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3gyc

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

    Title Crystal structure of putative glycoside hydrolase (YP_001304622.1) from Parabacteroides distasonis ATCC 8503 at 1.85 A resolution. To be published
    Site JCSG
    PDB Id 3gyc Target Id 394744
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS25354,YP_001304622.1 Molecular Weight 46183.39 Da.
    Residues 392 Isoelectric Point 5.34
    Sequence aksemafagkgeispraitmwdfswlerrwpgagyedwdqvldelsergynairidayphliaenpmkk wllkevwnqqdwgspdmnevqvqpnlnlflskckerdikvglsswyrldvdevclkldtpekladcwlt ilrsieedglldtilyvdlcnewpgdswapffaktypnvgwgnwykeeslrwmktslekmrqvypdmpf lysfdhgdvkkyeevdcsfldlyehhiwmaqqnggefyklvgygynrflpddyknvvknaervyrerpg ywqklltdkielmasvarknrrplvttecwglvdykdwpllkwdwvkdlcelgtitaartgmwvgvats nfcgpqfagmwrdvewhkrltsiirsspldesltknnevaakllkrl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.85 Rfree 0.205
    Matthews' coefficent 2.12 Rfactor 0.169
    Waters 417 Solvent Content 42.08

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3gyc
    1. Distributed structure determination at the JCSG
    H van den Bedem, G Wolf, Q Xu - Section D: Biological , 2011 - scripts.iucr.org
     

    Protein Summary

    Pfam update: sugar-binding family as it overlapped quite soon with cellulases: Cellulase-like, PF12876, Sugar-binding cellulase-like, CL CL0058.This is a putative cellulase family.

    This is a secreted protein of unknown function from a human gut bacteria with an N-terminal signal sequence that was removed from the cloned construct used for structure determination.

    It has not been assigned to any Pfam family. There are no conserved domains according to the Conserved Domain Database and PSI-BLAST indicates that this is a singleton protein.

    It is present as a dimer in the crystal structure but the in vivo or in vitro functional oligomerization state for this protein is unknown at this time.

    Fig1.png

    There is a prominent cavity in the protein (CASTp server) which is lined with mostly aromatic residues including Phe50, Trp103, Trp108, Trp141, Trp193, Trp206, Arg81 and His260 (in red sticks):

    Fig2_cavity.png

    This could be a ligand binding site.

    Residues Glu187, Glu330 and His260 could be a metal binding site providing hydrolase activity.

    The peptide bond between Cys332 and Trp333 in this region is a cis-peptide.

    Fig2A_EEH.png

    Cis-peptides are often seen in the active site of carbohydrate binding protein.

    FFAS shows very weak similarity (scores of -10.9 and -9.8) to an endoglucanase (PDB id 2z96) and mannosidase (glycoside hydrolase family, PDB id 1uuq). A search for other proteins of similar structure indicates some similarity to a beta-glycanase (Q-score 0.24, rmsd=2.68A over 235 Ca residues, 13% sequence identity, PDB id 1cec) and several other similar proteins.

    Superimposition of this structure onto the 1cec (cyan) and 1uuq (light green) shows their similarity:

    Fig3_1CECcyan_1UUGlimon.png

    Many of the residues of this protein near the activity/putative metal binding site mentioned above are conserved in the 1cec and 1uuq structures, especially the Glu-Glu-His forming the putative catalytic triad.

     Based on this analysis including the putative active site cavity, residues and cis-pepitde bond, this protein is likely to be a novel glycoside hydrolase. The genomic neighborhood (STRING server) of this protein includes proteins involved in sugar metabolism to which it may be functionally associated and which also supports the structure-based functional annotation for this protein. Since the protein is from the human gut bacteria, it may also have some role in modulating GI tract activities.

    Ligand Summary

    Reviews

    References

     

    No references found.

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