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The Open Protein Structure Annotation Network
PDB Keyword
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3fkh

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

    Title Crystal structure of Putative pyridoxamine 5'-phosphate oxidase (NP_601736.1) from CORYNEBACTERIUM GLUTAMICUM ATCC 13032 KITASATO at 2.51 A resolution. To be published
    Site JCSG
    PDB Id 3fkh Target Id 375029
    Molecular Characteristics
    Source Corynebacterium glutamicum atcc 13032
    Alias Ids TPS6822,NP_601736.1, 92226 Molecular Weight 15770.16 Da.
    Residues 137 Isoelectric Point 4.80
    Sequence mdnpvnilneqealerlqsvslgrvvvrrsdemdifpvnfivdkgaiyirtaegnklfsmnlnhdvlfe adevkdgkawsvvvrataeivrkldeiayadtlelkpwiptlkynyvrivpneitgreftlgeepery
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.51 Rfree 0.287
    Matthews' coefficent 2.37 Rfactor 0.243
    Waters 78 Solvent Content 48.17

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3fkh
    1. 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

    The target 375029 has not yet been annotated and is currently listed as a hypothetical protein on the JCSG PSCA server.

    However, a sequence based search identifies this protein to belong to the Pyridoxamine 5'-phosphate oxidase family of PFAM PF01243: Pyridoxamine 5'-phosphate oxidase.

    This annotation is confirmed by a comparison of the structure with its homologs (see table below) which immediately suggests that it is a FMN binding split-barrel protein.

    SSM Structural Homologs

    N
    PDB
    Q-score
    RMSD
    Title
    1 3cp3 , TOPSAN page 0.6767 1.310 CRYSTAL STRUCTURE OF CONSERVED PROTEIN OF UNKNOWN FUNCTION DIP1874 FROM CORYNEBACTERIUM DIPHTHERIAE
    2 2hq9, TOPSAN page 0.5748 1.738 CRYSTAL STRUCTURE OF A FAD-BINDING PROTEIN (NP_107146.1) FROM MESORHIZOBIUM LOTI AT 1.95 A RESOLUTION
    3 2hti , TOPSAN page 0.5259 2.044 CRYSTAL STRUCTURE OF BH0577 (10173191) FROM BACILLUS HALODURANS AT 2.50 A RESOLUTION
    4 3db0 , TOPSAN page 0.5142 1.868 CRYSTAL STRUCTURE OF PUTATIVE PYRIDOXAMINE 5'-PHOSPHATE OXIDASE (NP_472219.1) FROM LISTERIA INNOCUA AT 2.00 A RESOLUTION
    5 2fhq , TOPSAN page 0.4467 1.989 CRYSTAL STRUCTURE OF GENERAL STRESS PROTEIN FROM BACTEROIDES THETAIOTAOMICRON

     

    A superposition of these structures is shown below with the following color code: target (green), 2fhq (cyan), 2hq9 (magenta), 2hti (yellow), 3cp3 (pink), 3db0 (grey).

    all.png

     

    The protein assembles as a dimer (figure below) in the crystal structure as expected for a member of this family.

    FB9776D_dimer.png

     

    A closer comparison with 2hq9, another JCSG structure,  highlights the completeness of the structural homolgy.

    FB9776D_2hq9.png

    The target is in green while the 2hq9 is in orange. There is no FMN or FAD bound in the crytsal structure of this target. The FAD bound to 2hq9 is shown in stick representation to point out the location of the site of FAD/FMN.

     

    Note from PFAM:

    This is a putative pyridoxamine 5'-phosphate oxidase. This page says it matches PF01243, but when searched against the current set of Pfam models it didn't match anything. I have built a new family from it called Pyridox_ox_2 (PF12900), and have added it to the FMN-binding clan (CL0336). It is not the first structure for the clan.

    Ligand Summary

    Reviews

    References

     

    No references found.

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