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CSA entry for 1hqc
Original Entry
Title:
Hydrolase
Compound:
Ruvb
Mutant:
No
UniProt/Swiss-Prot:
Q56214-RUVB_THETH
EC Class:
3.6.1.3
Other CSA Entries:
Overview of all sites for 1hqc
Homologues of 1hqc
Entries for UniProt/Swiss-Prot: Q56214
Entries for EC: 3.6.1.3
Other Databases:
PDB entry: 1hqc
PDBsum entry: 1hqc
UniProt/Swiss-Prot: Q56214
IntEnz entry: 3.6.1.3
Literature Report:
Introduction:
Recombination 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.
Mechanism:
ATP 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.
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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
401 0
ElectrostaticTransition state
Acts to stabilise the pentavalent phosphate transition state through electrostatic contacts with the gamma phosphate.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11171970 Current protein Ligand is essential for catalysis
PubMed ID 11171970 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
THRA 146 146Sidechain
ElectrostaticTransition state
Acts to stabilise the pentavalent phosphate transition state that forms during the reaction through electrostatic contacts with the beta phosphate.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11171970 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 10464259 Related protein: POA812 Mutagenesis of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ARGA 205 205Sidechain
ElectrostaticTransition state
Stabilises the pentavalent phosphate transition state through electrostatic contacts with the gamma phosphate of ATP.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11171970 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 10464259 Related protein: POA812 Mutagenesis of residue
References:
1
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.
T. Hishida and H. Iwasaki and T. Yagi and H. Shinagawa
J Biol Chem 274, (36) 25335-42, (1999).
10464259
2
Crystal structure of the Holliday junction migration motor protein RuvB from Thermus thermophilus HB8.
K. Yamada and N. Kunishima and K. Mayanagi and T. Ohnishi and T. Nishino and H. Iwasaki and H. Shinagawa and K. Morikawa
Proc Natl Acad Sci U S A 98, (4) 1442-7, (2001).
11171970
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