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3gux

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

    Title Crystal structure of putative Zn-dependent exopeptidase (YP_001298628.1) from Bacteroides vulgatus ATCC 8482 at 1.80 A resolution. To be published
    Site JCSG
    PDB Id 3gux Target Id 390181
    Molecular Characteristics
    Source Bacteroides vulgatus atcc 8482
    Alias Ids TPS7687,YP_001298628.1, 3.40.630.10, 88199 Molecular Weight 35471.80 Da.
    Residues 313 Isoelectric Point 5.55
    Sequence gnsksrndrtetvdkevikapefdadsayqyiqvqadfgprvpntqahkecgeylagqlekfgakvynq yadliaydgtilksrniigaykpeskkrillcahwdsrpyadndpdpknhhtpilgvndgasgvgvlle iarqiqkeqpalgidivffdsedygipefydgkykqdtwclgsqywartphvqnynarygilldmvggk datfyyegysartarsemkkiwkkahelgygkyfvkedggetvddhiyvnklaripcvdiinydagnpq ssfgsfwhtvndtmenidrntlkavgqtvmdviynek
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.80 Rfree 0.232
    Matthews' coefficent 2.06 Rfactor 0.196
    Waters 282 Solvent Content 40.18

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3gux

    Protein Summary

    Member of Peptidase M28 family

     

    Gene BVU_1317 from Bacteroides vulgatus translates into the YP_001298628 protein. NCBI blast sequence alignment suggests BVU_1317 is a leucine aminopeptidase precursor from the peptidase family M28 (PF04389).

    Pre-SCOP classifies 3gux in the alpha/beta class, Zn-dependent exopeptidase superfamily, glutaminyl-peptide cyclotransferase-like family (?). Based on a DALI search, 3gux shows structural similarity to bacterial aminopeptidases like PDB:2ek8 (Z=28), PDB:1lok (Z=27), PDB:1tkj (Z=27), PDB:2dea (Z=27), PDB:1cp6 (Z=26).

    3gux structure shows two subunits in each asymmetric unit.  The interface interaction calculation can not suggest any oligomeric status other than monomer since lots of residues are not modeled in the structure due to poor electron density. The putative metal binding site in this structure could not be modeled.

     

    390181_1.png

     Figure 1. The monomer structure of 3gux.

     

    References,

    1.    Gilboa, R.,  Spungin-Bialik, A.,  Wohlfahrt, G.,  Schomburg, D.,  Blumberg, S.,  Shoham, G.  (2001) Interactions of Streptomyces griseus aminopeptidase with amino acid reaction products and their implications toward a catalytic mechanism.  Proteins   44: 490-504   (PDB: 1F2O)
     
    2.    Huang, K.F.,  Wang, Y.R.,  Chang, E.C.,  Chou, T.L.,  Wang, A.H.   (2008) A conserved hydrogen-bond network in the catalytic centre of animal glutaminyl cyclases is critical for catalysis.  Biochem.J.   411: 181-190   (PDB ID: 2ZEE)
     
    3.    Desmarais, W.,  Bienvenue, D.L.,  Bzymek, K.P.,  Petsko, G.A.,  Ringe, D.,  Holz, R.C.   (2006) The high-resolution structures of the neutral and the low pH crystals of aminopeptidase from Aeromonas proteolytica.  J.Biol.Inorg.Chem.   11: 398-408   (PDB: 1RTQ).
     
    4.    Huang, K.F.,  Liu, Y.L.,  Cheng, W.J.,  Ko, T.P.,  Wang, A.H.   (2005) Crystal structures of human glutaminyl cyclase, an enzyme responsible for protein N-terminal pyroglutamate formation  Proc.Natl.Acad.Sci.Usa   102: 13117-13122 (PDB ID: 2AFM)

    Ligand Summary

    Reviews

    References

     

    No references found.

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