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3qc2

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

    Title Crystal structure of a glycosyl hydrolase (BACOVA_03624) from Bacteroides ovatus at 2.30 A resolution. To be published
    Site JCSG
    PDB Id 3qc2 Target Id 416748
    Molecular Characteristics
    Source Bacteroides ovatus atcc 8483
    Alias Ids TPS33834,ZP_02066624.1, 333097 Molecular Weight 40958.09 Da.
    Residues 363 Isoelectric Point 8.13
    Sequence qssnhkenklpdwafggferpknvnpvispientkfycpltkdsiawesndtfnpaatlyngeivvlyr aedksgvgighrtsrlgyatstdgthfqrektpvfypdndsqkelewpggcedpriavtddglyvmmyt qwnrhvprlavatsrnlkdwtkhgpafakafdgkffnlgcksgsiltevvkgkqvikkvngkyfmywge ehvfaatsddlihwtpivnidgslkklfsprdgyfdshltecgppaiytpkgivllyngknhsgrgdkr ytanvyaagqalfdandptrfitrldepffrpmdsfeksgqyvdgtvfiegmvyfknkwylyygcadsk vgvavydpkrpakadplp
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.30 Rfree 0.2241
    Matthews' coefficent 2.66 Rfactor 0.1844
    Waters 346 Solvent Content 53.76

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3qc2

    Protein Summary

    Target ID 416748 from the gut bacterium Bacteroides ovatus can be classified as belonging to the Domain of Unknown Function (DUF377) (PF04041) Pfam Family. This family is represented by another JCSG structure, PDB ID 1vkd, a hyoptherical protein from Thermotoga maritima. Although the exact function of members of DUF377 (PF4041) is not known, members of this Pfam family are believed to be glycosidases. Shown below is a ribbons representation of the structure of target ID 416748 with the N-terminal end in blue and the C-terminal end in red.

     

    monomer.png

    The overall structure resembles a five-bladed beta propeller-like SCOP fold, Furthermore, based on structural similarity to PDB ID 1vkd, target ID 416748 most likely is a member of the arabinanase/levansucrase/invertase Superfamily. A DALI search shows that target ID 416748 has structural similarity to the following PDB entries:

     

    PDB ID
    Description
    DALI Z-Score rmsd (Ang) length of alignment
    number of residues in related target
    % sequence id Citation
    1vkd Predicted Glycolase (TM1225) from Thermotoga Maritima 31.1 2.5 274 326 26 Joint Center for Structural Genomics
    3k1u Beta-xylosidase, family 43 glycosyl hydrolase from Clostridium acetobutylicum 22.6 3.0 258 319 12 Midwest Center for Structural Genomics
    3aki exo-1,5-alpha-L-arabinofuranosidase complexed with alpha-L-arabinofuranosyl azido 22.5 3.0 259 448 14 Fujimoto Z et al.J Biol Chem (2010) [Ref]
     2b4w Hypothetical protein from leishmania major  22.0  3.0  255  292  15 Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
     3kst Endo-1,4-beta-xylanase (NP_811807.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482  21.3  2.5  239  291  14 Joint Center for Structural Genomics
     3c7f  glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase from bacillus subtilis in complex with xylotriose.  21.3  3.0  262  487  16  Vandermarliere et al. Biochem J. (2009) ([Ref]
     1yrz  xylan beta-1,4-xylosidase from Bacillus Halodurans C-125  21.1  2.7 245  522 13  Federov AA. et al. (unpublished)
     2ac1  cell-wall invertase from Arabidopsis thaliana  20.9  3.1  258  537  18 Verhaest, M. et al. Acta Cryst D (2006) [Ref]

     

    Ligand Summary

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