3AHI

H320A mutant of Phosphoketolase from Bifidobacterium Breve complexed with acetyl thiamine diphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structures of phosphoketolase: thiamine diphosphate-dependent dehydration mechanism

Suzuki, R.Katayama, T.Kim, B.-J.Wakagi, T.Shoun, H.Ashida, H.Yamamoto, K.Fushinobu, S.

(2010) J Biol Chem 285: 34279-34287

  • DOI: 10.1074/jbc.M110.156281
  • Primary Citation of Related Structures:  
    3AHJ, 3AHC, 3AHD, 3AHE, 3AHF, 3AHG, 3AHH, 3AHI

  • PubMed Abstract: 
  • Thiamine diphosphate (ThDP)-dependent enzymes are ubiquitously present in all organisms and catalyze essential reactions in various metabolic pathways. ThDP-dependent phosphoketolase plays key roles in the central metabolism of heterofermentative bac ...

    Thiamine diphosphate (ThDP)-dependent enzymes are ubiquitously present in all organisms and catalyze essential reactions in various metabolic pathways. ThDP-dependent phosphoketolase plays key roles in the central metabolism of heterofermentative bacteria and in the pentose catabolism of various microbes. In particular, bifidobacteria, representatives of beneficial commensal bacteria, have an effective glycolytic pathway called bifid shunt in which 2.5 mol of ATP are produced per glucose. Phosphoketolase catalyzes two steps in the bifid shunt because of its dual-substrate specificity; they are phosphorolytic cleavage of fructose 6-phosphate or xylulose 5-phosphate to produce aldose phosphate, acetyl phosphate, and H(2)O. The phosphoketolase reaction is different from other well studied ThDP-dependent enzymes because it involves a dehydration step. Although phosphoketolase was discovered more than 50 years ago, its three-dimensional structure remains unclear. In this study we report the crystal structures of xylulose 5-phosphate/fructose 6-phosphate phosphoketolase from Bifidobacterium breve. The structures of the two intermediates before and after dehydration (α,β-dihydroxyethyl ThDP and 2-acetyl-ThDP) and complex with inorganic phosphate give an insight into the mechanism of each step of the enzymatic reaction.


    Related Citations: 
    • Overexpression, crystallization and preliminary X-ray analysis of xylulose-5-phosphate/fructose-6-phosphate phosphoketolase from Bifidobacterium breve
      Suzuki, R., Kim, B.-J., Shibata, T., Iwamoto, Y., Katayama, T., Ashida, H., Wakagi, T., Shoun, H., Fushinobu, S., Yamamoto, K.
      (2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 941

    Organizational Affiliation

    Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Xylulose 5-phosphate/fructose 6-phosphate phosphoketolaseA845Bifidobacterium breveMutation(s): 1 
Gene Names: xfp
EC: 4.1.2.22 (PDB Primary Data), 4.1.2 (UniProt)
Find proteins for D6PAH1 (Bifidobacterium breve)
Explore D6PAH1 
Go to UniProtKB:  D6PAH1
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HTL
Query on HTL

Download CCD File 
A
2-ACETYL-THIAMINE DIPHOSPHATE
C14 H21 N4 O8 P2 S
GYRGKLZCJRVYRV-UHFFFAOYSA-O
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.426α = 90
b = 174.426β = 90
c = 163.809γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance