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The Open Protein Structure Annotation Network
PDB Keyword
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3f9t

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

    Title Crystal structure of L-tyrosine decarboxylase MfnA (EC 4.1.1.25) (NP_247014.1) from METHANOCOCCUS JANNASCHII at 2.11 A resolution. To be published
    Site JCSG
    PDB Id 3f9t Target Id 390948
    Molecular Characteristics
    Source Methanocaldococcus jannaschii dsm 2661
    Alias Ids TPS18308,NP_247014.1, 3.40.640.10, 289364 Molecular Weight 45047.83 Da.
    Residues 396 Isoelectric Point 6.74
    Sequence mrnmqekgvsekeileelkkyrsldlkyedgnifgsmcsnvlpitrkivdifletnlgdpglfkgtkll eekavallgsllnnkdayghivsggteanlmalrcikniwrekrrkglsknehpkiivpitahfsfekg remmdleyiyapikedytidekfvkdavedydvdgiigiagttelgtidnieelskiakenniyihvda afgglvipflddkykkkgvnykfdfslgvdsitidphkmghcpipsggilfkdigykryldvdapylte trqatilgtrvgfggactyavlrylgregqrkivnecmentlylykklkennfkpviepilnivaiede dykevckklrdrgiyvsvcncvkalrivvmphikrehidnfieilnsikrd
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.11 Rfree 0.192
    Matthews' coefficent 2.92 Rfactor 0.158
    Waters 407 Solvent Content 57.86

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3f9t
    1. Evolution of a novel lysine decarboxylase in siderophore biosynthesis
    M Burrell, CC Hanfrey, LN Kinch, KA Elliott - Molecular , 2012 - Wiley Online Library
     

    Protein Summary

     This protein is classified into both Pfam PF00282 (Pyridoxal-dependent decarboxylase conserved domain) and PF00266 (Aminotransferase Class V).

    There are 2 monomers in the asymmetric unit of the crystal structure forming a tight dimer. Crystal packing analysis suggests that this should be the stable oligomeric state in solution.

    Fig1_dimer.png

    Pyridoxal phosphate (PLP, cyan, above) was modeled at the putative active site in clear and unambiguous electron density from density modified, experimentally phased maps (below).

     Fig2eden.jpg

     

    In such PLP binding proteins, PLP is often found covalently attached to a lysine residue, forming a modified residue LLP by Schiff base formation. This is believed to be the ground state of such enzymes, as can be seen in another recently determined JCSG aminotransferase structure. Interestingly, the PLP in this structure does not form such a linkage with the neighboring lysine.

    Fig3A_Putativeactivesite.png

     

    The residues surrounding this PLP are Lys245, Asp206, Asn98, His 132, His 244, Thr 95, Thr285, Thr181. Residue Thr285 is from the other molecule forming the dimer since the binding site is in near the interface of the dimer.

    A search for other proteins of similar structure using EBI's SSM server show the top hits are E. coli GadB (2dgk.pdb, Z-score 8.5, 2.2A rmsd), glycine decarboxylase (P-Protein) of the glycine cleavage system (1wyu.pdb, Z-score=9.4, 2.31A rmsd, NifS-like protein (involved in FeS cluster assembly, 1eg5.pdb, Z-score=7.5, rmsd=2.5A) and other decarboxylases and aminotransferases.

    Ligand Summary

    PLP (Pyridoxal phosphate) was found at the putative active site.

    Reviews

    References

     

    No references found.

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