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The Open Protein Structure Annotation Network
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3u7z

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

    Title Crystal structure of a putative metal binding protein RUMGNA_00854 (ZP_02040092.1) from Ruminococcus gnavus ATCC 29149 at 1.30 A resolution. To be published
    Site JCSG
    PDB Id 3u7z Target Id 417407
    Molecular Characteristics
    Source Ruminococcus gnavus atcc 29149
    Alias Ids TPS45767,ZP_02040092.1, 324509 Molecular Weight 11010.20 Da.
    Residues 100 Isoelectric Point 3.91
    Sequence asegekhitvtvihgdqtenvfefdtdakylgevlesenlvdgesgeyglfittvdeetaddskqqwwc itkggeqvntsadqtpvsdgdafeltlkegy
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.30 Rfree 0.1887
    Matthews' coefficent 1.83 Rfactor 0.1379
    Waters 172 Solvent Content 32.85

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

     RUMGNA_00854 protein matches to the "lid domain" of gastric intrinsic factor (2BB6 and 2PMV), according to FFAS and HHPRED. This structure was solved using 2BB6 as a search template, despite very low sequence identity (<15%). The structure is highly conserved (1.3A rmsd for 86 aa). The residues involved in substrate binding in the homolog 2BB6 are not conserved in this structure.

     

    There is an unusual interaction between Cys100 and Lys128 (distance SG/NZ ~2.5A), likely suggesting some kind of reaction intermediate (?). The active site like enviroment near C100 could be an artifact of crystal packing.

     

    Many Ca2+ ions near acidic residues on the protein surface.

     

    Fig. 1 Monomer

    sp17946a.png

     

    Fig. 2 Cys100 and Lys128

    c100k128-sp17946a.png

     

    In papers describing 2BB6 and 2PMV papers this domain was said to have a novel fold. Strangely, despite being solved over 5 years ago, neither if these domains was classified in SCOP or CATH. Structure alignment suggest that it has a beta-Grasp-like fold ( RUMGNA_00854 in green, beta-Grasp (ubiquitin-like) domain from Hypothetical protein MTH1743 in red) - 2.65Å over 67 aa with 15% seq id

     

    SP17946.png

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page

    Files (3)

    FileSizeDateAttached by 
     c100k128-sp17946a.png
    sp17946A c100-k128
    189.96 kB22:40, 3 Oct 2011qxuActions
     SP17946.png
    beta-Grasp (ubiquitin-like) domain from Hypothetical protein MTH1743
    83.56 kB22:49, 14 Oct 2011adamActions
     sp17946a.png
    sp17946A
    96.45 kB22:31, 3 Oct 2011qxuActions
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