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The Open Protein Structure Annotation Network
PDB Keyword
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3g8y

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

    Title Crystal structure of SusD/RagB-associated esterase-like protein (YP_001301335.1) from Bacteroides vulgatus ATCC 8482 at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 3g8y Target Id 393239
    Molecular Characteristics
    Source Bacteroides vulgatus atcc 8482
    Alias Ids TPS24857,YP_001301335.1 Molecular Weight 44613.83 Da.
    Residues 390 Isoelectric Point 6.36
    Sequence yqpekhavvksdrgdgrllstyaivhemlkdthpqyayrsgmsaqeftqwqdgvraamveimkfpeikr qpspvcvktekkegyilekwefypfpksvstflvlkpehlkgavpgvlcipgsgrtkeglvgepgicdk ltedynnpkvsmalnmvkegyvavavdnaaageasdlecydkgwnydydvvsrfllelgwswlgytsyl dmqvlnwmkaqsyirkdrivisgfslgtepmmvlgvldkdiyafvyndflcqtqeravvmtkpdkenrr pfpnsirhlipgywryfnfpdvvaslaprpiifteggldrdfrlvqsayaasgkpenaefhhypkfadk avrkdvehldegldsktyfeavnvdppshyfknelvipwlrkvlk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.90 Rfree 0.209
    Matthews' coefficent 2.97 Rfactor 0.168
    Waters 472 Solvent Content 58.61

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3g8y
    1. Structure of the catalytic domain of glucuronoyl esterase Cip2 from Hypocrea jecorina
    PR Pokkuluri, NEC Duke, SJ Wood - Proteins: Structure, , 2011 - Wiley Online Library
     

    Protein Summary

    pfam note: This family overlapped with alpha-beta hudrolases, so I have
    ID Abhydrolase_7
    AC PF12715 and it put it into the same clan as other abhydrolases.

     

     

    Gene BVU_4111 from Bacteroides vulgatus ATCC 8482 encodes the YP_001301335 protein. A PSI-BLAST search using the NCBI database can not provide any hit other than hydrolases with ~22% seq.id.   No Pfam assignment is available for this protein.

    The YP_001301335 and the SusD/RagB family (Pfam:PF07980) proteins are encoded in the same genomic neighborhood. Other homologs of YP_001301335 encoded in similar neighborhood are emb:CAH07500.1 from Bacteroides fragilis NCTC 9343 and dbj:BAD48462.1 from Bacteroides fragilis YCH46.

    YP_001301335 has a predicted signal peptide (cleaved at position #17: SVCSL-CMVGN) and may be a bacterial lipoprotein. LipPred servers predicted signal peptides in YP_001301335 homologs (ABR41713, ZP_03299337, YP_098996) and ABR41713 is a lipoprotein, while ZP_03299337 and YP_098996 as non-lipoproteins.

    Pre-SCOP classifies 3g8y in the alpha/beta class, alpha/beta hydrolases superfamily. FFAS, SSM and Dali searches indicate that 3g8y is a structurally similar to esterases 1vlq and 3fvt (Z=19), and deacetylases, such as 1ods (Z=18), 2RAU (Z=17), and 1UFO (Z=16). The crystal interface interaction suggests that the biomolecule of protein YP_001301335.1  could be a dimer. In the current 3g8y model, there is an unknown electron density  near the conserved residues Ser  256, Asp 394 and His 398. Therefore, 3g8y, a SusD/RagB-associated esterase-like protein, has thioesterase-like residues in its putative active site cleft (Ser256, Asp394, and His398). However, the Asp394 side chain is in a different conformation compared to known thioesterases (i.e. PDB:1eh5).

     

     

    393239_1.png

     

    Figure 1. The 3g8y structure carries the conserved residues Ser 256, Asp 394 and His 398 for a putative hydrolase activity.

     

    393239_2.png

     

    Figure 2. Based on the 3g8y crystal interface interaction, the biomolecule of YP_001301335 could be a dimer based.

     

     

    393239_3.png

     

    Figure 3. 3g8y (green) is structurally similar to deacetylases 1JFR (Red), 1UFO (gray; Z=16) and 2RAU (blue; Z=17).

    Ligand Summary

    Reviews

    References

     

    No references found.

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