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

    Title Crystal structure of 3-keto-5-aminohexanoate cleavage enzyme (YP_293392.1) from Ralstonia eutropha JMP134 at 1.72 A resolution. To be published
    Site JCSG
    PDB Id 3c6c Target Id 381418
    Molecular Characteristics
    Source Ralstonia eutropha jmp134
    Alias Ids TPS1757,YP_293392.1, PF05853, 86556 Molecular Weight 31990.10 Da.
    Residues 297 Isoelectric Point 5.24
    Sequence msrkviltcavtgnapfnpkhpsmpitpaqiadacveaakagasvahihvrdpktgggsrdpvlfkevv drvrssgtdivlnltcglgafllpdpedeskalpesdvvpvaervkhledclpeiasldittgnqvegk lefvylnttrtlramarrfqelgikpelevfspgdilfgkqlieeglidgvplfqmvlgvlwgapaste tmiyqrnlipanaqwaafgigrdqmpmmaqaallggnvrvglednlylsrgvfatngqlverartvieh lgmsvatpdeardimglsrpa
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.72 Rfree 0.184
    Matthews' coefficent 2.92 Rfactor 0.153
    Waters 395 Solvent Content 57.81

    Ligand Information


    Google Scholar output for 3c6c
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
    2. 3-Keto-5-aminohexanoate Cleavage Enzyme
    M Bellinzoni, K Bastard, A Perret, A Zaparucha - Journal of Biological , 2011 - ASBMB
    3. Ligands in crystal structures that aid in functional characterization
    AE Speers, BF Cravatt - Acta Crystallographica Section F: Structural , 2010 - scripts.iucr.org

    Protein Summary

    Gene Reut_C6226 from Ralstonia eutropha jmp134 encodes the YP_293392 protein containing a classical TIM barrel fold. It is the first solved representative of a very large PFAM family PF05853  (prokaryotic family with unknown function DUF849, FFAS score: -107; or COG3246 from the COGs database, FFAS score: -103).  One of the members (CAM07313, 43% seq id) was characterized as a 3-keto-5-aminohexanoate cleavage enzyme that is involved in in the fermentation pathway of lysine (Kreimeyer et al. 2007).  The genome context analysis with the STRING server indicates functional association with Reut_C6225 (a NAD-dependent epimerase/dehydratase), and Reut_C6224 (a short-chain dehydrogenase/reductase).   

    A structural similarity search with DALI gives strong hits with other DUF849 proteins like PDB:3lot, PDB:3e02, PDB:3chv, PDB:3e49 and PDB:3fa5 (Z=39-37). 3c6c biomolecule is likely to be a tetramer. A weaker hit (Z=16) is detected with the pyridoxine 5'-phosphate synthase PDB:3gk0. 3c6c chelates a Ni metal via the side chains of residues H47, H49 and E250. Three ordered water molecules are observed in the vicinity.

    Ligand Summary





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