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3hbk

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

    Title Crystal structure of putative glycosyl hydrolase, was Domain of Unknown Function (DUF1080) (YP_001302580.1) from Parabacteroides distasonis ATCC 8503 at 2.36 A resolution. To be published
    Site JCSG
    PDB Id 3hbk Target Id 394752
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS25838,YP_001302580.1, 325883 Molecular Weight 27030.82 Da.
    Residues 244 Isoelectric Point 5.42
    Sequence teetakvvpmavitpainqltdqekaegwallfdgkttkgwrgahkdafpdhgwmvkdgelivqksdgs estnggdivtegeysafefsvdfkitegansgikyfvteqekqkgsayglefqllddakhpdaklyttf pgsrtlgslydlkksenihfngvgewntavvkvfpnnhvehwlngvkvleyergskefrdlvkgskyad psynaggafgeapkghillqdhgdevafrnikvkelk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.36 Rfree 0.245
    Matthews' coefficent 2.86 Rfactor 0.198
    Waters 77 Solvent Content 56.99

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Pfam Update: This protein is now in family PF06439.4 DUF1080 CL0004 Glycosyl hydrolase along with other structures.

     

    Gene BDI_1195 from Parabacteroides distasonis ATCC 8503 encodes the YP_001302580 amino acid sequence belonging to the DUF1080 group (PF06439). This bacterium is one of the most common fecal isolates.

     

    3hbk structure was determined at a resolution of 2.36 Angstroms by Se-Met multiwavelength anomalous dispersion. The construct used to generate protein for crystallization contains residues 29-268. Electron density for the first ten residues at the N-terminal end of the protein is disordered, and this region could not be modeled. The crystal structure indicates that a monomer is a significant oligomerization state in solution.

     

    Shown below are ribbon representations of the structure of 3hbk color coded with the N-terminal end in blue and the C-terminal end in red. Each image shows the structure from two different viewpoints. The core of the protein can be described as a jelly-roll-like structure, with the two core beta sheets surrounded by some short helices and several loops.

     

    monomer_view1.png

     

    monomer_view2.png

    Using 3hbk as query, DALI provides as top hits 3h3l (Z-scr=28), 3imm (Z-sr=20), 1oq1 (Z-scr=14), and 1mac (Z-scr=13).

    A secondary structure match from the Profunc server shows that the structure of 3hbk is similar to the following structures:

    RMSD(Ang) Seq ID    PDB ID           Structure Description

         2.31      23.6%       1mac     bacillus macerans endo-1,3-1,4-beta-glucanase
         2.49      22.9%       1u0a      beta-1,3-1,4- endoglucanase h(a16-m) in complex with beta-glucan tetrasaccharide
         2.46      22.4%       1glh      Cation binding to a bacillus (1,3-1,4)-beta-glucanase.
         2.40      20.1%       1gbg      Bacillus licheniformis beta-glucanase
         2.43      18.9%       1byhA    Molecular and active-site structure of a bacillus (1-3,1-4)- beta-glucanase
         2.53      22.4%       2ayhA     hybrid bacillus endo-1,3-1,4-beta-d-glucan 4- glucanohydrolase h(a16-m)
         2.50      19.0%       2a6wA    Crystal structure of emp46p carbohydrate recognition domain (crd), metal-free form
         2.53      16.7%       2yxsA     n-terminal domain of human galectin-8 with d-lactose
         2.61      18.7%       2a6vA      emp46p carbohydrate recognition domain (crd), potassium-bound form
         2.64      16.6%       2yv8A      Crystal structure of n-terminal domain of human galectin-8

    The top scoring structure from this similarity search, PDB ID 1mac, is a endo-1,3-1,4-beta glucanase (EC 3.2.1.73). This class of enzyme hydrolyzes beta 1,4 linkages adjacent to beta-1,3 linkages in polymeric carbohydrates.

     

    Shown below is a superposition of the alpha-carbon traces for the structures of 3hbk(green) and PDB ID 1mac (blue), an endoglucanase from Bacillus macerans. Both structures show a common jelly-roll structural core.

    394752_1mac_overlap.png

     

     Comparisons of the structure of 3hbk with that of 1mac, indicates the position of the putative active site. This comparison shows that the structure surrounding the putative active site of 3hbk is different from the structure of the active site region of 1mac. However, this comparison allows us to identify specific residues in 3hbk that are likely important for function.

     

    Shown below is a representation of the structure at the putative active site of 3hbk. A sulfate from the crystallization (SO4) and an ethylene glycol (EDO) from the crystallization/cryogen solutions were modeled into the structure. An acidic sidechain (Glu 145) is positioned at the center of the putative active site region.

    putative_active_site.bmp

     

     

    References

    Hahn, M., Olsen, O., Politz, O., Borriss, R., and Heinemann, U. (1995) J. Biol. Chem. Vol 270,No 7 pp. 3081-3088

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page

    Files (6)

    FileSizeDateAttached by 
     394752_1mac_overlap.png
    least quares overlap with PDB ID 1mac
    231.25 kB01:20, 5 Apr 2009haxelrodActions
     active_site_overlap2.bmp
    Comparison of GS13641A (green) and GS13641(cyan) putative active sites.
    994.98 kB21:27, 13 May 2009haxelrodActions
     GS13641A_GS13645A_overlap.png
    No description
    194.33 kB19:35, 13 May 2009haxelrodActions
     monomer_view1.png
    Ribbons representation-monomer view 1
    148.89 kB00:14, 5 Apr 2009haxelrodActions
     monomer_view2.png
    Ribbons representation-monomer view 2
    159.71 kB00:14, 5 Apr 2009haxelrodActions
     putative_active_site.bmp
    putative active site
    1525.93 kB02:44, 5 Apr 2009haxelrodActions
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