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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1qhg
Original Entry
Title:
Hydrolase
Compound:
Atp-dependent helicase pcra
Mutant:
No
UniProt/Swiss-Prot:
P56255-PCRA_BACST
EC Class:
No EC number available
Other CSA Entries:
Overview of all sites for 1qhg
Homologues of 1qhg
Entries for UniProt/Swiss-Prot: P56255
Other Databases:
PDB entry: 1qhg
PDBsum entry: 1qhg
UniProt/Swiss-Prot: P56255
Literature Report:
Introduction:
PcrA DNA helicase is a 3'-5' DNA helicase. It is a single-stranded DNA (ssDNA)-dependent ATPase that uses the free energy of ATP hydrolysis to unwind duplex DNA. PcrA is known to be essential in some species, such as Bacillus subtilis and Staphylococcus aureus, with roles in DNA repair and rolling circle replication.

This annotation covers the ATPase activity of PcrA.
Mechanism:
PcrA uses Glu 224 as a general base to deprotonate the water molecule that attacks the gamma phosphate of ATP. In addition, Lys 37, Arg 387, Arg 610 and an Mg2+ ion contact the triphosphate chain of ATP and stabilise negative charge in the transition state.
Sites:

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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
NA 699 0
ElectrostaticTransition state
Weakens the P-O bond that is broken, stabilising negative charge in the transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 10388562 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 10388562 Current protein Ligand is essential for catalysis

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
LYSA 37 0Sidechain
ElectrostaticTransition state
Interacts with the beta phosphate of ATP; stabilises negative charge in the transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 10388562 Current protein Conservation of residue
PubMed ID 10388562 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 10388562 Current protein Mutagenesis of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
GLUA 224 0Sidechain
Acid/baseWater
Deprotonates the water molecule that attacks the gamma phosphate of ATP.
Evidence from paper Evidence concerns Evidence type
PubMed ID 10388562 Current protein Structural similarity to homologue of known mechanism
PubMed ID 10388562 Current protein Mutagenesis of residue
PubMed ID 10388562 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 10388562 Current protein Conservation of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ARGA 610 0Sidechain
ElectrostaticTransition state
Polarises the gamma phosphate of ATP, stabilising negative charge in the transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 10388562 Current protein Conservation of residue
PubMed ID 10388562 Current protein Mutagenesis of residue
PubMed ID 10388562 Current protein Residue is positioned appropriately (ligand position known)
References:
1
DNA binding mediates conformational changes and metal ion coordination in the active site of PcrA helicase.
P. Soultanas and M. S. Dillingham and S. S. Velankar and D. B. Wigley
J Mol Biol 290, (1) 137-48, (1999).
10388562
2
Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism.
S. S. Velankar and P. Soultanas and M. S. Dillingham and H. S. Subramanya and D. B. Wigley
Cell 97, (1) 75-84, (1999).
10199404
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