Substrate connectivity effects in the transition state for cytidine deaminase

Biochemistry. 1998 Aug 25;37(34):11873-8. doi: 10.1021/bi980959n.


The binding properties of substrates and competitive inhibitors of Escherichia coli cytidine deaminase are compared with those of the fragments obtained by cutting these ligands at several positions including the glycosidic bond. In contrast with the normal substrate cytidine (kcat/Km = 2.6 x 10(6) M-1 s-1), cytosine is found to serve as an extremely slow substrate (kcat/Km = 1.8 x 10(-3) M-1 s-1), despite the ability of cytosine to enter any active site that can accommodate the normal substrate cytidine. Spontaneous nonenzymatic deamination proceeds at similar rates for cytosine and cytidine at pH 7 and 25 degrees C, indicating that substituent ribose exerts little effect on the intrinsic reactivity of cytidine in solution. Dividing knon by kcat/Km, the maximal Kd value of the enzyme's complex with the altered substrate in the transition state is estimated as 6.1 x 10(-8) M for cytosine, very much higher than the value (1.2 x 10(-16) M) estimated for cytidine. The Kd value of ribofuranose, the missing substituent, is roughly 1.8 x 10(-2) M, as indicated by the Ki values of D-ribose and 1-methyl-D-ribofuranoside as competitive inhibitors. Thus, the free energy of binding of the altered substrate in the transition state is 9.5 kcal/mol more favorable for the whole molecule cytidine than for the sum of those of its parts, cytosine plus ribofuranose. As a separate molecule, however, ribose shows no detectable effect on the enzyme's activity on cytosine. Connectivity effects of similar magnitude are indicated by the equilibrium binding affinities of inhibitors. Thus, the Ki value of the transition state analogue inhibitor zebularine hydrate (1.2 x 10(-12) M) is very much lower than the combined affinities of N-ribofuranosylurea (1.6 x 10(-4) M) and allyl alcohol (0.14 M), indicating that the glycoside bond, by its presence, exerts a connectivity effect of 9.9 kcal/mol on the observed free energy of binding.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Binding Sites
  • Cytidine / metabolism
  • Cytidine Deaminase / antagonists & inhibitors
  • Cytidine Deaminase / chemistry*
  • Cytidine Deaminase / metabolism*
  • Drug Synergism
  • Enzyme Inhibitors / metabolism
  • Escherichia coli / enzymology
  • Hydroxides / metabolism
  • Kinetics
  • Ligands
  • Models, Chemical
  • Pyrimidine Nucleosides / metabolism
  • Substrate Specificity


  • Enzyme Inhibitors
  • Hydroxides
  • Ligands
  • Pyrimidine Nucleosides
  • Cytidine
  • pyrimidin-2-one beta-ribofuranoside
  • hydroxide ion
  • Cytidine Deaminase