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2fg9

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

    Title Crystal structure of (np_811990.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.20 A resolution. To be published
    Site JCSG
    PDB Id 2fg9 Target Id 359120
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS1419,NP_811990.1, 2.30.110.10, 60683772, 60679947, 87266 Molecular Weight 18252.09 Da.
    Residues 159 Isoelectric Point 6.20
    Sequence mktiviedkqriesiilqadacfvgitdlegnpyvvpmnfgyendtlylhsgpeggkiemlqrnnnvci tfslghklvyqhkqvacsysmrsesamcrgkvefiedmeekrhaldiimrhytkdqfsysdpavrnvkv wkvpvdqmtgkvfglradekp
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.20 Rfree 0.245
    Matthews' coefficent 2.49 Rfactor 0.223
    Waters 46 Solvent Content 50.21

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2fg9
    1. Structural Basis of Murein Peptide Specificity of a [gamma]-D-Glutamyl-L-Diamino Acid Endopeptidase
    Q Xu, S Sudek, D McMullan, MD Miller, B Geierstanger - Structure, 2009 - Elsevier
     
    2. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
     
    3. The structure of a Xanthomonas general stress protein involved in citrus canker reveals its flavin-binding property
    E Hilario, Y Li, D Niks, L Fan - Acta Crystallographica Section D: , 2012 - scripts.iucr.org
     

    Protein Summary

    Gene BT_3078 from Bacteroides thetaiotaomicron vpi-5482 encodes the protein NP_811990.1 that belongs to the 'Pyridoxamine 5'-phosphate oxidase' family (PF01243) and a 'predicted flavin-nucleotide-binding protein' COG (GOG3467).  It is highly similar to a number of proteins annotated as 5-nitroimidazole antibiotic resistance proteins, but the origin of those protein annotations is unclear.  The protein shares the same genomic neighborhood as Ribonuclease R (Q8A378), according to the STRING database.


    NP_811990.1 structure, 2fg9, belongs to 'PNP-oxidase-like' family of SCOP (FMN-binding split barrel superfamily and fold), and is classified in pre-SCOP as a new protein domain within this family.   

    Similar structures to 2fg9 identified by DALI include: with Zscr=16, 2hti and 2fur; with Zscr=15, 2hq9 and 1w3p, a NIMA-related protein. The  'NimA-related protein DR0842' protein domain belonging to the same SCOP family is a type of reductase that converts the nitro group of the 5-nitroimidazole antibiotic into a non-bactericidal amine (i.e. these are 5-nitroimidazole antibiotic resistance proteins).

    2fg9 is the first structure of the 'PNP-oxidase-like' SCOP family to be solved with FAD as a ligand (the observed co-factor/ligand combinations in other structures of the same family are: FMN, PLP, FMN+PLP, PYR, PYR+MTR and CIT).

    2fg9 was solved as an hexamer (3x homodimer) and this was confirmed by SEC/SLS and analysis of the crystallographic packing of the protein using the PQS server.  However, since the interactions observed between dimers involve the expression tag, it is likely that the real biologically relevant form is a dimer, in conformance with the remaining proteins in the same SCOP family (this was also noted in the deposited PDB file).

    Ligand Summary



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