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The Open Protein Structure Annotation Network
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3h3l

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

    Title Crystal structure of PUTATIVE SUGAR HYDROLASE (YP_001304206.1) from Parabacteroides distasonis ATCC 8503 at 1.59 A resolution. To be published
    Site JCSG
    PDB Id 3h3l Target Id 394755
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS25356,YP_001304206.1, 370930 Molecular Weight 27269.33 Da.
    Residues 240 Isoelectric Point 4.95
    Sequence agtqtaqtqaldsdgiptggewitmfdgktlngwrgycrqdvplgwvvedgsitykgsdnkadtgfgdl iydkkfknfvfeiewkidkagnsgifytaqeiegtpiyysspeyqlldnenmpdawegcdgnrqagavy dmimpdpqpvkpygnwnktrivvynqrvihymndvkilefqfgtpvwralvdhskfskfstspekcpea ydlmlqcgkqpgyigmqdhgygvcfrnirikel
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 3
    Resolution (Å) 1.59 Rfree 0.185
    Matthews' coefficent 2.44 Rfactor 0.170
    Waters 488 Solvent Content 49.66

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3h3l
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    2. Ligands in crystal structures that aid in functional characterization
    AE Speers, BF Cravatt - Acta Crystallographica Section F: Structural , 2010 - scripts.iucr.org
     

    Protein Summary

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

    Gene BDI_2876 from Parabacteroides distasonis atcc 8503 encodes the YP_001304206 protein that belongs to Pfam group DUF1080 (PF06439). STRING genome context analysis indicates a strong hit (score 0.85) with BDI_2875, a putative galactosamine-6-phosphate isomerase.

    monomer.png

    Shown above is a ribbon representation of the 3h3l structure. The EBI-PISA oligomeric prediction server and analytical size exclusion chromatography  provide supporting evidence that a dimer is a significant oligomerization state in solution. Shown below is a ribbons representation of the dimer with one subunit in blue and a second in red.

     

    dimer.png

    dimer_active_site.png

    Shown above is a representation of the solvent excluded surface of the structure of the dimer of 3h3l facing toward the putative active site cleft. TRIS molecules are represented as cylinders and are located within the cleft at the putative active site. The individual monomers are shown in yellow and blue.

     

    putative_active_site (1).bmp

     

    Shown here is a close-up view of the structure surrounding the putative active site of 3h3l. The bound TRIS ligand is shown (labled TRS) along with superimposed 2fo-fc omit map electron density.

     

    The fastSCOP fold prediction server indicates that target ID 394755 described here is structurally similar to those proteins belonging to the concanavalin A-like lectins/glucanases. In particular the structure of target ID is similar  to that of thrombospondin C-terminal domain from humans (PDB ID 1ux6). A search of the PDB using the DALI server shows as top hits 3hbk (Z-scr=28), 3imm (Z-sr=20),  followed by 1oq1 (Z-scr=14), and 1mac (Z-scr=13) and others:

    PDB ID    rmsd (Å)   %seq id  nalgn  name
    1oq1             3.2             12      180    Unk. Func.Galectin-fold-like fold B. subtilis
    2a6x             2.8              10     158    Y east   Emp46p carbohydrate recognition
    1mac            2.6              10     154   Bac. macerans endo-1,3-1,4-beta-glucanase
    1gbg             2.9              10     156   BAC LICHENIFORMIS BETA-GLUCANASE
    2ayh             2.8                9    154     Bacillus 1,3-1,4-Beta-Glucanase  

     

    Shown here are ribbon representations of SSM superposition of the coordinates of the monomer of 3h3l (green). with top scoring DALI hits. PDB ID 1mac is in cyan, PDB ID 1OQ1 is in magenta, and PDB ID 1GBG is in yellow. This superpositioning indicates that 3h3l contains two alpha-helices at the edge of the beta jelly-roll that are absent in the related structures. These two helices are involved in dimer formation.
     
    overlap_DALI.png

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page

    Files (6)

    FileSizeDateAttached by 
     dimer.png
    ribbons representation dimer
    513.52 kB00:22, 18 Mar 2009haxelrodActions
     dimer_active_site.png
    No description
    321.54 kB17:03, 13 May 2009haxelrodActions
     dimer_cleft.png
    No description
    182.62 kB20:03, 13 May 2009haxelrodActions
     monomer.png
    ribbons representation monomer
    447.6 kB00:22, 18 Mar 2009haxelrodActions
     overlap_DALI.png
    Superposition of top four DALI hits
    208.21 kB18:49, 13 May 2009haxelrodActions
     putative_active_site (1).bmp
    No description
    1207.08 kB21:57, 12 May 2009haxelrodActions
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