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

    Title Crystal structure of putative cystathionine beta-lyase involved in aluminum resistance (NP_470671.1) from LISTERIA INNOCUA at 2.12 A resolution. To be published
    Site JCSG
    PDB Id 3fd0 Target Id 390899
    Molecular Characteristics
    Source Listeria innocua clip11262
    Alias Ids TPS18305,NP_470671.1, 3.40.640.10, 87446 Molecular Weight 44611.23 Da.
    Residues 408 Isoelectric Point 4.91
    Sequence mteiqtirkkveqqitslqnetdeiaefnqakvldafqenkvsdfhfnpstgygyddegrdtlervyas vfkteaalvrpqiisgthaistvlfgilrpgdellyitgepydtleeivgirsegqgslkdfqigydav pllpngeidypavskkisantkmigiqrsrgyadrpsftiekikemvtfvkninpniivfvdncygefv erieptevgadiiagsliknpggglaktggyiagrntlvdlcgyrlttpgigreagaslysllemyqgf flaphvtaqaikgarftaamlaefgveadplwdakrtdliqsvsfhskdkmiafaqaiqaaspvnahvl pigaympgyeddvimaagtfiqgasleltadgpirepyqlyvqggltyehvkiavtraiensl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.12 Rfree 0.188
    Matthews' coefficent 3.23 Rfactor 0.152
    Waters 512 Solvent Content 61.96

    Ligand Information


    Google Scholar output for 3fd0
    1. N-Acylpolyamine inhibitors of HDM2 and HDMX binding to p53
    R Hayashi, D Wang, T Hara, JA Iera, SR Durell - Bioorganic & medicinal , 2009 - Elsevier

    Protein Summary

    This protein is annotated as belonging to 2 Pfams: PF06838 (Aluminium resistance protein) and PF01053 (Cys/Met metabolism PLP-dependent enzyme). Both of these are under the Pfam clan CL0061, the PLP-dependent aminotransferase superfamily.

    Other proteins of similar sequence and proteins structures with significant sequence similarities can be found using the BLAST and FFAS links provided above.

    This represents the first crystal structure of a member of PF06838. Another JCSG structure belonging to this family is also currently being solved, target 391679

    The protein exists as a dimer in the asymmetric unit of the crystal structure as shown below. Residue Lys226 in both chains has been modified by covalent modification with PLP via a Schiff base formation between lysine and bound PLP. This residue has therefore been modeled as LLP (in cyan below). This is at the putative active site of both protomers. There is clear and unambiguous electron density in the density modified experimentally phased maps for this.


    However, crystal packing analysis suggests that a tetramer may be the stable oligomeric form in solution:


    The PLP/LLP in the density modified experimentally phased maps is shown below:



    Even though this is the first structure from Pfam PF06838 of an aluminium resistance protein, JCSG has recently solved several structures of PLP-bound proteins from this Pfam clan CL0061. Some of them have bound PLP and some have lysine-bound PLP thus forming a modified lysine LLP. Most of them are classified as aminotransferases of different kinds belonging to different Pfams under this clan. They also show some differences in oligomerization.

    Interestingly, most of them are probably dimers as opposed to  the prediction of this as a tetramer, and the relative orientation of the monomers also appears to be different.

    For a summary of the JCSG structures belonging to Pfam Clan CL0061, see this link.


    A search for proteins of similar structure using the SSM server at EBI returns hits with many PLP-dependent enzymes such as those with PDB ids 1gc0, 1pff, 3cog, etc. but the top hit has a Q-score of only 0.32 with a 2.4A r.m.s.d. and 20% sequence identity.



    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. 

    Ligand Summary




    No references found.

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