Induced fit on sugar binding activates ribokinase

J Mol Biol. 1999 Jul 30;290(5):1009-18. doi: 10.1006/jmbi.1999.2938.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Diphosphate / metabolism
  • Adenosine Triphosphate / metabolism
  • Apoenzymes / chemistry
  • Apoenzymes / metabolism
  • Binding Sites
  • Catalysis
  • Crystallization
  • Crystallography, X-Ray
  • Dimerization
  • Enzyme Activation
  • Escherichia coli / enzymology
  • Models, Chemical
  • Models, Molecular
  • Molecular Sequence Data
  • Oxygen / chemistry
  • Oxygen / metabolism
  • Phosphorylation
  • Phosphotransferases (Alcohol Group Acceptor) / chemistry*
  • Phosphotransferases (Alcohol Group Acceptor) / metabolism*
  • Protein Structure, Secondary
  • Ribose / metabolism*


  • Apoenzymes
  • Adenosine Diphosphate
  • Ribose
  • Adenosine Triphosphate
  • Phosphotransferases (Alcohol Group Acceptor)
  • ribokinase
  • Oxygen

Associated data

  • PDB/1RK2
  • PDB/1RKA
  • PDB/1RKS