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3e49

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

    Title Crystal structure of prokaryotic domain of unknown function (DUF849) with a TIM barrel fold (YP_556190.1) from BURKHOLDERIA XENOVORANS LB400 at 1.75 A resolution. To be published
    Site JCSG
    PDB Id 3e49 Target Id 381357
    Molecular Characteristics
    Source Burkholderia xenovorans lb400
    Alias Ids TPS7312,YP_556190.1, PF05853, 87215 Molecular Weight 33885.76 Da.
    Residues 310 Isoelectric Point 6.18
    Sequence mgssrkviitcavtgaihtpsmspylpvtpdevaqasigaaeagaavihlhardprdgrptqdpaafae flpriksntdavinlttggsphmtveerlrpathympelaslnmgsmnfglypmlerfkefahgwereh lersrdlvfkntfadiefilktcggngtrfefecydtshlynlahfvdrklatppffvqtvfgllggig phpedlahmrrtadrlfgadyvwsilgagrhqiplasigaaqganvrvgledslwiapgelaetnaaqv rkirqvieglslevaspaeartmlglkgpqnvnf
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 1.75 Rfree 0.218
    Matthews' coefficent 2.22 Rfactor 0.177
    Waters 955 Solvent Content 44.55

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3e49
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    2. Ligands in crystal structures that aid in functional characterization
    AE Speers, BF Cravatt - Acta Crystallographica Section F: Structural , 2010 - scripts.iucr.org
     
    3. 3-Keto-5-aminohexanoate Cleavage Enzyme
    M Bellinzoni, K Bastard, A Perret, A Zaparucha - Journal of Biological , 2011 - ASBMB
     
    4. High Yield Recombinant Expression, Characterization and Homology Modeling of Two Types of Cis-epoxysuccinic Acid Hydrolases
    GZ Cui, S Wang, Y Li, YJ Tian, Y Feng, Q Cui - The Protein Journal, 2012 - Springer
     

    Protein Summary

    Gene Bxe_C0966 from Burkholderia xenovorans lb400 encodes the protein YP_556190 that belongs to PFAM PF05853 which is the family of prokaryotic proteins of unknown function (DUF849).  Kreimeyer et al. (reference #1) identified a protein, CAM07313, from a collection of waterwater metagenomics sequences, that shares sequence similarity with DUF849 (E-value: 1.2e-99).  They characterized CAM07313 as a 3-keto-5-aminogexoanoate 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.

    The 3e49 monomer structure is a Tim-barrel surrounded by helices (Fig 1). There is a Zn ion located in the center of the core of the protein (Fig 1). Indeed this structure is 60% identical to PDB:3e02 (Z=53), another JCSG solved structure (381354 ).  Additionally, this protein shares sequence and structural similarity with other structures solved by JCSG: a prokaryotic domain of unknown function (DUF849) with a TIM barrel fold (YP_164873.1) from Silicibacter pomeroyi DSS-3 (TOPSAN page, PDB:3chv, Z=40); a putative 3-keto-5-aminohexanoate cleavage enzyme (YP_293392.1) from Ralstonia eutropha JMP134 (TOPSAN page, PDB:3c6c, Z=38); PDB:3lot (Z=51); PDB:3fa5 (Z=40).

    PU6423E_PU6423C.png

    Fig 1. 3e49 structure (green) superimposed on 3e02 (cyan). The Zn ion bound to each target is shown by the sphere representation.

    PU6423E_PU6423C_AS.png

    Fig 2. Putative active site residues conservation (H49, H51, and E258) between 3e49 (green) and 3e02 (cyan).

    PU6423E_tetramer.png

    Fig 3. The biologically relevant oligomer for 3e49 is a dimer of dimers, like for 3e02. However, all four chains are present in the crystallographic asu of 3e49, unlike in 3e02, where crystal symmetry provides the associating chains.

         

    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

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