1XC3

Structure of a Putative Fructokinase from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural studies of ROK fructokinase YdhR from Bacillus subtilis: insights into substrate binding and fructose specificity.

Nocek, B.Stein, A.J.Jedrzejczak, R.Cuff, M.E.Li, H.Volkart, L.Joachimiak, A.

(2011) J.Mol.Biol. 406: 325-342

  • DOI: 10.1016/j.jmb.2010.12.021
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The main pathway of bacterial sugar phosphorylation utilizes specific phosphoenolpyruvate phosphotransferase system (PTS) enzymes. In addition to the classic PTS system, a PTS-independent secondary system has been described in which nucleotide-depend ...

    The main pathway of bacterial sugar phosphorylation utilizes specific phosphoenolpyruvate phosphotransferase system (PTS) enzymes. In addition to the classic PTS system, a PTS-independent secondary system has been described in which nucleotide-dependent sugar kinases are used for monosaccharide phosphorylation. Fructokinase (FK), which phosphorylates d-fructose with ATP as a cofactor, has been shown to be a member of this secondary system. Bioinformatic analysis has shown that FK is a member of the "ROK" (bacterial Repressors, uncharacterized Open reading frames, and sugar Kinases) sequence family. In this study, we report the crystal structures of ROK FK from Bacillus subtilis (YdhR) (a) apo and in the presence of (b) ADP and (c) ADP/d-fructose. All structures show that YdhR is a homodimer with a monomer composed of two similar α/β domains forming a large cleft between domains that bind ADP and D-fructose. Enzymatic activity assays support YdhR function as an ATP-dependent fructose kinase.


    Organizational Affiliation

    Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, IL 60439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative fructokinase
A
302Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: gmuE (ydhR)
EC: 2.7.1.4
Find proteins for O05510 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O05510
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
PT
Query on PT

Download SDF File 
Download CCD File 
A
PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.180 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 112.660α = 90.00
b = 112.660β = 90.00
c = 75.087γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
autoSHARPphasing
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2012-10-10
    Type: Database references
  • Version 1.4: 2017-10-11
    Type: Refinement description