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The Open Protein Structure Annotation Network
PDB Keyword
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377395

    Table of contents
    1. 1. Ligand Summary

    Site JCSG
    Status Diffraction-quality Crystals
    Target Id 377395
    Molecular Characteristics
    Source Lactobacillus delbrueckii bulgaricus atcc baa-365
    Alias Ids TPS6975, Molecular Weight 43992.97 Da.
    Residues 390 Isoelectric Point 5.02
    Sequence maekqydfthvpkrqgnsikwgvlkekelpmwiaemdfkiapeimasmeeklkvaafgyesvpaeyykavadweei ehrarpkedwcvfasgvvpaisamvrqftspgdqilvqepvynmfysviegngrrvissdliyenskysvnwadl eeklatpsvrmmvfcnphnpigyawseeevkriaelcakhqvllisdeihgdlvltdeditpaftvdwdaknwvv slispsktfnlaalhaacaiipnpdlraraeesfflagigepnllaipaaiaayeeghdwlrelkqvlrdnfaya reflakevpevkvldsnasylawvdisalgmnaedfckylrektgliisagngyrgnghefvrinlacpkelvid gmqrlkqgvlnlnn
      BLAST   FFAS
    Ligand Information
    Ligands
    Metals
    Google Scholar output for

    Ligand Summary

     Ligands: Acetate ion, PLP molecules

     

     

     

     

     

    Protein YP_813084.1 is from Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC BAA-365), which belongs to the Pfam 00155.  There are two subunits in each asymmetric unit to form a tight dimer.  The result from NCI Blast sequence match indicates this target may be PLP-dependent aminotransferase or Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose. PLP molecule from crystallization condition as additive is modeled in the conserved active site with clear electron density support in each subunit.  The covalent bond distance between the C4 atom  of  PLP and NZ atomof Lys 233 indicates a Schiff Base formation in each subunit.There are three domains in each monomer of YP_813084.1. The PLP locates in the cavity formed by these three domains at the interface between two subunits. One Acetate from crystallization condition has clear H-Bond interaction with Arg 364. Acetate anion should be considered as the analogue of COO- in the external substrate aldimine. Interestingly, Asn 170 has strong H-Bond with PLP, but has no directly interaction with Acetate ion in the structure.

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    Figure 1.   The over all structure of protein YP_813084.1.

     

    3.png

    Figure 2.  Protein YP_813084.1 forms a tigher dimer.

     

     

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    Figure 3. Based on it function prediction, one PLP molecule from crystallization condition as additive

    is modeled in the the active site with clear electron density support.  This PLP molecule covalently links

    with the NZ of conserved residue Lys 233. 

     

     


    Refrence 

    1.     Krupka, H.I.,  Huber, R.,  Holt, S.C.,  Clausen, T.  (2000) Crystal structure of cystalysin from Treponema denticola: a pyridoxal 5'-phosphate-dependent protein acting as a haemolytic enzyme.  EMBO J.   19: 3168-3178   (PDB: 1C7N)

    2.    Clausen, T.,  Schlegel, A.,  Peist, R.,  Schneider, E.,  Steegborn, C.,  Chang, Y.S.,  Haase, A.,  Bourenkov, G.P.,  Bartunik, H.D.,  Boos, W.  (2000) X-ray structure of MalY from Escherichia coli: a pyridoxal 5'-phosphate-dependent enzyme acting as a modulator in mal gene expression.  EMBO J.   19: 831-842  (PDB: 1D2F)

     

    3.    Bertoldi M, Cellini B, Laurents DV, Borri Voltattorni C. (2008)Folding pathway of the pyridoxal 5'-phosphate C-S lyase MalY from Escherichia coli. Biochem J. 2005 Aug 1;389(Pt 3):885-98.

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