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The Open Protein Structure Annotation Network
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3fdb

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

    Title Crystal structure of putative PLP-dependent beta-cystathionase (NP_940074.1) from CORYNEBACTERIUM DIPHTHERIAE at 1.99 A resolution. To be published
    Site JCSG
    PDB Id 3fdb Target Id 390709
    Molecular Characteristics
    Source Corynebacterium diphtheriae nctc 13129
    Alias Ids TPS14603,NP_940074.1, 3.40.640.10, 289761 Molecular Weight 41720.05 Da.
    Residues 376 Isoelectric Point 5.13
    Sequence mqfpsiedlrarntmkwtrygqgvlplwvaesdfstcpavlqaitdavqreafgyqpdgsllsqataef yadrygyqarpewifpipdvvrglyiaidhftpaqskvivptpayppffhllsatqregifidatggin lhdvekgfqagarsillcnpynplgmvfapewlnelcdlahrydarvlvdeihaplvfdgqhtvaagvs dtaasvcititapskawniaglkcaqiifsnpsdaehwqqlspvikdgastlgliaaeaayrygtdfln qevaylknnhdfllheipkripgakitpmqatylmwidfrdttiegspseffiekakvamndgawfged gtgfcrlnfatsrevleeaidrmakavshht
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.99 Rfree 0.175
    Matthews' coefficent 3.51 Rfactor 0.147
    Waters 435 Solvent Content 64.98

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3fdb

    Protein Summary

    Gene aecD (DIP1736) translates into the NP_940074 protein from Corynebacterium diphtheriae, a pathogenic bacterium that causes diphtheria.  The sequence alignment suggests this protein carries a PLP-dependent domain for aminotransferase class I and II (PF00155). The NCBI protein entry NP_940074 has been annotated as a putative pyridoxal 5-phosphate (PLP)-dependent βeta C-S lyase. Analysis of DIP1736 genome context indicates a functional link (score 0.9) with a putative methionine biosynthesis related protein (DIP0630) and a putative cysteine synthase (DIP1890).

    Pre-SCOP classifies 3fdb in the alpha/beta class, PLP-dependent transferases superfamily, cystathionine synthase-like family. According to DALI, 3fdb structure is similar to a putative C-S lyase PDB:3dzz (Z=47), cystalysin 1C7O (Z=46), aminotransferase PDB:3kax (Z=44) and the MalY protein PDB:1d2f (Z=41). 3fdb structure shows a conserved binding site for a PLP molecule.  One PLP molecule with covalent bond distance to Lys 222 is modeled in 3fdb with clear electron density support.  This PLP molecule, covalently linked to Lys 222, has H-Bond interactions with Tyr 114, Asn160, Asp 188 and His 191. There is one 3fdb molecule in each asymmetric unit.  The interface interaction suggests that the likely biomolecule is a dimer. 

       

    390709_1.png

       

       

     Figure 1. The 3fdb molecule packs in a tri-angle shape with a cavity for PLP binding.

       

       

    390709_3.png

       

       

     Figure 2. The biomolecule of 3fdb is a dimer based on interface interaction.

       

       

    390709_4.png

       

    Figure 3. 3fdb (green) is structurally similar to 1C7O (Z=46), 1C7N (Z=46), 1D2F (Z=41) and 2DOU (Z=38) with a conserved PLP binding site. 

       

    390709_2.png

       

     Figure 4. A PLP molecule, from the protein expression medium, is modeled in the 3fdb structure.  The PLP molecule is covalently linked to Lys 222 and has H-Bond interactions with Tyr 114, Asn160, Asp 188 and His 191.

       

       

     References:

    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: 1C7O)

    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 ID: 1D2F)

    3.    Weyand, S.,  Kefala, G.,  Weiss, M.S.   (2007) The Three-dimensional Structure of N-Succinyldiaminopimelate Aminotransferase from Mycobacterium tuberculosis  J.Mol.Biol.   367: 825-838   (PDB ID: 2O0R)

    Ligand Summary

    PLP -pyridoxal 5'-phosphate

    Reviews

    References

     

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