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3urz

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

    Title Crystal structure of a hypothetical protein (BACOVA_03105) from Bacteroides ovatus ATCC 8483 at 2.19 A resolution. To be published
    Site JCSG
    PDB Id 3urz Target Id 416729
    Molecular Characteristics
    Source Bacteroides ovatus atcc 8483
    Alias Ids TPS33827,ZP_02066110.1, 327419 Molecular Weight 24152.33 Da.
    Residues 207 Isoelectric Point 9.02
    Sequence qsvdemlqkvsaaieagqngqavsyfrqtialnidrtemyywtnvdknseissklatelalaykknrny dkaylfykellqkapnnvdcleacaemqvcrgqekdalrmyekilqleadnlaaniflgnyyyltaeqe kkkletdykklssptkmqyaryrdglsklfttryekarnslqkvilrfpsteaqktldkilriekevnr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.19 Rfree 0.2397
    Matthews' coefficent 3.08 Rfactor 0.2173
    Waters 55 Solvent Content 60.12

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3urz

    Protein Summary

    The  hypothetical protein protein BACOVA_03105 (ZP_02066110.1) is a divergent member of PFAM PF07719(the match is below PFAM significance threshold), so it could possibly be a new family in the TRP clan. This particular subfamily of TRP repeat proteins is typical for human gut, but also for environmental Bacteroidetes. None of the proteins in this sub-family was studied experimentally for its function.

    The monomer structure is shown below.

    SP16541B.png

     

    There are two monomers in the crystallographic asymmetric unit. Each monomer binds two Zinc atoms (magenta spheres in figures above and below). The coordination of each Zn atoms is provided by two monomers, shown below.

    SP16541B_ZN250.png SP16541B_ZN260.png

     

    There are over 1000 solved structures with TRP repeats, not surprisingly PDB BACOVA_03105 structure picks up a lot of hits in structure similarity searches. The top 10 DALI hits are shown below.

    N PDB Z-score RMSD LALI NRES %ID Description
    1 2vgy 10.8 2.4 122 132 14 Chaperone Sycd
    2 2q7f 10.8 4.6 157 194 14 Yrrb Protein
    3 2e2e 10.8 3.4 135 171 17 Formate-dependent Nitrite Reductase Complex Nrfg
    4 3hym 10.6 4.4 154 301 12 Anaphase-promoting Complex Subunit Cdc26
    5 3ks2 10.5 3.2 123 137 19 Chaperone Protein Ipgc
    6 2vgx 10.4 2.4 115 134 14 Chaperone Sycd
    7 3gyz 10.3 2.6 118 143 19 Chaperone Protein Ipgc
    8 2hyz 10.3 3.6 132 136 24 Synthetic Consensus Tpr Protein
    9 3pe3 10.2 4.9 147 701 16 Udp-n-acetylglucosamine--peptide N-
    10 1fch 10.1 3.7 142 297 14 Peroxisomal Targeting Signal 1 Receptor

     

     

     A superposition of this protein (green) over 2vgy (blue) indicates the similarities between them.

    SP16541B_2vgy.png

    However, 2vgy does not have any metal bound to it.

     

    Interestingly, all the top hits in structural similarity are involved in protein-protein interactions, Yrrb in peptide binding with a unsusual peptide binding cavity - is it conserved here?

     

    What do you think about these unusual (for a TRP repeat protein) elongated helices at the C-terminal. They are used to form contacts with the second molecule in the crystallographic dimer.

     

    Most TRP structures are curved with a "supertwist". Ours appears unusually straight. I'm not clear what it means.

    Ligand Summary

    Reviews

    References

     

    No references found.

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