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3taw

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

    Title Crystal structure of a Hypothetical glycoside hydrolase (BDI_3141) from Parabacteroides distasonis ATCC 8503 at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 3taw Target Id 393092
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS24373,YP_001304469.1 Molecular Weight 39572.27 Da.
    Residues 355 Isoelectric Point 5.02
    Sequence avsetisetawcldgferptgvnpvikplptkfycpmredsvaweesdtfnpaatiydgkivvmyraed nsaqgigsrtsrlgyatstdgihferdtkpafypakdnqaenecpggtedpriamtedgtyvllytqwn rkvprlavatskdlkhwtkfgpafekayngkfkdeatksaslvttlkgdkqviakvngkyfmywgeknv yaatsdnlidwdplldengellklfsprsgyfdsqltecgppailtkdgivllyngknepgekgdtayp ansycagqalfdvnnptkligrldkpflqptddfeksgqypagtvfveglvyyrnkwylyygcadsfva vavsdkqlnf
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.70 Rfree 0.1718
    Matthews' coefficent 2.31 Rfactor 0.1490
    Waters 332 Solvent Content 46.72

    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.

     

    Target ID 393092 is a member of the  DUF377 (PF04041) Pfam family. Shown below are two representations of the monomer. 

    monomer_view1.pngmonomer_view2.png

    A DALI search of the Protein Data Bank shows that target ID 393092 shows similarity to the following structures. The top scoring hits are related JCSG structures.
     
    PDB ID DALI Z-score rms overlap (Angstroms) length of alignment number of residues  %sequence id  Description
    3r67 61.4 0.9 346 349 70 Crystal structure of a putative glycosidase (BT_4094) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.30 A resolution
    3qc2 58.8 1.3 343 357 67 Crystal structure of a glycosyl hydrolase (BACOVA_03624) from Bacteroides ovatus at 2.30 A resolution
    1vkd 32.4 2.2 273 326 27 Crystal structure of hypothetical protein (TM1225) from Thermotoga maritima at 2.10 A resolution
    3qz4 23.0 2.9 258 306 14 Crystal structure of an Endo-1,4-beta-xylanase D (BT_3675) from Bacteroides thetaiotaomicron VPI-5482 at 1.74 A resolution
    3k1u 22.9 3.1 256 314 14 X-ray crystal structure of beta-xylosidase, family 43 glycosyl hydrolase from Clostridium acetobutylicum at 1.55 A resolution
    3aki 22.8 3.2 258 448 14 Crystal structure of exo-1,5-alpha-L-arabinofuranosidase complexed with alpha-L-arabinofuranosyl azido

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (2)

    FileSizeDateAttached by 
     monomer_view1.png
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    209.88 kB21:14, 19 Jul 2011haxelrodActions
     monomer_view2.png
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    182.28 kB21:14, 19 Jul 2011haxelrodActions
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