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The Open Protein Structure Annotation Network
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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 393142
    Molecular Characteristics
    Source Bacteroides fragilis nctc 9343
    Alias Ids TPS20982,YP_211496.1, 324027 Molecular Weight 30962.74 Da.
    Residues 290 Isoelectric Point 5.58
    Sequence eqedkvsgektlavvsassddrpstrgiindntyalgvfrttantyaplynvkhiysggewgaddvikv dyrnasffayypyhtatgnyaglaggttltlqaqlfnagedicygageasgggpvsvynpfveflnmkh ayarlrltltrgekfdktkkcniqnitfksnnanfyltrsldiastagatggsavaagyvhnpnvniat gksvtyeymfppqpldgskltilvtvdgvtrscdistlgssldsgkyygvsltftdvgiilssavvtvn nfggqgntqvdtel
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.90 Rfree 0.2108
    Matthews' coefficent 2.09 Rfactor 0.1685
    Waters 314 Solvent Content 41.15

    Ligand Information
    Ligands
    Metals

    Jmol

     

    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.

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