1RKA

THE APO FORM OF E. COLI RIBOKINASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.4 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:  
    1RKA, 1RK2, 1RKS

  • 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 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
    • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (RIBOKINASE)A309Escherichia coliMutation(s): 0 
Gene Names: rbsK
EC: 2.7.1.15
Find proteins for P0A9J6 (Escherichia coli (strain K12))
Explore P0A9J6 
Go to UniProtKB:  P0A9J6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.210 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.97α = 90
b = 61.97β = 90
c = 127.834γ = 120
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-08-31
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Advisory, Data collection
  • Version 1.4: 2019-11-13
    Changes: Database references