1RKS

E. COLI RIBOKINASE IN COMPLEX WITH D-RIBOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Induced fit on sugar binding activates ribokinase.

Sigrell, J.A.Cameron, A.D.Mowbray, S.L.

(1999) J.Mol.Biol. 290: 1009-1018

  • DOI: 10.1006/jmbi.1999.2938
  • Primary Citation of Related Structures:  
  • Also Cited By: 1GQT

  • PubMed Abstract: 
  • The enzyme ribokinase phosphorylates ribose at O5* as the first step in its metabolism. The original X-ray structure of Escherichia coli ribokinase represented the ternary complex including ribose and ADP. Structures are presented here for the apo en ...

    The enzyme ribokinase phosphorylates ribose at O5* as the first step in its metabolism. The original X-ray structure of Escherichia coli ribokinase represented the ternary complex including ribose and ADP. Structures are presented here for the apo enzyme, as well as the ribose-bound state and four new ternary complex forms. Combined, the structures suggest that large and small conformational changes play critical roles in the function of this kinase. An initially open apo form can allow entry of the ribose substrate. After ribose binding, the active site lid is observed in a closed conformation, with the sugar trapped underneath. This closure and associated changes in the protein appear to assist ribokinase in recognition of the co-substrate ATP as the next step. Binding of the nucleotide brings about further, less dramatic adjustments in the enzyme structure. Additional small movements are almost certainly required during the phosphoryltransfer reaction. Evidence is presented that some types of movements of the lid are allowed in the ternary complex, which may be critical to the creation and breakdown of the transition state. Similar events are likely to take place during catalysis by other related carbohydrate kinases, including adenosine kinase.


    Related Citations: 
    • Structure of Escherichia Coli Ribokinase in Complex with Ribose and Nucleotide 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
    • Purification, Characterization, and Crystallization of Escherichia Coli Ribokinase
      Sigrell, J.A.,Cameron, A.D.,Jones, T.A.,Mowbray, S.L.
      (1997) Protein Sci. 6: 2474
    • 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


    Organizational Affiliation

    Department of Molecular Biology, Uppsala University, Uppsala, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (RIBOKINASE)
A
309Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rbsK
EC: 2.7.1.15
Find proteins for P0A9J6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A9J6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
RIB
Query on RIB

Download SDF File 
Download CCD File 
A
RIBOSE
C5 H10 O5
HMFHBZSHGGEWLO-AIHAYLRMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.229 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 95.210α = 90.00
b = 95.210β = 90.00
c = 154.460γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-08-31
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2018-04-04
    Type: Data collection