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The Open Protein Structure Annotation Network
PDB Keyword
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381354

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

    Site JCSG
    Status Crystallized
    Target Id 381354
    Molecular Characteristics
    Source Burkholderia xenovorans lb400
    Alias Ids TPS7311, Molecular Weight 34101.21 Da.
    Residues 310 Isoelectric Point 6.01
    Sequence mkqskkiiitcavtgsihtptmspylpitpeeivkegvaaaeagaamlhlhardplngrpsqdpdlfmrflpqlke rtdailnittggglgmslderlaparaarpevasmnmgslnfnisqaaakfdtfkfdwerpylagtrdfilsntf sqiergmtelgasgtrfefecydvghlynlahfvdrklveppfflqcvfgilggigadpenllhmrtiadrlfgq dyylsvlaagrhqmpfvtmsailggnvrvgledslysgkgqlatsnaeqvrkirriieelsldiatpdearamlk tkganetsf
      BLAST   FFAS
    Ligand Information
    Ligands
    Metals

    Protein Summary

     

    Gene Bxe_C0271 from Burkholderia xenovorans lb400 encodes the YP_555544 amino acid sequence that belongs to the DUF849 group (PF05853). Kreimeyer et al. (reference #1) idenitified a protein, CAM07313, from a collection of water metagenomics sequences, that shares sequence similarity with DUF849 (E-value: 1.2e-99).  They characterized CAM07313 as a 3-keto-5-aminohexoanoate cleaveage enzyme.  Thus, CAM07313 provides a possible functional annotation for DUF849.  However, many bacterial genomes have multiple proteins that share sequence similarity to DUF849.  Additionally, some of the microbes that have proteins with sequence similarity to DUF849 cannot ferment lysine.

    3e02 has a monomer structure composed of  a Tim-barrel surrounded by helices (Fig 1). There is a Zn ion located in the center of the core of the protein which interacts with a couple of histidine residues (H49, H51) and glutamate (E258).

    PU6423C.png

    Fig 1. 3e02 monomer structure with Zn ion in the core of the protein.

     

    PU6423C_as (1).png

    Fig 2. Active site and interaction of Zn ion with residues H49, H51, and E258.

    PU6423C_tetramer.png

    Fig 3. The 3e02 protein arranges a dimer of dimer in the crystal environment and the resulting tetramer may represent the biological oligomer.

     

    The significant structural homologs of 3e02 (apart from 3e49, a 60% identical sequence with a Dali Z-scr of 53) are a putative 3-keto-5-aminohexanoate cleavage enzyme (YP_293392.1) from Ralstonia eutropha JMP134 (Dali Z-scr=38; TOPSAN page, PDB id: 3c6c) and a prokaryotic domain of unknown function (DUF849) with a TIM barrel fold (YP_164873.1) from Silicibacter pomeroyi DSS-3 (Dali Z-scr=40; TOPSAN page, PDB id: 3chv) as returned by a SSM search. Both of these structures were determined at JCSG and are very similar to this target (Fig 4). All three have conserved metal sites and interacting residues suggesting functional similarity. A sequence alignment of these proteins is shown in Fig 5.

    3c6c_3chv_target.png

     

    Fig 4: 3e02 (green) is structurally similar to 3c6c (cyan), and 3chv (magenta).

    alignment.png
    Fig 5. Sequence aligment showing conserved residues (red) involved in (Zn) metal binding.

     

    References

    1. Kreimeyer A, Perret A, Lechaplais C, Vallenet D, Médigue C, Salanoubat M, Weissenbach J.  Identification of the last unknown genes in the fermentation pathway of lysine.  J Biol Chem. 2007 Mar 9;282(10):7191-7. Epub 2006 Dec 13.  PMID: 17166837

    Ligand Summary

    ZN ion: X-ray Flourescence excitation and wavelength scans, anomalous difference fouriers, and geometry support the modeling of Zn ion.

    Ethylene glycol (EDO) from cryo solution is also modeled in the structure. 

    Reviews

    References

     

    No references found.

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