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The Open Protein Structure Annotation Network
PDB Keyword
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3i4g

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

    Title Crystal structure of SusD-like carbohydrate binding protein BF1063 from Bacteroides fragilis YCH46 (YP_210668.1) from Bacteroides fragilis NCTC 9343 at 1.35 A resolution. To be published
    Site JCSG
    PDB Id 3i4g Target Id 396566
    Molecular Characteristics
    Source Bacteroides fragilis nctc 9343
    Alias Ids TPS25933,YP_210668.1, BIG_773 Molecular Weight 60173.15 Da.
    Residues 527 Isoelectric Point 5.17
    Sequence cdlerypltdlseetfwnsesnaelaltslyrgsltdgveynpsdwwsyhgmimmehlsdnafdrrgen npffkissgnltadnafikrywetsykrigycnrflvgiqnssesekktrmiaearflratqyfylasy fknvplvenvltgeeannvtktsqadilkwcvteftaaaadlprfsaipageagrackqaalaflgrtc mlqkdwksgakafhdimelgdnainanyqelfypstgtsnkenifyiqylenylgtglpqhalsakdgg wslvnpaadlyesyefkdgtpfsyddprydpsnlgkdrdprldytiyyngaifmgteykmspdysaakk ekldytseasrtgfmmrkyfeestpindvqsangltpviryaevllgyleclvednqtitqgildetin avrgrasvnmppvtevtpaklreivrherrielamegirywdimrwgiahevlsqkiwgapypgstqya tttkevdptgnyrwyvgkrafrnptdytwpipqseqninpnlrd
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.35 Rfree 0.157
    Matthews' coefficent 2.12 Rfactor 0.138
    Waters 752 Solvent Content 41.86

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Bacteroides species are anaerobic bacteria with predominant components of the bacterial florae of mucous membranes.   Unlike to E. coli which can grow both with and without oxygen, but both Bacteroides  and Bacteroides can be found in the same place: the intestine.  Because of the bacterial florae of mucous membranes, Bacteroides usually case endogenous infections and develop in all body sites, including the CNS, the head, the neck, the chest, the abdomen, the pelvis, the skin, and the soft tissues. Unfortunately, the Bacteroides are very good at finding ways to become resistant to all of the antibiotics that we use so developing new ways to fight the bugs is a great importance. 
     
    The B fragilis group, a member of the Bacteroidaceae family, includes B fragilis (causes the most clinical infections), Bacteroides distasonis, Bacteroides ovatus, Bacteroides thetaiotaomicron, and Bacteroides vulgatus. These bacteria are resistant to penicillins, mostly through the production of beta-lactamase. They are part of the normal GI florae and predominate in intra-abdominal infections and infections that originate from those florae. Enterotoxigenic B fragilis (ETBF) is also a potential cause of diarrhea.
     
    Gene BF0978 from Bacteroides fragilis nctc encodes the YP_210668 protein with 546 residues.  This target has been annotated as Putative outer membrane protein probably involved in nutrient binding.  The NCBI blast classifies YP_210668 inside the SusD superfamily. Dali search indicates that this target is a structural homolog to SusD protein, essential for starch binding and utilization by Bacteroides thetaio-taomicron, a prominent adaptive forager of glycans in the distal human gut mcirobiota. 

    3i4g structure has an α-helical fold mainly comprising of α helices, four sets of 2-stranded antiparallel β sheet, and multiple reverse turns. Based on structural similarity to 3CK7, 3i4g also carries an arc-shaped binding pocket, which it complements the helical structure of starch and imposes this conformation on bound maltoheptose as seen in 3CK7. A MES buffer molecule is founded in this conserved arc-binding pocket. 
     

    396566_1.png

    Figure 1.  3i4g monomer has a similarlly shaped putative active site as an arch for binding starch, as in its structural homolog 3CK7. The protein is a monomer.

     

     

    396566_2.png

    Figure 2. The biomolecule of 3i4g (green) is a structural homolog to 3CK7.

     

    396566_3.png

     

    Figure 3.  In 3i4g (green),  the arc-shape is not as hydrophobic as in its structural homolog 3CK7.

     

    Reference,

     

    1.  Koropatkin, N.M.,  Martens, E.C.,  Gordon, J.I.,  Smith, T.J. (2008) Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices. Structure 16: 1105-1115

     

    Ligand Summary

    MES buffer anion

    Reviews

    References

     

    No references found.

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