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The Open Protein Structure Annotation Network
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3luu

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

    Title Crystal structure of Protein with unknown function which belongs to Pfam DUF971 family (AFE_2189) from Acidithiobacillus ferrooxidans ATCC 23270 at 1.93 A resolution. To be published
    Site JCSG
    PDB Id 3luu Target Id 381806
    Molecular Characteristics
    Source Acidithiobacillus ferrooxidans atcc 23270
    Alias Ids TPS7334,AFE_2189, PF06155, 87240 Molecular Weight 11408.36 Da.
    Residues 100 Isoelectric Point 5.56
    Sequence msdprtqpleirplmisrvmevdwadghtsrltfehlrvecpcaeckghtpdqaqivtgkehvsvvevv pvghyavqlhfsdghntgiftweylrrldae
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.93 Rfree 0.221
    Matthews' coefficent 2.43 Rfactor 0.196
    Waters 45 Solvent Content 49.33

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3luu
    1. Crystal structure of human gamma-butyrobetaine hydroxylase
    K Tars, J Rumnieks, A Zeltins, A Kazaks - Biochemical and , 2010 - Elsevier
     
    2. Structural and Mechanistic Studies on _-Butyrobetaine Hydroxylase
    IKH Leung, TJ Krojer, GT Kochan, L Henry - Chemistry & biology, 2010 - Elsevier
     

    Protein Summary

    Gene Lferr_0978 from Acidithiobacillus ferrooxidans atcc 23270 encodes the YP_002219431 protein, a member of PFAM DUF971, a large family ( >500 members) with broad phylogenetic distribution in bacteria and eukaryotes, including humans. A domain homologous to Lferr_0978 is present highly conserved in the eukaryotic THLM (Epsilon-N-trimethyllysine hydroxylase (EC 1.14.11.8) ) gene responsible for the conversion of epsilon-N-trimethyllysine to beta-hydroxy-N-epsilon-trimethyllysine, the first step in the L-carnitine biosynthesis  (Vaz et al., 2001 [PubMed 11431483]). However, the catalytic domain of the THLM protein is located at its C-terminus, while the domain homologous to Lferr_0978 is found at the N-terminus and its function is unknown.

    A 2nd iteration with Psi-Blast detects a 46% seq. id. with a predicted phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (ZP_00943662). Genomic neighbourhood analysis of a homologue (52% seq. id.) of Lferr_0978, Mmc1_1632, suggests possible involvement in quinone biosynthesis (0.7 scored link between Mmc1_1632 and Mmc1_3492, a quinone methyltransferase).

    Pre-SCOP classifies 3luu in the alpha+beta class, NE0471 N-terminal domain-like fold. Dali provides only a weak hit (Z=5) with the hypothetical protein NE0471 2auw.

    Lferr_0978 sequence shows traces of an ancient duplication, with a conserved DGH motif.

     

    VMEVDWADGH-TSRLTFEHLR

    +++ ++DGH T T+E+LR

    AVQLHFSDGHNTGIFTWEYLR

     

    This internal repeat is also seen in the 3luu structure, which consists of two bbba repeats, with an antiparallel beta sheet with a 123 topology. The conserved DGH motif is located on the loop between the second and third beta strand in each repeat, this motif is also well conserved in the entire family.

    3luu structure strongly resembles another JCSG structure, 3k8r, with rmsd 2.8A for 67 Ca, and identical internal repeat which also consists of an internal repeat of a similar bbba motif. Even the mutual position of the two repeats is highly similar in both structures. The corresponding families, DUF971 and DUF3532, do not show any significant sequence similarity, however, based on their structural similarity they may be distantly homologous.

    An intriguing feature involves a Zinc ion (not present in crystallization conditions) chelated by residues H36, E40 and E100  which are located near the assymetric interface of two monomers and help the formation of an assymetric dimer. As a result, a superhelical bundle would be formed in the crystal lattice. This Zinc binding site does not appear to be highly conserved.

     

    Fig 1. 3luu monomer

    pu6502a.png

    Fig 2. 3luu assymetric dimer

    pu6502a-dimer.png

    Fig 3. helical bundle

    helical-bundle.png

    Fig 4. 3llu (mypro) sequence alignment and mapping of conserved aa (dark)

    aline-pu6502a.png

    consv.png

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page

    Files (5)

    FileSizeDateAttached by 
     aline-pu6502a.png
    pu6502a seq align
    83.2 kB00:02, 27 Jan 2010qxuActions
     consv.png
    pu6502a conservation
    135.83 kB00:01, 27 Jan 2010qxuActions
     helical-bundle.png
    helical bundle of pu6502a
    168.79 kB23:28, 26 Jan 2010qxuActions
     pu6502a-dimer.png
    assymetric dimer of pu6502a
    119.56 kB23:28, 26 Jan 2010qxuActions
     pu6502a.png
    monomer of pu6502a
    102.77 kB23:28, 26 Jan 2010qxuActions
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