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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
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS26593,YP_211437.1, 324049
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

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

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    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
     

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    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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