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

Currently 6GUA does not have a wwPDB validation 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

  • 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.,Laboratoire de Chémoinformatique, UMR 7140 CNRS-Université de Strasbourg, 1 rue Blaise Pascal, Strasbourg 67000, France. Electronic address: dhorvath@unistra.fr.,Structural Biology, Zoological Institute, Kiel University, Am Botanischen Garten 1-9, 24118 Kiel, Germany. Electronic address: axel.scheidig@strubio.uni-kiel.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable phosphoketolase
A, B, C, D, E, F, G, H
822Lactococcus lactis subsp. lactis (strain IL1403)Mutation(s): 0 
EC: 4.1.2.-
Find proteins for Q9CFH4 (Lactococcus lactis subsp. lactis (strain IL1403))
Go to UniProtKB:  Q9CFH4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

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

Download SDF File 
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 = 158.100α = 90.00
b = 141.500β = 90.29
c = 161.150γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

Currently 6GUA does not have a wwPDB validation report.



Entry History 

Deposition Data

Revision History 

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