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    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of carbon-sulfur lyase involved in aluminum resistance (YP_878183.1) from CLOSTRIDIUM NOVYI NT at 2.90 A resolution. To be published
    Site JCSG
    PDB Id 3gwp Target Id 391679
    Related PDB Ids 3i16 
    Molecular Characteristics
    Source Clostridium novyi nt
    Alias Ids TPS14655,YP_878183.1, 3.40.640.10, 382580 Molecular Weight 47156.36 Da.
    Residues 426 Isoelectric Point 5.15
    Sequence mlestkqflkkynindrvlklyetamndiqnqfkilddirefnqlkvlnafqeeriseahftnssgygy gdigrdsldavyarvfntesalvrphfvngthalgaalfgnlrpgntmlsvcgepydtlhdvigitens nmgslkefginykqvdlkedgkpnleeiekvlkedesitlvhiqrstgygwrralliediksivdcvkn irkdiicfvdncygefmdtkeptdvgadliagsliknigggiaptggylagtkdciektsyrltvpgig gecgstfgvvrsmyqglflaphismealkgailcsrimelagfevmpkydekrsdiiqsikfndkdkli efckgiqtgspidsfvscepwdmpgytdqvimaagafiqgssielsadapirepyiaylqggltfdhak igilialsrivk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 2.90 Rfree 0.271
    Matthews' coefficent 2.32 Rfactor 0.223
    Waters Solvent Content 46.95

    Ligand Information


    Google Scholar output for 3gwp

    Protein Summary

    Pfam Class: This sequence matches the Pfam entry Alum_res (PF06838).

    Target ID 391679 is a 47.1 kilodalton, 426 amino acid long protein encoded by Clostridium novyi nt , a strain whose toxins genes have been deleted. This strain has been utilized for cancer therapy.  The structure reported here has been refined to a moderate resolution of 2.9 Angstroms, and the structure indicates that this target belongs to the SCOP Superfamily of PLP-dependent transferases. A search of the PFAM database shows that this target belongs to the PF06838 Alum_res PFAM group.This family represents the aluminium resistance protein, which confers resistance to aluminium in bacteria (1) In addition, over expression on some Al-induced genes confer aluminum resistance in transgenic Arbidopsis. One of these genes is a glutathione S-transferase gene, parB. (2) Among the highlights of the structure determination reported here, is the presence of a bound pyridoxal-5'-phosphate cofactor, and this observation is consistent with Target ID 391679 belonging to the PLP_aminotran Pfam clan (CL0061).This clan is a functionally-diverse group of proteins.

    Primary phasing of this target was accomplished by molecular replacement using the structure Solved by MR using with the recently determined JCSG structure 3fd0 as a search model. This model sequence has ~50% id over ~97% length to Target ID 391679.

    Shown below is a ribbon representation of the structure of a monomer of target ID 391679 color coded according to the amino acid sequence position with the N-terminal end in blue and the C-terminal end an red. The structure indicates that a pyridoxal-5'-phosphate (magenta) is bound to Lys 243 in a Schiff base (aldimine) linkage.



     Crystal packing analysis indicates that a tetamer (shown below) is a biologically-significant oligomerization state.






    Related Structures

    A search of the PDB using NCBI VAST show the following structures are similar to that of YP_878183.1

    PDB ID 3fd0-Crystal Structure Of Putative Cystathionine Beta-Lyase Involved In Aluminum Resistance (Np_470671.1) From Listeria Innocua At 2.12 A Resolution. SeqID=49% rmsd overlap=1.2 Å

    PDB ID 1N8P-Crystal Structure Of Cystathionine Gamma-Lyase From Yeast SeqID=17% rmsd overlap=2.9 Å

    PDB ID 1E5E-Methionine Gamma-Lyase (Mgl) From Trichomonas Vaginalis In Complex With Propargylglycine SeqID=14%  rmsd overlap=2.4 Å

    PDB ID 1QGN-Cystathionine Gamma Synthase from Nicotiana tabacum SeqID=17%  rmsd overlap=2.4 Å

    For these related structures, the biologically significant oligomerization state is a tetramer.


    Shown below is an amino acid sequence alignment between YP_878183.1 and closely related structures from the PDB identified from the VAST search.  Conserved residues include Tyr 68,Tyr 69, Gly 73, Ser 75, Gly 99, Ala 102, Gly 114, Asp 217, Gly 233, Asp 235, Ser 240, Gly 247, Gly 292,  Pro 297.  The sidechain of one of these residues, Asp 217, is within hydrogen bonding contact distance of the pyridoxal-5-phosphate ring nitrogen atom and is likely to play a role in the catalytic mechanism of YP_878183.1.




    Shown below is a superpositioning of the active site structures of YP_878183.1 (green) and PDB ID 3FD0 (cyan) (a putative cystathione beta-lyase. This superpositioning shows the active sites are quite similar suggesting MG9652S and 3FD0 perform a similar role. A corresponding active site comparison of the structures of YP_878183.1 and PDB ID 1N8P (a cystathionine-gamma-lyase from yeast) shows the active site structures to be quite different (not shown). A more detailed structural comparison between YP_878183.1 and PDB ID 3DF0 versus related cystathione-gamma-lyases that are functionally characterized could enhance our understanding of the role of the two former JCSG targets. In addition cystathionine-gamma-lyases are responsible for the production of H2S in mammals, and H2S is an endogeneous gastrotransmitter associated with various diseases such as hypertension, diabetes, haemorrhagic shock, and pancreatitis(3).













    (1). Jo J, Jang YS, Kim KY, Kim MH, Kim IJ, Chung WI; , Biochem Biophys Res Commun 1997;239:835-839.: Isolation of ALU1-P gene encoding a protein with aluminum tolerance activity from Arthrobacter viscosus

    (2).Sasaki et al. Plant Cell Physio. 44 2003 S84

    (3).  Sun et al. (2008) Published on November 19, 2008 J. Biol. Chem in press.




























    Ligand Summary




    No references found.

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