Biochemistry I   Spring & Fall Terms

Carbonic Anhydrase Mechanism

  Y 90°   Y -90°
  X 90°   X -90°

  Reaction Steps:
  1. Start: Active Site
  2. CO2 Binding
  3. Nucleophilic Attack
  4. HCO3- Dissociation
  5. H+ Dissociation/Shuttle
  6. His 64 Rotation/Flip
  7. Return to Start

  Reaction Sequence
    H-Bond Distances (Å)

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Carbonic Anhydrase Mechanism
Carbonic Anhydrase catalyzes the reversible hydration of CO2 to form bicarbonate anion and a proton:
CO2 + H2O <==> HCO3- + H+
The turnover number (kcat) for the hydration reaction is about 106 sec-1.

The numbered buttons show the sequence of steps in the hydration reaction:
  1. Start: Active Site The zinc is coordinated by the imidazole rings of three histidines (94, 96, and 119) and an OH- ion. The geometry of the active site is tetrahedral.
  2. CO2 Binding A water molecule (HOH338) is displaced by CO2. The main chain NH of Thr 199 orients and polarizes the CO2 molecule.
  3. Nucleophilic Attack The zinc-bound OH- attacks the carbon of CO2 to form HCO3-, labeled "BCT".
  4. HCO3- Dissociation A water molecule (HOH263) replaces the HCO3- product.
  5. H+ Dissociation/Shuttle The proton product dissociates from HOH263 and is transferred in three steps along a "wire" of H-bonded waters to His 64.
  6. His 64 Rotation/Flip The protonated His 64 side chain rotates from the "in" postion to the "out" position where it is exposed to bulk solvent on the enzyme exterior.
  7. Return to Start After releasing the H+ product, His 64 rotates back to the starting (in) postion. The enzyme is then ready for another cycle of catalysis. (Repeat the sequence at step 2.)
The rate limiting step in the reaction is H+ dissociation, i.e. steps 5-7 above.

"Reaction Sequence" This button shows all seven steps with a 1.0 sec delay between each.
  H-Bond Distances (Å) are between the waters in the proton dissociation pathway.

Carbonic Anhydrase Mechanism: Animation of the seven steps using chemical structures (in a pop-up window).

The structure and proposed mechanism of carbonic anhydrase is described by:
Hakansson K, Carlsson M, Svensson LA, Liljas A. (1992) "Structure of native and apo carbonic anhydrase II and structure of some of its anion-ligand complexes." J Mol Biol 227: 1192     PubMed [2CBA.pdb]
(Coordinates for HCO3- are from 1CAM.pdb; coordinates for CO2 were added to the 2CBA.pdb file.)

Back to the Carbonic Anhydrase Structure page.

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