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The Open Protein Structure Annotation Network
PDB Keyword
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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
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS14603,NP_940074.1, 3.40.640.10, 289761
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

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

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3fdb

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    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

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    (Z=47), cystalysin 1C7O (Z=46), aminotransferase
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    (Z=44) and the MalY protein
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    (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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