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Search The CSA
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Catalytic Site Atlas

CSA LITERATURE entry for 1hqc

E.C. nameDNA helicase
SpeciesThermus thermophilus (Bacteria)
E.C. Number (IntEnz) 3.6.4.12
CSA Homologues of 1hqcThere are 20 Homologs
CSA Entries With UniProtID Q5SL87
CSA Entries With EC Number 3.6.4.12
PDBe Entry 1hqc
PDBSum Entry 1hqc
MACiE Entry 1hqc

Literature Report

IntroductionRecombination in bacteria requires the isomerisation of the Holliday junction in a process revolving around the activities of three enzymes each with specific functions. RuvB, the second of the three enzymes involved, catalyses the migration of the branches of DNA before the cleavage step occurs, so that the cleavage and rejoining can produce recombinant products. It works by using ATP hydrolysis to power conformational change in the DNA binding domain, restructuring the Holliday junction. The ATP binding domain shows homology to the AAA family (ATP associated activities) in that it has a Rossman fold and both Walker A and Walker B motifs. Here, the enzyme from Thermus thermophilus is analysed; it displays significant sequence identity with the E.coli enzyme and both share similar active sites and probable catalytic mechanisms, as well as the same overall fold.
MechansimATP hydrolysis occurs through nucleophilic attack by water on the electrophilic phosphorous atom of the gamma phosphate of ATP to produce a pentavalent phosphate transition state, stabilised by contacts with Mg2+, Arg 205 and Thr 146. Collapse of this intermediate releases ADP and Pi, and is used to drive the conversion of the inactive homoheptamer to a homohexameric structure, thus causing branch migration of the DNA.
Reaction

Catalytic Sites for 1hqc

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
ThrA146146macie:sideChainActs to stabilise the pentavalent phosphate transition state that forms during the reaction through electrostatic contacts with the beta phosphate.
ArgA205205macie:sideChainStabilises the pentavalent phosphate transition state through electrostatic contacts with the gamma phosphate of ATP.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
ThrB146146macie:sideChainActs to stabilise the pentavalent phosphate transition state that forms during the reaction through electrostatic contacts with the beta phosphate.
ArgB205205macie:sideChainStabilises the pentavalent phosphate transition state through electrostatic contacts with the gamma phosphate of ATP.

Literature References

Notes:
Hishida T
Role of walker motif A of RuvB protein in promoting branch migration of holliday junctions. Walker motif a mutations affect Atp binding, Atp hydrolyzing, and DNA binding activities of Ruvb.
J Biol Chem 1999 274 25335-25342
PubMed: 10464259
Yamada K
Crystal structure of the Holliday junction migration motor protein RuvB from Thermus thermophilus HB8.
Proc Natl Acad Sci U S A 2001 98 1442-1447
PubMed: 11171970
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