6GUA

Xylulose 5-phosphate phosphoketolase from Lactococcus lactis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.212 

    wwPDB Validation 3D Report Full Report


    This is version 1.1 of the entry. See complete history


    Literature

    Crystal structure of a xylulose 5-phosphate phosphoketolase. Insights into the substrate specificity for xylulose 5-phosphate.

    Scheidig, A.J.Horvath, D.Szedlacsek, S.E.

    (2019) J Struct Biol 207: 85-102

    • DOI: 10.1016/j.jsb.2019.04.017
    • Primary Citation of Related Structures:  
      6GUA

    • PubMed Abstract: 
    • Phosphoketolases (PK) are TPP-dependent enzymes which play essential roles in carbohydrate metabolism of numerous bacteria. Depending on the substrate specificity PKs can be subdivided into xylulose 5-phosphate (X5P) specific PKs (XPKs) and PKs which ...

      Phosphoketolases (PK) are TPP-dependent enzymes which play essential roles in carbohydrate metabolism of numerous bacteria. Depending on the substrate specificity PKs can be subdivided into xylulose 5-phosphate (X5P) specific PKs (XPKs) and PKs which accept both X5P and fructose 6-phosphate (F6P) (XFPKs). Despite their key metabolic importance, so far only the crystal structures of two XFPKs have been reported. There are no reported structures for any XPKs and for any complexes between PK and substrate. One of the major unknowns concerning PKs mechanism of action is related to the structural determinants of PKs substrate specificity for X5P or F6P. We report here the crystal structure of XPK from Lactococcus lactis (XPK-Ll) at 2.1 Å resolution. Using small angle X-ray scattering (SAXS) we proved that XPK-Ll is a dimer in solution. Towards better understanding of PKs substrate specificity, we performed flexible docking of TPP-X5P and TPP-F6P on crystal structures of XPK-Ll, two XFPKs and transketolase (TK). Calculated structure-based binding energies consistently support XPK-Ll preference for X5P. Analysis of structural models thus obtained show that substrates adopt moderately different conformation in PKs active sites following distinct networks of polar interactions. Based on the here reported structure of XPK-Ll we propose the most probable amino acid residues involved in the catalytic steps of reaction mechanism. Altogether our results suggest that PKs substrate preference for X5P or F6P is the outcome of a fine balance between specific binding network and dissimilar catalytic residues depending on the enzyme (XPK or XFPK) - substrate (X5P or F6P) couples.


      Related Citations: 
      • Preliminary X-ray crystallographic analysis of the D-xylulose 5-phosphate phosphoketolase from Lactococcus lactis.
        Petrareanu, G., Balasu, M.C., Zander, U., Scheidig, A.J., Szedlacsek, S.E.
        (2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 805

      Organizational Affiliation

      Department of Enzymology, Institute of Biochemistry of the Romanian Academy, Spl. Independentei 296, Bucharest 060031, Romania. Electronic address: stefan.szedlacsek@biochim.ro.



    Macromolecules
    Find similar proteins by:  (by identity cutoff)  |  Structure
    Entity ID: 1
    MoleculeChainsSequence LengthOrganismDetailsImage
    Probable phosphoketolaseABCDEFGH822Lactococcus lactis subsp. lactis Il1403Mutation(s): 0 
    Gene Names: LL1502L138230
    EC: 4.1.2
    Find proteins for Q9CFH4 (Lactococcus lactis subsp. lactis (strain IL1403))
    Explore Q9CFH4 
    Go to UniProtKB:  Q9CFH4
    Protein Feature View
    Expand
     ( Mouse scroll to zoom / Hold left click to move )
    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    TPP
    Query on TPP

    Download CCD File 
    A, B, C, D, E, F, G, H
    THIAMINE DIPHOSPHATE
    C12 H19 N4 O7 P2 S
    AYEKOFBPNLCAJY-UHFFFAOYSA-O
     Ligand Interaction
    PO4
    Query on PO4

    Download CCD File 
    A, B, C, E, G, H
    PHOSPHATE ION
    O4 P
    NBIIXXVUZAFLBC-UHFFFAOYSA-K
     Ligand Interaction
    MG
    Query on MG

    Download CCD File 
    A, B, C, D, E, F, G, H
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.95 Å
    • R-Value Free: 0.261 
    • R-Value Work: 0.212 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 158.1α = 90
    b = 141.5β = 90.29
    c = 161.15γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    XDSdata reduction
    XSCALEdata scaling
    MOLREPphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2019-05-22
      Type: Initial release
    • Version 1.1: 2019-06-19
      Changes: Data collection, Database references