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3on6

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

    Title Crystal structure of a Bacterial protein of unknown function (BACOVA_03626) from Bacteroides ovatus at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 3on6 Target Id 416738
    Molecular Characteristics
    Source Bacteroides ovatus atcc 8483
    Alias Ids TPS33830,ZP_02066626.1, 327421 Molecular Weight 52635.20 Da.
    Residues 460 Isoelectric Point 6.05
    Sequence itnsdfviqqdntkinnyqtnrpetskrlfvsqaveqqiahikqlltnarlawmfencfpntldttvhf dgkddtfvytgdihamwlrdsgaqvwpyvqlankdaelkkmlagvikrqfkcinidpyanafnmnsegg ewmsdltdmkpelherkweidslcypirlayhywkttgdasifsdewltaiakvlktfkeqqrkedpkg pyrfqrkteraldtmtndgwgnpvkpvgliasafrpsddattfqflvpsnffavtslrkaaeilntvnk kpdlakecttlsneveaalkkyavynhpkygkiyafevdgfgnqllmddanvpslialpylgdvkvndp iyqntrkfvwsednpyffkgtagegiggphigydmiwpmsimmkaftsqndaeiktcikmlmdtdagtg fmhesfhkndpknftrswfawqntlfgelilklvnegkvdllnsiq
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.70 Rfree 0.1663
    Matthews' coefficent 2.18 Rfactor 0.1333
    Waters 1204 Solvent Content 43.54

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3on6
    1. Analysis of a New Family of Widely Distributed Metal-independent _-Mannosidases Provides Unique Insight into the Processing of N-Linked Glycans
    KJ Gregg, WF Zandberg, JH Hehemann - Journal of Biological , 2011 - ASBMB
     

    Protein Summary

     BACOVA_03626 protein is a member of our DUF1237 family. Structures of two related proteins are already known (2nvp and 2p0v). Many of the proteins in the family have been annotated as being members of the Twin-arginine translocation pathway. However, I think this is based on the match of the sequence to the Twin-arginine translocation pathway signal peptide rather than any definitive function. Both Pfam and PIRSF have these sequences in families on unknown function. Superfamily have some of the proteins classified as belonging to their Six-hairpin glycosidases superfamily (based on the structures above). This is also confirmed by distant sequence similarity, as detected by FFAS and HHpred, to various families in the  6_Hairpin (CL0059) PFAM clan, for instance to Amylo-alpha-1,6-glucosidase (PF06202) and Plant neutral invertase (PF04863). All these proteins are classified by Carbohydrate-Active enZYmes Database or CAZy (http://www.cazy.org/) as clans GH-L and GH-M.

     DUF1237 (Pfam 06824) Pfam family contains over 260 (PFAM count) or over 860 (PSI-BLAST count on NR-60 + various metagenomics datasets) members, most of them hypothetical proteins whose function is uncertain. This Pfam family is currently represented by two other structures in the PDB. These include PDB ID 2NVP and PDB ID 2P0V, two structures determined by the Northeast Structural Genomics Consortium.

    A recent paper from Boraston group [Ref] identified DFU1237 family as a new family of glycosyl hydrolases (GH125). BACOVA_0362 and its homologs are exo-α1,6-mannosidases, specific for N-linked glycans. Cleaving this bond is a critical step in  infection by microbial pathogens and colonization by microbial symbionts. Unfortunately this effort appears to be independent of the JCSG (and other PSI centers).

     

    SP16731A_monomer.png

     

     

     

     

    Shown here is a ribbons representation of the structure of BACOVA_03626 proteins (target ID 416738_ color coded with the N-terminal end in blue and the C-terminal end in red. The structure of target ID is similar to those found in the alpha/alpha torid SCOP fold belonging to the six-harpin glycosidases SUPERFAMILY.

     

     

     

     

     

    dimer.png

     

     

    Shown here is a ribbons representation of the predicted dimer for target ID 416738 with the individual monomers colored in blue and yellow. Analytical size exclusion chromatography with static light scattering supports the assignment of a dimer as a significant oligomerization state.

     

     

     

     

     

     

     

     

    A DALI search reveals that target ID 416738 has structural similarity to the following targets. The sequence and structural similarity  betwen target ID 416738 and several glucoamylases suggests protein BACOVA_03626  (target ID 416738) is also a glucoamylase.

     

    PDB ID
    DALI Z-score
    length of alignment
    number of residues in PDB ID
    % sequence identity
    rmsd overlap (Angstroms)
    Description
    Citation
    2P0V_A 70.9 443 443 95 0.3 Crystal structure of BT3781 protein from Bacteroides thetaiotaomicron, Northeast Structural Genomics Target BtR58  
    2NVP_A 57.1 421 430 44 1.2 X-Ray Crystal Structure of Protein CPF_0428 from Clostridium perfringens. Northeast Structural Genomics Consortium Target CpR63.  
    1LF6_A 31.3 342 674 13 2.9 CRYSTAL STRUCTURE OF BACTERIAL GLUCOAMYLASE [Ref]
    1UG9_A 29.9 348 1019 12 3.0

    Crystal Structure of Glucodextranase from Arthrobacter globiformis I42

     
    [Ref]
    1LF9_A 27.7 343 674 13 2.9 CRYSTAL STRUCTURE OF BACTERIAL GLUCOAMYLASE COMPLEXED WITH ACARBOSE
     
    [Ref]
    1AYX_A 27.3 338 492 12 2.9

    CRYSTAL STRUCTURE OF GLUCOAMYLASE FROM SACCHAROMYCOPSIS FIBULIGERA AT 1.7 ANGSTROMS

     
     
    [Ref]
    2F6D_A 24.8 338 492 12 2.9 Structure of the complex of a glucoamylase from Saccharomycopsis fibuligera with acarbose [Ref]
    1V7X_A 24.6 350 779 11 3.8 Crystal structure of Vibrio proteolyticus chitobiose phosphorylase in complex with GlcNAc and sulfate [Ref]
    1AGM_A 24.3 321 470 12 2.8 Refined structure for the complex of acarbose with glucoamylase from Aspergillus awamori var. x100 to 2.4 angstroms resolution [Ref]

     

     

     

     

    Ligand Summary

    Reviews

    References

     

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    Files (2)

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     dimer.png
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    268.64 kB16:34, 27 Aug 2010haxelrodActions
     SP16731A_monomer.png
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    251.34 kB16:31, 27 Aug 2010haxelrodActions
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