Carbonate dehydratase (beta class)

 

Beta-carbonic anhydrases are found in a variety of higher plants, simple eukaryotes, eubacteria and archaea. they catalyse the interconversion of carbon dioxide and bicarbonate. These are zinc-containing metalloenzymes.

 

Reference Protein and Structure

Sequence
P61517 UniProt (4.2.1.1) IPR001765 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
1i6p - CRYSTAL STRUCTURE OF E. COLI BETA CARBONIC ANHYDRASE (ECCA) (2.0 Å) PDBe PDBsum 1i6p
Catalytic CATH Domains
3.40.1050.10 CATHdb (see all for 1i6p)
Cofactors
Zinc(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:4.2.1.1)

water
CHEBI:15377ChEBI
+
carbon dioxide
CHEBI:16526ChEBI
→
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

After association of carbon dioxide with the binding site, Asp 44 (activated by binding with zinc and electrostatic interaction with Arg 46) acts as a base to abstract a proton from the water molecule. This yields a nucleophilic hydroxide that binds the zinc which further activates it for nucleophilic attack of the carbon dioxide to generate zinc-bound bicarbonate. Loss of the proton is catalysed by Asp 44 again acting as a base to transfer the proton to the solvent, and the product leaves the active site.

Catalytic Residues Roles

UniProt PDB* (1i6p)
Cys42, Cys101, His98 Cys42A, Cys101A, His98A Coordinate the zinc ion metal ligand
Asp44 Asp44A Acts as a base to deprotonate the attacking water nucleophile and the substrate. metal ligand, proton acceptor
Arg46 Arg46A Activates Asp 44. increase basicity, electrostatic stabiliser
*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

proton transfer, coordination, bimolecular nucleophilic addition, overall reactant used, overall product formed, decoordination from a metal ion

References

  1. Smith KS et al. (2002), J Bacteriol, 184, 4240-4245. Roles of the Conserved Aspartate and Arginine in the Catalytic Mechanism of an Archaeal  -Class Carbonic Anhydrase. DOI:10.1128/jb.184.15.4240-4245.2002. PMID:12107142.
  2. Rowlett RS (2014), Subcell Biochem, 75, 53-76. Structure and catalytic mechanism of β-carbonic anhydrases. DOI:10.1007/978-94-007-7359-2_4. PMID:24146374.
  3. Cronk JD et al. (2001), Protein Sci, 10, 911-922. Crystal structure of E. coli β-carbonic anhydrase, an enzyme with an unusual pH-dependent activity. DOI:10.1110/ps.46301. PMID:11316870.
  4. Mitsuhashi S et al. (2000), J Biol Chem, 275, 5521-5526. X-ray Structure of β-Carbonic Anhydrase from the Red Alga, Porphyridium purpureum , Reveals a Novel Catalytic Site for CO2 Hydration . DOI:10.1074/jbc.275.8.5521. PMID:10681531.

Step 1. Asp44, activated by electrostatic interactions with zinc and Arg46, acts as a base to abstract a proton from the water. This generates a hydroxide ion which can bind to the zinc.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Arg46A electrostatic stabiliser
Cys42A metal ligand
Asp44A metal ligand
His98A metal ligand
Cys101A metal ligand
Arg46A increase basicity
Asp44A proton acceptor

Chemical Components

proton transfer, coordination

Step 2. The hydroxide is now activated for nucleophilic attack on the carbon dioxide.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Cys42A metal ligand
Asp44A metal ligand
His98A metal ligand
Cys101A metal ligand

Chemical Components

ingold: bimolecular nucleophilic addition, overall reactant used

Step 3. Deprotonation is catalyzed by Asp 44 transferring the proton to the solvent, allowing the product to leave the active site.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Cys42A metal ligand
Asp44A metal ligand
His98A metal ligand
Cys101A metal ligand
Arg46A increase basicity
Arg46A electrostatic stabiliser
Asp44A proton acceptor

Chemical Components

overall product formed, decoordination from a metal ion, proton transfer
Download: Image, Marvin File

Step 1. Asp44, activated by electrostatic interactions with zinc and Arg46, acts as a base to abstract a proton from the water. This generates a hydroxide ion which can bind to the zinc.

Step 2. The hydroxide is now activated for nucleophilic attack on the carbon dioxide.

Step 3. Deprotonation is catalyzed by Asp 44 transferring the proton to the solvent, allowing the product to leave the active site.

Products.

Contributors

Gary McDowell, Gemma L. Holliday, James Willey