Carbonate dehydratase (gamma class)

 

Gamma-class carbonic anhydrase (Cam) from Methanosarcina thermophila catalyses the reversible hydration of carbon dioxide to bicarbonate. There are three distinct classes of carbonic anhydrases (alpha, beta and gamma). In M. thermophila, Cam activity increases when the substrate for growth is acetate, suggesting the involvement of this enzyme in acetate catabolism.

 

Reference Protein and Structure

Sequence
P40881 UniProt (4.2.1.1) IPR011004 (Sequence Homologues) (PDB Homologues)
Biological species
Methanosarcina thermophila TM-1 (Archaea) Uniprot
PDB
1qrg - A CLOSER LOOK AND THE ACTIVE SITE OF GAMMA-CARBONIC ANHYDRASES: HIGH RESOLUTION CRYSTALLOGRAPHIC STUDIES OF THE CARBONIC ANHYDRASE FROM METHANOSARCINA THERMOPHILA (1.72 Å) PDBe PDBsum 1qrg
Catalytic CATH Domains
2.160.10.10 CATHdb (see all for 1qrg)
Cofactors
Cobalt(3+) (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

Glu 62 deprotonates a water molecule liganded to Co. This proton is then abstracted by Glu 84 (and ultimately shuttled out to buffer.) This hydroxyl ligand then abstracts a proton from the adjacent liganded water molecule. The newly formed hydroxide ligand is stabilised by hydrogen bonding to Gln 75. CO2 is polarised by Asn 202 to make the carbon more attractive for nucleophilic attack. The hydroxide ligand nucleophilically attacks the carbon atom of CO2, resulting in a bound HCO3-. An oxygen atom of HCO3- displaces a liganded water molecule from Coto form a bidentate HCO3- ligand. HCO3- undergoes a bidentate transition state where the proton either rotates (Lindskog) or transfers (Lipscomb) to the non-metal-bound oxygen of HCO3-. Glu 62 destabilises HCO3- by hydrogen bonding to it. A water molecule replaces one of the bound oxygens of the HCO3- ligand. A second water molecule replaces the other bound oxygen atom of HCO3-, displacing it completely from Co.

Catalytic Residues Roles

UniProt PDB* (1qrg)
Glu96 Glu62A Acts as a base by deprotonating a water molecule liganded to Zn. Destabilises HCO3- ligand by hydrogen bonding to it, aiding its detachment from Zn. proton acceptor, electrostatic destabiliser, electrostatic stabiliser, proton donor
Glu118 Glu84A Abstracts a proton from Glu 62 and shuttles it up to the surface buffer. proton acceptor
His115, His156, His151 His81A, His122A, His117A(AA) Bind the metal ion. metal ligand
Asn236 Asn202A(AA) Polarises CO2, assisting the nucleophilic attack of HO-. increase electrophilicity, electrostatic stabiliser
Gln109 Gln75A(AA) Stabilises the hydroxide ligand, readying it for nucleophilic attack on CO2. 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, proton relay, bimolecular nucleophilic addition, overall reactant used, overall product formed, decoordination from a metal ion, coordination to a metal ion, native state of cofactor regenerated

References

  1. Zimmerman SA et al. (2006), Biochemistry, 45, 5149-5157. Proposal for a Hydrogen Bond Network in the Active Site of the Prototypic γ-Class Carbonic Anhydrase†. DOI:10.1021/bi052507y. PMID:16618104.
  2. Ghiasi M et al. (2017), Comput Theor Chem, 1109, 42-57. Activation modelling of β- and γ-class of carbonic anhydrase with amines and amino acids: Proton transfer process within the active site from thermodynamic point of view. DOI:10.1016/j.comptc.2017.03.041.
  3. Ferry JG (2010), Biochim Biophys Acta, 1804, 374-381. The gamma class of carbonic anhydrases. DOI:10.1016/j.bbapap.2009.08.026. PMID:19747990.
  4. Iverson TM et al. (2000), Biochemistry, 39, 9222-9231. A closer look at the active site of gamma-class carbonic anhydrases: high-resolution crystallographic studies of the carbonic anhydrase from Methanosarcina thermophila. PMID:10924115.

Step 1. Glu 62 deprotonates a water molecule liganded to Co. This hydroxyl ligand then abstracts a proton from the adjacent liganded water molecule. The newly formed hydroxide ligand is stabilised by hydrogen bonding to Gln 75.

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Catalytic Residues Roles

Residue Roles
Gln75A(AA) electrostatic stabiliser
Glu62A electrostatic stabiliser
His81A metal ligand
His122A metal ligand
Glu62A proton acceptor

Chemical Components

proton transfer, proton relay

Step 2. The proton bound to Glu62 is then abstracted by Glu84 where it is shuttled into the solution. CO2 is polarised by Asn 202 to make the carbon more attractive for nucleophilic attack. The hydroxide ligand nucleophilically attacks the carbon atom of CO2, resulting in a bound HCO3-.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asn202A(AA) electrostatic stabiliser
Gln75A(AA) electrostatic stabiliser
Asn202A(AA) increase electrophilicity
His81A metal ligand
His122A metal ligand
His117A(AA) metal ligand
Glu84A proton acceptor
Glu62A proton donor

Chemical Components

ingold: bimolecular nucleophilic addition, overall reactant used, overall product formed

Step 3. An oxygen atom of HCO3- displaces a liganded water molecule from Co to form a bidentate HCO3- ligand.

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Catalytic Residues Roles

Residue Roles
His81A metal ligand
His122A metal ligand
His117A(AA) metal ligand

Chemical Components

decoordination from a metal ion, coordination to a metal ion

Step 4. Glu 62 destabilises HCO3- by hydrogen bonding to it. A water molecule replaces one of the bound oxygens of the HCO3- ligand.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu62A electrostatic destabiliser
His81A metal ligand
His122A metal ligand
His117A(AA) metal ligand

Chemical Components

decoordination from a metal ion, coordination to a metal ion

Step 5. A second water molecule replaces the other bound oxygen atom of HCO3-, displacing it completely from Co.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His81A metal ligand
His122A metal ligand
His117A(AA) metal ligand

Chemical Components

native state of cofactor regenerated, decoordination from a metal ion, coordination to a metal ion
Download: Image, Marvin File

Step 1. Glu 62 deprotonates a water molecule liganded to Co. This hydroxyl ligand then abstracts a proton from the adjacent liganded water molecule. The newly formed hydroxide ligand is stabilised by hydrogen bonding to Gln 75.

Step 2. The proton bound to Glu62 is then abstracted by Glu84 where it is shuttled into the solution. CO2 is polarised by Asn 202 to make the carbon more attractive for nucleophilic attack. The hydroxide ligand nucleophilically attacks the carbon atom of CO2, resulting in a bound HCO3-.

Step 3. An oxygen atom of HCO3- displaces a liganded water molecule from Co to form a bidentate HCO3- ligand.

Step 4. Glu 62 destabilises HCO3- by hydrogen bonding to it. A water molecule replaces one of the bound oxygens of the HCO3- ligand.

Step 5. A second water molecule replaces the other bound oxygen atom of HCO3-, displacing it completely from Co.

Products.

Contributors

Ellie Wright, Gemma L. Holliday