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The Open Protein Structure Annotation Network
PDB Keyword
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2lrg

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

    Title NMR structure of the protein YP_001300941.1 from Bacteroides vulgatus. To be Published
    Site JCSG
    PDB Id 2lrg Target Id 393196
    Related PDB Ids 3u6g 
    Molecular Characteristics
    Source Bacteroides vulgatus atcc 8482
    Alias Ids TPS24847,YP_001300941.1, 324109 Molecular Weight 13417.15 Da.
    Residues 125 Isoelectric Point 4.77
    Sequence asdfqtgihkiviqqsgdtdsfevsvsiggadkggpaklyndkgeyigdsysaqirtatmscctngnaf fmtcagsvssiseagkrlhitvigyiddkevnrlekeyitdgntlietfsvstkei
      BLAST   FFAS

    Structure Determination
    Method NMR Chains 1

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    BVU_3708 from Bacteroides vulgatus (target 393196) is a founding member of a new PFAM family DUF4425 (PF14466), which will be released as a part of PFAM 26.0 release (probably).  BVU_3708 is a second member of this family, the first (2lge, 2lg7) was solved by JCSG using NMR. Interestingly, 2lge appeared to be an ORFan as BLAST was not able to find any homologs but can be matched to the same family by HHM. This relation is confirmed by structural similairty between these two proteins (see below). The structure was determined at a resolution of 1.35 Angstroms, and consists of beta-sandwich like fold.

     

     

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    monomer_view1.bmp

    Shown above is a representation of the monomeric structure of target ID 393196 (N-teminal end in blue, C-terminal end in red). The structure is essentialy composed of two five-stranded anti-parallel beta sheets that are spaced together to form a sandwich.

     

     

    dimer.bmp


    Analytical size exclusion chromatography and crystal packing suggest that the dimer (shown above) is a significant oligomerzation state in solution. A search of the PDB using with the DALI database shows only one other structure with a Z-score above 10, the NMR structure of a metal binding protein from Parabacteroides distasonis that was determined by JCSG, PDB ID 2lge. These two proteins are founding members of a new PFAM family DUF4425 (PF14466).

     

     

     

    Sho2lge_to_target.bmp

     

    Shown above is superpositioning of the structures of target ID 393196 (green) and PDB ID 2lge (purple). (DALI Z-score 13.1, rmsd 2.1 Ang, alignment length 113 amino acids). The two targets show an overall sequence identity of 13%.

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

    Ligand Summary

    Reviews

    References

     

    No references found.

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