection of residual antibiotics in food products.  Nitroreductases  typically require NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer.  The structure described here was determined at a resolution of 2.0 Angstroms using single wavelength anomalous dispersion methods (SAD).

     

    dimer.png

     Shown here is a ribbon representation of the structure of the dimer of NP_765521.1 color coded with the N-terminal region in blue and the C-terminal region in red. An FMN, tightly bound to each monomer is shown in the red sticks. The crystal structure indicates that the dimer represented here is a significant oligomerization state. Recently refined JCSG structures similar to NP_765521.1 also include YP_001089721.1 from Clostridium difficile 630 and NP_904626.1 from Porphyromonas gingivalis w83. The refined coordinates for NP_76552.1 were used as a template to search for structurally-similar proteins using the fastSCOP evolutionary classification server. This serarch shows that NP_766552.1 most likely belongs to the NADH oxidase/flavin reductase SCOP family. An NCBI VAST search shows several targets in the Protein Data Bank that show a similar structure. Among these targets are PDB ID 2B67 (Nitroreductase Family Protein from Streptococcus pneumoniae TIGR4, rmsd 1.85 Angstroms, seq id 25%), PDB ID 1NOX (NADH Oxidase from Thermus thermophilus; rmsd 1.62 Angstroms, 25% sequence id), PDB ID 2HAY ( The Crystal Structure of the Putative NAD(P)H-Flavin Oxidoreductase from Streptococcus pyogenes M1 GAS; ), PDB ID 1ICU (the structure of E.coli Nitroreductase Complex with Nicotinic Acid), and PDB ID 3BEM ( Crystal Structure Of Putative Nitroreductase Ydfn (2632848) From Bacillus Subtilis At 1.65 A Resolution).

     

    Shown below is a representation of the structure of NP_765521.1 in the vicinity of the putative active site.  One monomer in the dimer is shown in yellow ribbons and the symmetry-related dimer is shown in blue ribbons. A bound FNM (red sticks) is also shown superimposed on 2fo-fc electron density. An unknown ligand (represented by red spheres and its corresponding electron density) is situated near one face of the bound FMN cofactor.

    active_site.bmp

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (2)

    FileSizeDateAttached by 
    active_site.bmp
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    776.3 kB23:31, 6 Mar 2009haxelrodActions
     dimer.png
    No description
    238.18 kB22:05, 10 Feb 2009haxelrodActions
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