.
The Open Protein Structure Annotation Network
PDB Keyword
.

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
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Molecular Characteristics
    Source
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Alias Ids
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    TPS24307,NP_765521.1, 3.40.109.10, 323977
    Molecular Weight
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Da.
    Residues
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Isoelectric Point
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Sequence
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
      BLAST   FFAS

    Structure Determination
    Method XRAY
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Chains 4
    Resolution (Å)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Rfree
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Matthews' coefficent 2.16 Rfactor 0.146
    Waters
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Solvent Content 43.13

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    Ligand Information
    Ligands
    Metals

    Jmol

     
    parameter 'target' could not convert from 'list' to 'str' (click for details)
    Google Scholar output for 3gbh

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    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.

    Tag page
    • No tags

    Files (2)

    FileSizeDateAttached by 
    active_site.bmp
    No description
    776.3 kB23:31, 6 Mar 2009haxelrodActions
     dimer.png
    No description
    238.18 kB22:05, 10 Feb 2009haxelrodActions
    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch