1GQT

Activation of Ribokinase by Monovalent Cations


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report



Literature

Activation of Ribokinase by Monovalent Cations.

Andersson, C.E.Mowbray, S.L.

(2002) J Mol Biol 315: 409

  • DOI: 10.1006/jmbi.2001.5248
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Carbohydrate kinases frequently require a monovalent cation for their activity. The physical basis of this phenomenon is, however, usually unclear. We report here that Escherichia coli ribokinase is activated by potassium with an apparent K(d) of 5 m ...

    Carbohydrate kinases frequently require a monovalent cation for their activity. The physical basis of this phenomenon is, however, usually unclear. We report here that Escherichia coli ribokinase is activated by potassium with an apparent K(d) of 5 mM; the enzyme should therefore be fully activated under physiological conditions. Cesium can be used as an alternative ion, with an apparent K(d) of 17 mM. An X-ray structure of ribokinase in the presence of cesium was solved and refined at 2.34 A resolution. The cesium ion was bound between two loops immediately adjacent to the anion hole of the active site. The buried location of the site suggests that conformational changes will accompany ion binding, thus providing a direct mechanism for activation. Comparison with structures of a related enzyme, the adenosine kinase of Toxoplasma gondii, support this proposal. This is apparently the first instance in which conformational activation of a carbohydrate kinase by a monovalent cation has been assigned a clear structural basis. The mechanism is probably general to ribokinases, to some adenosine kinases, and to other members of the larger family. A careful re-evaluation of the biochemical and structural data is suggested for other enzyme systems.


    Related Citations: 
    • Structure of Escherichia Coli Ribokinase in Complex with Ribose and Dinucleotide Determined to 1.8 A Resolution: Insights Into a New Family of Kinase Structures.
      Sigrell, J.A., Cameron, A.D., Jones, T.A., Mowbray, S.L.
      (1998) Structure 6: 183
    • Ribokinase from Escherichia Coli K12. Nucleotide Sequence and Overexpression of the Rbsk Gene and Purification of Ribokinase
      Hope, J.N., Bell, A.W., Hermodson, M.A., Groarke, J.M.
      (1986) J Biol Chem 261: 7663
    • Induced fit on sugar binding activates ribokinase.
      Sigrell, J.A., Cameron, A.D., Mowbray, S.L.
      (1999) J Mol Biol 290: 1009

    Organizational Affiliation

    Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBOKINASE
A, B, C, D
309Escherichia coli K-12Mutation(s): 0 
Gene Names: rbsKb3752JW3731
EC: 2.7.1.15
Find proteins for P0A9J6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A9J6
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACP
Query on ACP

Download CCD File 
A, B, C
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
RIB
Query on RIB

Download CCD File 
A, B, C, D
RIBOSE
C5 H10 O5
HMFHBZSHGGEWLO-AIHAYLRMSA-N
 Ligand Interaction
CS
Query on CS

Download CCD File 
A, B, C, D
CESIUM ION
Cs
NCMHKCKGHRPLCM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.453α = 90
b = 62.767β = 90
c = 339.277γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-01-28
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2018-04-18
    Changes: Advisory, Atomic model, Data collection, Database references