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3nuz

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

    Title Crystal structure of a putative acetyl xylan esterase (BF1801) from Bacteroides fragilis NCTC 9343 at 2.30 A resolution. To be published
    Site JCSG
    PDB Id 3nuz Target Id 393240
    Molecular Characteristics
    Source Bacteroides fragilis nctc 9343
    Alias Ids TPS26593,YP_211437.1, 324049 Molecular Weight 45781.12 Da.
    Residues 397 Isoelectric Point 8.61
    Sequence aqsdgwspkdhnliksvredgrflssygvvhamlrntepryafhrdfspkefrkwqkglrhameeimkf pqiknspapvcikreqregyrlekwefyplpkcvstflvlipdninkpvpailcipgsggnkeglagep giapklndrykdpkltqalnfvkegyiavavdnpaageasdlerytlgsnydydvvsryllelgwsylg yasyldmqvlnwmktqkhirkdrivvsgfslgtepmmvlgtldtsiyafvyndflcqtqeraevmtmpd kngrrpfpnsirhlipdfwknfnfpdivaalaprpiilteggldrdldlvrkayaivgtpdnvkiyhyk kfsdpdtrknveylpegldrneyfrmvnvdgpnhyfkselvvpwlrklleer
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 6
    Resolution (Å) 2.30 Rfree 0.182
    Matthews' coefficent 2.66 Rfactor 0.152
    Waters 254 Solvent Content 53.80

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3nuz
    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
     
    2. Tetartohedral twinning could happen to you too
    P Roversi, E Blanc, S Johnson - Section D: Biological , 2012 - scripts.iucr.org
     

    Protein Summary

    Structure of a human gut bacteria putative PUL protein reveals a glycan modification acetyl esterase

    (Pfam update: On building, this overlapped immediately with Peptidase_S15 PF02129, Abhydrolase_5 PF12695, Abhydrolase_6 PF12697 and BAAT_C PF08840)

    This protein is annotated as a putative acetyl xylan esterase protein, possibly due to the next closest FFAS hit with PDB 1v1q (15% seq id).

    However, this is likely to be a human gut symbiont putative PUL protein that is actually a glycan modification acetyl esterase.

    B. thetaiotaomicron has 88 PULs (Polysaccharide Utilization Loci), including 866 genes, ~18% of its genome (Ref1).
    PULs characterized by presence of SusC/SusD proteins and contain glycan-degrading enzymes. 
    Some PULs also encode enzymes for removal of glycan modifications (e.g. the sulfatase and acetyl esterase), which is likely a prerequisite step in degrading the underlying backbone (Ref1).
     
    This protein is in SusD gene locus and crystal structure reveals it to be esterase-like. 
    So this is likely to be a PUL glycan modifying acetyl esterase.

     
    Pfam CL0028:AB_hydrolase (CL0028), Alpha/Beta hydrolase fold

    JCSG has solved another similar structure of a protein annotated as a SusD/RagB-associated esterase-like protein PDB ids 3g8y (~68% seq id) which is described here. Structural comparisons made with other esterases, but connection to PUL and specific functional implication not done for 3g8y.

    There are 6 molecules in the asymmetric unit that form 3 dimers:

    Fig1.png

    Structure of dimer:

    Fig1dimer.png

    Location of active site (superposed on 1v1q in cyan):

    Fig2activesite.png

    Zoom of active site (1v1q in cyan and blue): Putative active site residues are Ser256, Asp279 and His398.

    Fig3activezoom.png
     

    References:

    1. Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm”
    J Biol Chem. 2009 Sep 11;284(37):24673-7 , Martens EC, Koropatkin NM, Smith TJ, Gordon JI. 
     

    Ligand Summary

    Reviews

    References

     

    No references found.

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