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3h3i

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

    Title Crystal structure of Putative lipid binding protein (NP_811174.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.20 A resolution. To be Published
    Site JCSG
    PDB Id 3h3i Target Id 393040
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS25259,NP_811174.1, 324995 Molecular Weight 16486.28 Da.
    Residues 149 Isoelectric Point 4.21
    Sequence acdndtepggtavekmagdwwvtvnafidgkevedpfgaghlqmstyntasnsetemwlddlgnfweyk lkvnvnyaartfsttgfvdnvtyeskvkitdgkvlekaattpsgmpadsivymvqfdddedgltykvsg frrtgfpaddf
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 3
    Resolution (Å) 2.20 Rfree 0.232
    Matthews' coefficent 2.42 Rfactor 0.187
    Waters 210 Solvent Content 49.21

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3h3i
    1. Probing Oxygen Activation Sites in Two Flavoprotein Oxidases Using Chloride as an Oxygen Surrogate
    PR Kommoju, Z Chen, RC Bruckner, FS Mathews - Biochemistry, 2011 - ACS Publications
     

    Protein Summary

    Gene BT_2261 from Bacteroides thetaiotaomicron vpi-5482 encodes the NP_811174 protein that belongs to a small family of lipid-binding proteins found in Bacteroidetes. Pfam suggests it might be a hydrolase: PF12888, Lipid-binding putative hydrolase, CL CL0058. This clan has many structures.

     

    This is a secreted protein (may be a lipoprotein also) from the human gut microbe B. thetaiotaomicron without any annotation in Pfam. It appears to be a bacteroides/humat gut-specifc protein.

    FFAS shows weak hits but statistically significant hits only to Major Urinary Protein I (PDB id 1i04, score -12.1, cyan) and to alpha-2U-globulin (PDB id 2a2g, score -10.7, magenta):

    GS_1i04.pngGS_2a2g.png

    but this protein (green) does not have the prominent helix that is present in the other two.

     Major Urinary Protein I is a lipocalin. There is only one example of a crystal structure of a bacterial lipocalin, the E. coli Blc protein (1qwd.pdb, yellow):

    GS_1qwd.png

     

    The E. coli Blc protein has longer strands in the curved beta sheet and also has the helix that is missing in this protein.

    A search for other similar structures using SSM indicates primary similarity to avidin which has many practical applications and numerous crystal structures, for example, 2a5b.pdb (~3A rmsd over 97 aligned Ca residues, ~12% sequence identity, in pink):

    GS_2a5b.png

    The avidin also does not have the helix and the curved beta sheet is very similar in size to this protein.

    Bacterial avidins are streptavidin, purified from the bacterium, Streptomyces avidinii (Ref. 1):

     

    Therefore, of all the proteins mentioned, the most structural similarity is to the avidin and streptavidin.

     

    A survey of the genomic neighborhood shows the presence of several proteins of unknown function and an outer membrane protein.

     

    Further analysis of this structure will be done toward a more detailed description at a later date.

     

    References:

    1.Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation, W A Hendrickson, A Pähler, J L Smith, Y Satow, E A Merritt, and R P Phizackerley

    Ligand Summary

    Reviews

    References

     

    No references found.

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