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Catalytic Site Atlas

CSA LITERATURE entry for 1q3q

E.C. namechaperonin ATPase
SpeciesThermococcus sp. (Archaea)
E.C. Number (IntEnz) 3.6.4.9
CSA Homologues of 1q3qThere are 34 Homologs
CSA Entries With UniProtID P61112
CSA Entries With EC Number 3.6.4.9
PDBe Entry 1q3q
PDBSum Entry 1q3q
MACiE Entry M0179

Literature Report

IntroductionChaperonins 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.
MechansimAsp 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 Mg2+ 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.
Reaction

Catalytic Sites for 1q3q

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
ThrA9797macie:sideChainThr 97 hydrogen bonds to the gamma phosphate of ATP during the transition states and intermediate, stabilising charge build-up.
ThrA9898macie:sideChainThr 98 hydrogen bonds to the gamma phosphate of ATP during the transition states and intermediate, stabilising charge build-up.
AspA6464macie:sideChainAsp 64 holds and polarises a water molecule for inline attack on the gamma-phosphate of ATP.
AspA393393macie:sideChainAsp 393 holds and polarises a water molecule for inline attack on the gamma-phosphate of ATP.
Loss of water - Asp 393 interaction after ATP hydrolysis may be the trigger for conformational change and chaperonin opening,

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
ThrB9898macie:sideChainThr 98 hydrogen bonds to the gamma phosphate of ATP during the transition states and intermediate, stabilising charge build-up.
ThrB9797macie:sideChainThr 97 hydrogen bonds to the gamma phosphate of ATP during the transition states and intermediate, stabilising charge build-up.
AspB6464macie:sideChainAsp 64 holds and polarises a water molecule for inline attack on the gamma-phosphate of ATP.
AspB393393macie:sideChainAsp 393 holds and polarises a water molecule for inline attack on the gamma-phosphate of ATP.
Loss of water - Asp 393 interaction after ATP hydrolysis may be the trigger for conformational change and chaperonin opening,

Annotated By Reference To The Literature - Site 3 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
ThrC9898macie:sideChainThr 98 hydrogen bonds to the gamma phosphate of ATP during the transition states and intermediate, stabilising charge build-up.
ThrC9797macie:sideChainThr 97 hydrogen bonds to the gamma phosphate of ATP during the transition states and intermediate, stabilising charge build-up.
AspC6464macie:sideChainAsp 64 holds and polarises a water molecule for inline attack on the gamma-phosphate of ATP.
AspC393393macie:sideChainAsp 393 holds and polarises a water molecule for inline attack on the gamma-phosphate of ATP.
Loss of water - Asp 393 interaction after ATP hydrolysis may be the trigger for conformational change and chaperonin opening,

Annotated By Reference To The Literature - Site 4 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
ThrD9898macie:sideChainThr 98 hydrogen bonds to the gamma phosphate of ATP during the transition states and intermediate, stabilising charge build-up.
ThrD9797macie:sideChainThr 97 hydrogen bonds to the gamma phosphate of ATP during the transition states and intermediate, stabilising charge build-up.
AspD6464macie:sideChainAsp 64 holds and polarises a water molecule for inline attack on the gamma-phosphate of ATP.
AspD393393macie:sideChainAsp 393 holds and polarises a water molecule for inline attack on the gamma-phosphate of ATP.
Loss of water - Asp 393 interaction after ATP hydrolysis may be the trigger for conformational change and chaperonin opening,

Literature References

Notes:
Shomura Y
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.
J Mol Biol 2004 335 1265-1278
PubMed: 14729342
Ditzel L
Crystal structure of the thermosome, the archaeal chaperonin and homolog of CCT.
Cell 1998 93 125-138
PubMed: 9546398
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