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CSA entry for 1e7l
Original Entry
Title:
Endonuclease
Compound:
Recombination endonuclease vii
Mutant:
Yes
UniProt/Swiss-Prot:
P13340-END7_BPT4
EC Class:
3.1.22.4
Other CSA Entries:
Overview of all sites for 1e7l
Homologues of 1e7l
Entries for UniProt/Swiss-Prot: P13340
Entries for EC: 3.1.22.4
Other Databases:
PDB entry: 1e7l
PDBsum entry: 1e7l
UniProt/Swiss-Prot: P13340
IntEnz entry: 3.1.22.4
Literature Report:
Introduction:
Endonuclease VII from Bacteriophage t4 is a junction-resolving enzyme. It has a broad substrate specificity, and recognises a variety of branched DNA structures and other structural perturbations in DNA such as Y-junctions, heteroduplex loops and abasic sites.

Mechanism:
This enzyme catalyses a one step reaction which proceeds through a pentavalent transition state. His 41 acts as a general base to deprotonate water, activating it for nucleophilic attack on the phosphorus atom. This causes the P-O3' bond to break, and at the same time, His 105' protonates the O3' atom of the leaving group. Ca2+ (and possibly His 43) stabilise the pentavalent transition state.

Sites:

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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
HISA 41 41Sidechain
Acid/baseWater
His 41 acts as a general base, deprotonating a water molecule and activating it for nucleophilic attack on the phosphorus atom.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11327769 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 11327769 Current protein Mutagenesis of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
HISA 43 43Sidechain
ElectrostaticTransition state
Stabilises charge on phosphate group in transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11327769 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
GLUA 65 65Sidechain
ElectrostaticTransition state
Stabilises charge on phosphate group in transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11327769 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ZNA1165 0
ElectrostaticTransition state
Ca2+ stabilises the pentavalent transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11327769 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
HISB 105 105Sidechain
Acid/baseSubstrate
His 105 acts as a general acid by protonating the O3' atom on the leaving group as it leaves.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11327769 Current protein Mutagenesis of residue
PubMed ID 11327769 Current protein Residue is positioned appropriately (ligand position known)
Notes:

References:
1
Conformational flexibility in T4 endonuclease VII revealed by crystallography: implications for substrate binding and cleavage.
H. Raaijmakers and I. Törö and R. Birkenbihl and B. Kemper and D. Suck
J Mol Biol 308, (2) 311-23, (2001).
11327769
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