.
The Open Protein Structure Annotation Network
PDB Keyword
.

3sy6

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

    Title Crystal structure of a fimbrial protein BF1861 [Bacteroides fragilis NCTC 9343] (BF1861) from Bacteroides fragilis NCTC 9343 at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 3sy6 Target Id
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Molecular Characteristics
    Source
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Alias Ids
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    TPS20982,YP_211496.1, 324027
    Molecular Weight
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Da.
    Residues
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Isoelectric Point
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Sequence
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
      BLAST   FFAS

    Structure Determination
    Method XRAY
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Chains 2
    Resolution (Å)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Rfree
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Matthews' coefficent 2.09 Rfactor 0.1685
    Waters
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Solvent Content 41.15

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    Ligand Information
    Ligands
    Metals

    Jmol

     
    parameter 'target' could not convert from 'list' to 'str' (click for details)
    Google Scholar output for 3sy6

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    Protein Summary

    Pfam Update: There is one other structure 1vkd, in that family, that is described thus in TOPSAN: Protein Summary The gene TM1225 from Thermotoga maritima encodes the NP_229030 protein from the DUF377 group (PF04041). The protein belongs to the glycosyl hydrolases 43 superfamily COG2152. The genomic neighborhood of TM1225 shows the presence (score 0.8) of a transcriptional regulator XylR-related (TM1224). SCOP classifies 1vkd in the all beta class, 5-bladed beta propeller fold, arabinase/levansucrase/invertase superfamily, TM1225-like family. 1vkd shows structural similarity (Dali Z=22) to many beta-xylosidases like 3cpn, 1yrz, 2exh, or 3c2u. Glycosyl hydrolases are a big and widespread family of enzymes that hydrolyse the glycosidic bonds between carbohydrates or between a carbohydrate and an aglycone moiety. On the basis of sequence and structural similarity, the glycoside hydrolase family belongs to the beta-fructosidase (furanosidase) family of glycosyl hydrolases [1]. The enzyme, most probably, acts on a furanoside residue (fructose, arabinose and ribose). So, solution of this should confirm that. There were certainly overlaps to the GH family when I ran jackhmmer.

     

     

    The structure of target id 393142 was determined at a resolution of 1.9 Å by three wavelength Se-MAD phasing. A search of the Pfam database target indicates this target belongs to an un-assigned Pfam family based on amino acid sequence alone. Shown below is a ribbons representation of the monomer color-coded with the N-terminal end in blue and the C-terminal end in red.

     

    monomer.png

     


    The structure appears to contain two sub-domains with each subdomain resembling a two layered ß-sandwich. However these two sub-domains show significant structural differences. For the most part, the N-terminal half on the sequence comprises one sub-domain and the C-terminal half the second sub-domain. However, the sub-domains are intertwined so that non-contiguous regions of the sequence are inter-dispersed among the two sub-domains.

    Crystal packing suggets that a dimer is a significant oligiomeric form. Shown below is a view of the dimer with a non-crystallographic two-fold axis relating the two monomers in the dimer. One momomer is in yellow and the second monomer is in blue. In this view, the non-crystallographic two-fold axis is pointing perpendicular into and out of the plane of the screen.

    dimer_view2.png


    One of the two sub-domains is involved in the dimerization, and this dimerization leads to the formation of an 8-stranded ß-sheet. More specifically, a pairing of the C-terminal ß-strands is observed in the dimer.

     

    Tabulated below are entries in the PDB that show structural similarity to target id 393412 as determined by a DALI search. The structural similarity search suggests that target id 393142 is a fimbral assembly protein.

     

    PDB ID DALI Z-Score rmsd overlap (Å) number of residues aligned total residues % sequence id description
    3liu 10.7 4.0 218 373 11 Putative cell adhesion protein (YP_001304840.1) from Parabacteroides distasonis ATCC 8503 at 2.05 A resolution
    3r4r 10.6 4.6 206 267 10 Hypothetical fimbrial assembly protein (BDI_3522) from Parabacteroides distasonis ATCC 8503 at 2.38 A resolution
    3gf8 6.6 3.8 192 284 11 Putative polysaccharide binding proteins (DUF1812) (NP_809975.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.20 A resolution
    3pay 6.5 3.7 187 309 10 putative adhesin (BACOVA_04077) from Bacteroides ovatus at 2.50 A resolution

     

    Shown below is ribbon representation of the overlap between the structures of target ID 393142 (green) and PDB ID 3liu (blue), a putative fimbral assembly protein.

     

    3liu_overlap.png

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page
    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch