Chaperonin ATPase

 

Chaperonins are essential multisubunit assemblies that promote facilitated protein folding in concert with ATP hydrolysis - forming a 'cage' around the protein as it folds, with the 'timer' for protein release provided by ATP hydrolysis. Group II chaperonins are found in archaea and the eukaryotic cytosol. The mechanism for ATP hydrolysis of all chaperonins is the same, but the way this is linked to opening and closing of the cavity is different.

 

Reference Protein and Structure

Sequence
P61112 UniProt IPR012714 (Sequence Homologues) (PDB Homologues)
Biological species
Thermococcus sp. JCM 11816 (Archaea) Uniprot
PDB
1q3s - Crystal structure of the chaperonin from Thermococcus strain KS-1 (FormIII crystal complexed with ADP) (3.0 Å) PDBe PDBsum 1q3s
Catalytic CATH Domains
3.30.260.10 CATHdb 1.10.560.10 CATHdb (see all for 1q3s)
Cofactors
Magnesium(2+) (1) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:5.6.1.7)

ATP(4-)
CHEBI:30616ChEBI
+
water
CHEBI:15377ChEBI
→
hydrogenphosphate
CHEBI:43474ChEBI
+
hydron
CHEBI:15378ChEBI
+
ADP(3-)
CHEBI:456216ChEBI
Alternative enzyme names: Chaperonin,

Enzyme Mechanism

Introduction

Asp 64 and Asp 393 bind and polarise a water molecule, which becomes nucleophilic enough to perform inline displacement on the gamma-phosphate of ATP. A pentacovalent intermediate is formed. The negative charges on the gamma-phosphate group are stabilised by contacts with Thr 97, Thr 98 and an Mg(II) ion, lowering the free energies of transition states and the intermediate. The intermediate collapses to yield the products of ATP hydrolysis: ADP and free orthophosphate.

Catalytic Residues Roles

UniProt PDB* (1q3s)
Asp393 Asp393A Asp 393 holds and polarises a water molecule for inline attack on the gamma-phosphate of ATP. Upon the loss of water the Asp 393 interaction after ATP hydrolysis may be the trigger for conformational change and chaperonin opening, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
Asp64 Asp64A Asp 64 holds and polarises a water molecule for inline attack on the gamma-phosphate of ATP. hydrogen bond acceptor, electrostatic stabiliser
Thr97 Thr97A Thr 97 hydrogen bonds to the gamma phosphate of ATP during the transition states and intermediate, stabilising charge build-up. hydrogen bond donor, electrostatic stabiliser
Thr98 Thr98A Thr 98 hydrogen bonds to the gamma phosphate of ATP during the transition states and intermediate, stabilising charge build-up. hydrogen bond donor, 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, bimolecular nucleophilic addition, overall reactant used, intermediate formation, unimolecular elimination by the conjugate base, intermediate collapse, intermediate terminated, overall product formed, native state of enzyme regenerated

References

  1. Ditzel L et al. (1998), Cell, 93, 125-138. Crystal Structure of the Thermosome, the Archaeal Chaperonin and Homolog of CCT. DOI:10.1016/s0092-8674(00)81152-6. PMID:9546398.
  2. An YJ et al. (2017), Nat Commun, 8, 827-. Structural and mechanistic characterization of an archaeal-like chaperonin from a thermophilic bacterium. DOI:10.1038/s41467-017-00980-z. PMID:29018216.
  3. Shomura Y et al. (2004), J Mol Biol, 335, 1265-1278. Crystal Structures of the Group II Chaperonin from Thermococcus strain KS-1: Steric Hindrance by the Substituted Amino Acid, and Inter-subunit Rearrangement between Two Crystal Forms. DOI:10.1016/j.jmb.2003.11.028. PMID:14729342.

Step 1. Asp393 deprotonates water, which attacks the gamma phosphate of ATP in a nucleophilic addition, resulting in a pentavalent phosphate intermediate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Thr97A hydrogen bond donor, electrostatic stabiliser
Thr98A hydrogen bond donor, electrostatic stabiliser
Asp64A hydrogen bond acceptor, electrostatic stabiliser
Asp393A hydrogen bond acceptor
Asp393A proton acceptor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic addition, overall reactant used, intermediate formation

Step 2. The pentavalent intermediate collapses, releasing orthophosphate and ADP, which deprotonates Asp393.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Thr97A hydrogen bond donor, electrostatic stabiliser
Thr98A hydrogen bond donor, electrostatic stabiliser
Asp64A hydrogen bond acceptor, electrostatic stabiliser
Asp393A hydrogen bond donor
Asp393A proton donor

Chemical Components

ingold: unimolecular elimination by the conjugate base, proton transfer, intermediate collapse, intermediate terminated, overall product formed, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. Asp393 deprotonates water, which attacks the gamma phosphate of ATP in a nucleophilic addition, resulting in a pentavalent phosphate intermediate.

Step 2. The pentavalent intermediate collapses, releasing orthophosphate and ADP, which deprotonates Asp393.

Products.

Contributors

Gemma L. Holliday, Daniel E. Almonacid, Jonathan T. W. Ng, James Torrance, Charity Hornby