1XUP

ENTEROCOCCUS CASSELIFLAVUS GLYCEROL KINASE COMPLEXED WITH GLYCEROL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of Enterococcal Glycerol Kinase in the Absence and Presence of Glycerol: Correlation of Conformation to Substrate Binding and a Mechanism of Activation by Phosphorylation

Yeh, J.I.Charrier, V.Paulo, J.Hou, L.Darbon, E.Clairborn, A.Hol, W.G.J.Deutscher, J.

(2004) Biochemistry 43: 362-367

  • DOI: 10.1021/bi034258o
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The first structure of a glycerol kinase from a Gram-positive organism, Enterococcus casseliflavus, has been determined to 2.8 A resolution in the presence of glycerol and to 2.5 A resolution in the absence of substrate. The substrate-induced closure ...

    The first structure of a glycerol kinase from a Gram-positive organism, Enterococcus casseliflavus, has been determined to 2.8 A resolution in the presence of glycerol and to 2.5 A resolution in the absence of substrate. The substrate-induced closure of 7 degrees is significantly smaller than that reported for hexokinase, a model for substrate-mediated domain closure that has been proposed for glycerol kinase. Despite the 78% level of sequence identity and conformational similarity in the catalytic cleft regions of the En. casseliflavus and Escherichia coli glycerol kinases, remarkable structural differences have now been identified. These differences correlate well with their divergent regulatory schemes of activation by phosphorylation in En. casseliflavus and allosteric inhibition in E. coli. On the basis of our structural results, we propose a mechanism by which the phosphorylation of a histidyl residue located 25 A from the active site results in a 10-15-fold increase in the activity of the enterococcal glycerol kinase.


    Organizational Affiliation

    Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA. Joanne_Yeh@brown.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycerol kinase
O, X
487Enterococcus casseliflavusMutation(s): 0 
Gene Names: glpK
EC: 2.7.1.30
Find proteins for O34153 (Enterococcus casseliflavus)
Go to UniProtKB:  O34153
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
O, X
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: 2.75 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.010α = 90.00
b = 107.670β = 90.00
c = 201.450γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
MLPHAREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance