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The Open Protein Structure Annotation Network
PDB Keyword
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3fcr

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

    Title Crystal structure of putative aminotransferase (YP_614685.1) from SILICIBACTER SP. TM1040 at 1.80 A resolution. To be published
    Site JCSG
    PDB Id 3fcr Target Id 391382
    Molecular Characteristics
    Source Silicibacter sp. tm1040
    Alias Ids TPS20225,YP_614685.1, 3.40.640.10, 336999 Molecular Weight 49754.61 Da.
    Residues 457 Isoelectric Point 5.24
    Sequence mlkndqldqwdrdnffhpsthlaqhargesanrviktasgvfiedrdgtklldafaglycvnvgygrqe iaeaiadqarelayyhsyvghgteasitlakmildrapknmskvyfglggsdanetnvkliwyynnilg rpekkkiisrwrgyhgsglvtgsltglelfhkkfdlpveqvihteapyyfrredlnqteeqfvahcvae lealieregadtiaafigepilgtggivpppagyweaiqtvlnkhdillvadevvtgfgrlgtmfgsdh yglepdiitiakgltsayaplsgsivsdkvwkvleqgtdengpighgwtysahpigaaagvanlkllde lnlvsnagevgaylnatmaealsqhanvgdvrgegllcavefvkdrdsrtffdaadkigpqisaklleq dkiiarampqgdilgfappfcltraeadqvvegtlravkavlg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.80 Rfree 0.254
    Matthews' coefficent 2.14 Rfactor 0.205
    Waters 321 Solvent Content 42.59

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3fcr
    1. Reversed Enantiopreference of an __Transaminase by a Single_Point Mutation
    M Svedendahl, C Branneby, L Lindberg - , 2010 - Wiley Online Library
     
    2. Distributed structure determination at the JCSG
    H van den Bedem, G Wolf, Q Xu - Section D: Biological , 2011 - scripts.iucr.org
     
    3. Crystal structures of the Chromobacterium violaceum__transaminase reveal major structural rearrangements upon binding of coenzyme PLP
    MS Humble, KE Cassimjee, M Hkansson - FEBS , 2012 - Wiley Online Library
     
    4. Key Amino Acid Residues for Reversed or Improved Enantiospecificity of an __Transaminase
    MS Humble, KE Cassimjee, V Abedi - , 2012 - Wiley Online Library
     

    Protein Summary

    This protein is annotated as a class III aminotransferase belonging to Pfam PF00202.This family is a member of the Pfam Clan CL0061 which includes many PLP-dependent enzymes of the superfamily of PLP-dependent aminotransferases.

    Several other structures of proteins belonging to this Pfam Clan but members of PF00155 (class I and II amino transferases) with bound PLP have also been recently solved at the JCSG. These include the proteins with JCSG target ids 391714 (in which the PLP is covalently linked to a lysine by Schiff base formation forming a LLP) and 391594 (3ele.pdb). PF01063 (Class IV aminotransferase) and PF00266 (Class V aminotransferase) proteins structures solved at JCSG belonging to same clan include targets 282701 (3csw.pdb) and 354073 (1vjo.pdb), respectively. This also includes PF00266 (Class V aminotransferase) represented by 390948 which also has the PLP-dependent decarboxylase domain.

    3fcr is present as a monomer in the crystal structure and there is a PLP molecule (green) bound at the putative active site. An unidentified ligand (UNL) has also been modeled near this PLP:

    Fig1.png

    A combination of Fo-Fc difference density, omit map, and comparison with structurally similar PLP-dependent aminotransferases led to the modeling of the PLP. The figure below shows the final PLP model in original Fo-Fc and 2Fo-Fc electron density prior to modeling and refinement and also shows the UNL (red spheres):

    PLP_LLP_UNL.jpg

    It is also noteworthy that the pyridoxal-5'-phosphate adduct is present in 2 forms, as free PLP and as covalently bound to Lys288 as LLP. This may represent some functional or reaction mechanism characteristic.

     

    Crystal packing analysis (using PISA) suggests that a dimer should be the stable oligomeric form in solution for 3fcr:

    Fig2.png

     These different aminotransferase appear to exhibit variations in dimerization and in PLP binding which could reflect their functional differences. For example, a superpositioning of 3fcr protein structure to that of 391714 illustrates this:

    Fig3.png

     A search for structurally similar proteins using SSM (EBI) shows most significant hits with dialkylglycine decarboxylases (PDB ids 1m0n Ref1, 1d7s, 1dge, 1dka, etc.) and acetylornithine aminotransferase (PDB ids 1vef, 2e54, etc.).

     

    References:

    1. Aminophosphonate inhibitors of dialkylglycine decarboxylase: structural basis for slow binding inhibition. Liu W, Rogers CJ, Fisher AJ, Toney MD. Biochemistry, 2002 Oct 15;41(41):12320-8.

    Ligand Summary

    PLP bound at the putative active site. Shown above in green and cyan.

    Reviews

    References

     

    No references found.

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    Files (4)

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    231.56 kB17:13, 28 Oct 2008debanuActions
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     Fig3.png
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    777.81 kB18:13, 28 Oct 2008debanuActions
     PLP_LLP_UNL.jpg
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    311.04 kB00:06, 13 Nov 2008debanuActions
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