Glycerol Kinase H232R with Glycerol

Experimental Data Snapshot

  • Resolution: 1.73 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.216 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Structural characterizations of glycerol kinase: unraveling phosphorylation-induced long-range activation

Yeh, J.I.Kettering, R.Saxl, R.Bourand, A.Darbon, E.Joly, N.Briozzo, P.Deutscher, J.

(2009) Biochemistry 48: 346-356

  • DOI: https://doi.org/10.1021/bi8009407
  • Primary Citation of Related Structures:  
    3D7E, 3FLC, 3H3N, 3H3O, 3H45, 3H46

  • PubMed Abstract: 

    Glycerol metabolism provides a central link between sugar and fatty acid catabolism. In most bacteria, glycerol kinase plays a crucial role in regulating channel/facilitator-dependent uptake of glycerol into the cell. In the firmicute Enterococcus casseliflavus, this enzyme's activity is enhanced by phosphorylation of the histidine residue (His232) located in its activation loop, approximately 25 A from its catalytic cleft. We reported earlier that some mutations of His232 altered enzyme activities; we present here the crystal structures of these mutant GlpK enzymes. The structure of a mutant enzyme with enhanced enzymatic activity, His232Arg, reveals that residues at the catalytic cleft are more optimally aligned to bind ATP and mediate phosphoryl transfer. Specifically, the position of Arg18 in His232Arg shifts by approximately 1 A when compared to its position in wild-type (WT), His232Ala, and His232Glu enzymes. This new conformation of Arg18 is more optimally positioned at the presumed gamma-phosphate location of ATP, close to the glycerol substrate. In addition to structural changes exhibited at the active site, the conformational stability of the activation loop is decreased, as reflected by an approximately 35% increase in B factors ("thermal factors") in a mutant enzyme displaying diminished activity, His232Glu. Correlating conformational changes to alteration of enzymatic activities in the mutant enzymes identifies distinct localized regions that can have profound effects on intramolecular signal transduction. Alterations in pairwise interactions across the dimer interface can communicate phosphorylation states over 25 A from the activation loop to the catalytic cleft, positioning Arg18 to form favorable interactions at the beta,gamma-bridging position with ATP. This would offset loss of the hydrogen bonds at the gamma-phosphate of ATP during phosphoryl transfer to glycerol, suggesting that appropriate alignment of the second substrate of glycerol kinase, the ATP molecule, may largely determine the rate of glycerol 3-phosphate production.

  • Organizational Affiliation

    Department of Structural Biology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15260, USA. jiyeh@pitt.edu

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycerol kinaseA [auth X],
B [auth O]
506Enterococcus casseliflavusMutation(s): 1 
Gene Names: glpK
Find proteins for O34153 (Enterococcus casseliflavus)
Explore O34153 
Go to UniProtKB:  O34153
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34153
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PO4

Download Ideal Coordinates CCD File 
G [auth X],
L [auth O]
O4 P
Query on GOL

Download Ideal Coordinates CCD File 
C [auth X],
H [auth O]
C3 H8 O3
Query on EDO

Download Ideal Coordinates CCD File 
D [auth X]
E [auth X]
F [auth X]
I [auth O]
J [auth O]
D [auth X],
E [auth X],
F [auth X],
I [auth O],
J [auth O],
K [auth O]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.73 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.812α = 90
b = 200.464β = 90
c = 56.505γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-11-01
    Changes: Data collection, Refinement description