Carbonate dehydratase (alpha class)

 

Carbonic acid anhydrase is able to catalyse the conversion of carbon dioxide to carbonic acid and vice versa. This is important in metabolism because it enables the creation of carbonic acid, a very important buffer in the blood which has a vital role in human physiology.

 

Reference Protein and Structure

Sequence
P00918 UniProt (4.2.1.1) IPR023561 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1ca2 - REFINED STRUCTURE OF HUMAN CARBONIC ANHYDRASE II AT 2.0 ANGSTROMS RESOLUTION (2.0 Å) PDBe PDBsum 1ca2
Catalytic CATH Domains
3.10.200.10 CATHdb (see all for 1ca2)
Cofactors
Zinc(2+) (1) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:4.2.1.1)

carbon dioxide
CHEBI:16526ChEBI
+
water
CHEBI:15377ChEBI
→
hydrogencarbonate
CHEBI:17544ChEBI
+
hydron
CHEBI:15378ChEBI
Alternative enzyme names: Anhydrase, Carbonate anhydrase, Carbonic acid anhydrase, Carbonate dehydratase, Carbonic anhydrase A, Carboxyanhydrase, Carbonic dehydratase, Carbonate hydro-lyase,

Enzyme Mechanism

Introduction

The reaction proceeds in two steps. First, an OH- bound to the Zinc ion attacks the carbon dioxide substrate forming bicarbonate and leaving a water at the Zinc ion. Polarisation of the C=O bond of carbon dioxide is achieved by Thr 199. Following this step, the OH- is regenerated by deprotonation of a water molecule by His 64, with Zinc acting to increase the polarity of the OH bond by withdrawing electrons from the oxygen atom.

Catalytic Residues Roles

UniProt PDB* (1ca2)
Thr198 Thr199(197)A The interaction between the Thr199 and hydroxide serve to enhance the nucleophilicity of the hydroxide and help orient the substrate (CO2) in the active site. hydrogen bond acceptor, hydrogen bond donor, activator, electrostatic stabiliser, increase nucleophilicity
Glu106 Glu106(105)A Hydrogen bonds to the hydroxyl of Thr199, activating it activator, hydrogen bond acceptor, electrostatic stabiliser
His64 His64(63)A Is able to deprotonate a water molecule allowing the formation of the catalytic nucleophile OH-. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
His94, His96, His119 His94(93)A, His96(95)A, His119(118)A Forms part of the catalytic zinc binding site. metal ligand
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

bimolecular nucleophilic addition, overall reactant used, overall product formed, coordination to a metal ion, proton transfer, native state of enzyme regenerated

References

  1. Fisher Z et al. (2005), Biochemistry, 44, 1097-1105. Structural and Kinetic Characterization of Active-Site Histidine as a Proton Shuttle in Catalysis by Human Carbonic Anhydrase II†,‡. DOI:10.1021/bi0480279. PMID:15667203.
  2. Supuran CT et al. (2003), Med Res Rev, 23, 146-189. Carbonic anhydrase inhibitors. DOI:10.1002/med.10025. PMID:12500287.
  3. Huang S et al. (1998), J Mol Biol, 283, 301-310. Crystal structure of carbonic anhydrase from Neisseria gonorrhoeae and its complex with the inhibitor acetazolamide. DOI:10.1006/jmbi.1998.2077. PMID:9761692.
  4. Lindskog S (1997), Pharmacol Ther, 74, 1-20. Structure and mechanism of carbonic anhydrase. DOI:10.1016/s0163-7258(96)00198-2. PMID:9336012.
  5. Tu CK et al. (1989), Biochemistry, 28, 7913-7918. Role of histidine 64 in the catalytic mechanism of human carbonic anhydrase II studied with a site-specific mutant. DOI:10.1021/bi00445a054. PMID:2514797.
  6. Eriksson AE et al. (1988), Proteins, 4, 274-282. Refined structure of human carbonic anhydrase II at 2.0 Å resolution. DOI:10.1002/prot.340040406. PMID:3151019.

Step 1. The interactions between the zinc bound hydroxide, Thr199 and Gu106 serve to enhance the nucleophilicity of the hydroxide and help to orient the substrate (carbon dioxide) in the active site [PMID:12500287]. Zinc activated water attacks the carbon of carbon dioxide in a nucleophilic addition, which results in the bicarbonate moiety being bound to the zinc in a bidentate manner.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His119(118)A metal ligand
His94(93)A metal ligand
His96(95)A metal ligand
Glu106(105)A hydrogen bond acceptor, electrostatic stabiliser, activator
Thr199(197)A hydrogen bond acceptor, hydrogen bond donor, electrostatic stabiliser, activator, increase nucleophilicity

Chemical Components

ingold: bimolecular nucleophilic addition, overall reactant used, overall product formed, coordination to a metal ion

Step 2. The bicarbonate ion formed at the end of the first step is displaced by a water molecules before this step occurs [PMID:12500287]. His64 deprotonates the zinc bound water.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu106(105)A hydrogen bond acceptor, activator, electrostatic stabiliser
Thr199(197)A hydrogen bond acceptor, hydrogen bond donor, activator, electrostatic stabiliser
His64(63)A hydrogen bond acceptor
His119(118)A metal ligand
His94(93)A metal ligand
His96(95)A metal ligand
His64(63)A proton acceptor

Chemical Components

proton transfer

Step 3. Evidence suggests that upon receiving the proton from the water, the His64 flips from the "in" configuration to the "out" configuration to deliver its proton to the solution. It is possible there is a longer proton relay chain present [PMID:15667203].

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu106(105)A hydrogen bond acceptor, electrostatic stabiliser
Thr199(197)A hydrogen bond acceptor, hydrogen bond donor, electrostatic stabiliser
His64(63)A hydrogen bond donor
His119(118)A metal ligand
His94(93)A metal ligand
His96(95)A metal ligand
His64(63)A proton donor

Chemical Components

proton transfer, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. The interactions between the zinc bound hydroxide, Thr199 and Gu106 serve to enhance the nucleophilicity of the hydroxide and help to orient the substrate (carbon dioxide) in the active site [PMID:12500287]. Zinc activated water attacks the carbon of carbon dioxide in a nucleophilic addition, which results in the bicarbonate moiety being bound to the zinc in a bidentate manner.

Step 2. The bicarbonate ion formed at the end of the first step is displaced by a water molecules before this step occurs [PMID:12500287]. His64 deprotonates the zinc bound water.

Step 3. Evidence suggests that upon receiving the proton from the water, the His64 flips from the "in" configuration to the "out" configuration to deliver its proton to the solution. It is possible there is a longer proton relay chain present [PMID:15667203].

Products.

Contributors

Gemma L. Holliday, Peter Sarkies