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3k11

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

    Title Crystal structure of Putative glycosyl hydrolase (NP_813087.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.80 A resolution. To be Published
    Site JCSG
    PDB Id 3k11 Target Id 396201
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS25879,NP_813087.1, 326095 Molecular Weight 50219.26 Da.
    Residues 444 Isoelectric Point 5.63
    Sequence kkavindsntplhllqpayqgtygdltpeqvkkdidrvfayidketparvvdkntgkvitdytamgdea qlergafrlasyewgvtysaliaaaettgdkrytdyvqnrfrflaevaphfkrvyeekgktdsqllqil tphalddagavctamiklrlkdeslpvdgliqnyfdfiinkeyrladgtfarnrpqrntlwlddmfmgi pavaqmsrydkeaknkylaeavkqflqfadrmfipekglyrhgwvesstdhpafcwarangwalltace lldvlpedypqrpkvmdyfrahvrgvtalqsgegfwhqlldcndsyletsataiyvyclahainkgwid aiaygpvaqlgwhavagkineegqvegtcvgtgmafdpafyyyrpvnvyaahgygpvlwagaemirlln tqhpqmndsavqyyqekqkttapifavdse
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.80 Rfree 0.171
    Matthews' coefficent 3.81 Rfactor 0.150
    Waters 469 Solvent Content 67.72

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3k11
    1. Quantum efficiency of the minor channel for excitation migration from B800 to B875 bacteriochlorophyll fractions in purple bacteria
    AY Borisov, AP Gaydukova - Supplemental Series A: Membrane and Cell , 2009 - Springer
     

    Protein Summary


    Gene BT_4176 from Bacteriodes thetaiotaomicron vpi-5482  encodes the NP_813087.1 protein with 465 residues and an isoelectric point of 5.83. The NCBI blast sequence alignment indicates that this protein contains a conserved domain belonging to the glycosyl hydrolase 88 family (PF07470). 

    Pre-SCOP classifies 3k11 in the all alpha class, six-hairpin glycosidases superfamily, YteR protein family.

    A structural similarity search via SSM and Dali sever show that 3k11 is a structurally related to the YteR proteins (2gh4, 2d8l, and 1nc5 with Z-scr=43) and to the unsaturated glucuronyl hydrolase (2d5j, Z-scr=28) with conserved putative active site, consisting of Arg286, Trp290, Asp 222 and Ser347. An ethylene glycol molecule from crystallization is modeled in the active site. The interface interaction suggests that the biomolecule of 3k11 is a trimer.  
     

     

     

    396201_1.png

    Figure 1. Structure 3k11 mainly consists of helices with a conserved putative active site formed by: Arg286, Trp290, Asp 222 and Ser347.

     

     

    396201_2.png

    Figure 2. Biomolecule of 3k11 may be a trimer.

     

     

     396201_3.png

     Figure 3. The 3k11 putative active site with conserved residues.

     

     

    Reference,


    Zhang R, Minh T, Lezondra L, Korolev S, Moy SF, Collart F, Joachimiak A. "1.6 A crystal structure of YteR protein from Bacillus subtilis, a predicted lyase." Proteins. 2005 60(3):561-5

    Ligand Summary

    Reviews

    References

     

    No references found.

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