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The Open Protein Structure Annotation Network
PDB Keyword
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3lm3

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

    Title Crystal structure of PROTEIN OF UNKNOWN FUNCTION (YP_001304447.1) from Parabacteroides distasonis ATCC 8503 at 1.44 A resolution. To be published
    Site JCSG
    PDB Id 3lm3 Target Id 394748
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS25834,YP_001304447.1 Molecular Weight 51831.97 Da.
    Residues 448 Isoelectric Point 5.84
    Sequence aadpvvvpanmepltiegnrfvtlcimirttpwevsrdvklhprdevdwhtlegvralreafatnnpng rltwgftmnaledgrknyreirdyvvecqkkygdevtyfpgyfpamylprervnremseaieiiskmvg ngyrpqsimggflsadnlrylaekenihvahaviwsqhnidgggadgspsypfypstehfckpaqgksd fidcvnldgwtmdficarrsgqtghgidgynsrrgvgpietykgwgldlghrevmhteaihfdkgleln gfgwvaniweaqmvhefgkdlicdamkmwvtgtkerwpdthfvtfgefgelwrkqyksnddwnyrfver gsglgdsynnleikwfmnkefrlallrdwhtknspayvidftrydlqahepadpspekpakdwslinki nqkalrpqdkpvlidklekedqdlirkyypellk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.44 Rfree 0.160
    Matthews' coefficent 2.20 Rfactor 0.141
    Waters 569 Solvent Content 44.16

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3lm3

    Protein Summary

    BDI_3119 gene from Parabacteroides distasonis atcc 8503 encodes the YP_001304447 protein that belongs to a very small protein cluster (four homologs in finished genomes, ~8 in metagenomics samples) within a larger (~50 members) new protein family of hypothetical proteins highly overrepresented in gut microbes. Interestingly it includes, both Gram negative (gut and environmental Bacteroidetes) and Gram positive (Clostridia, E. rectale) bacteria. The genomic neighbor of BDI_3119 (BDI_3118) is a typical representative of this new family; therefore BDI_3119 and BDI_3118 form a pair of (very divergent) paralogs, which are part of a P. distastonis probable polysaccharide utilization operon (SusC-homolog, SusD-homolog, BDI_3119, BDI_3118, beta-galactosidase, beta-galactosidase).

    Pre-SCOP classifies 3lm3 temptatively inside the metallo-dependent hydrolases superfamily, hydantoinase catalytic domain family. The 3lm3 structure contains two domains, the N-terminal seven stranded alpha/beta barrel (it looks like an unfinished TIM barrel) that are found in glycoside hydrolase/deacetylases (eg: the allantoinase PDB:3cl7, PDB:1z7a, with a score Z=19.0, the glucanotransferase PDB:1k1y [Z=17], or the alpha-amylase PDB:2b5d [Z=15]). The C-terminal domain contains a alpha-beta(4)-alpha structural motif that is found in many proteins, but its functional role is not clear. The active site residues of the puuE allantoinase 3cl7 are not conserved in 3lm3, suggesting the function of BDI_3119 is likely different.

     

     

     

    Fig 1. 3lm3 structure

    gs13565a.png

    Fig 2. Structure superposition of 3lm3 with 3cl7

    gs13565a-vs-1cl7.png

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page

    Files (2)

    FileSizeDateAttached by 
     gs13565a-vs-1cl7.png
    gs13565a vs 1cl7
    200.15 kB20:25, 25 Jan 2010qxuActions
     gs13565a.png
    gs13565a monomer
    196.42 kB23:45, 22 Jan 2010qxuActions
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