Get   for     ? 
 Site search     ? 
Catalytic Site Atlas Version 2.2.12
Find Annotated Site: PDB code:
Swiss-Prot code:
EC number:
Help
CSA entry for 1znv
Original Entry
Title:
Hydrolase/protein binding
Compound:
Colicin e7 immunity protein
Mutant:
Yes
UniProt/Swiss-Prot:
-
Q03708-CEA7_ECOLI
Q47112-IMM7_ECOLI
EC Class:
3.1.-.-
Other CSA Entries:
Overview of all sites for 1znv
Homologues of 1znv
Entries for UniProt/Swiss-Prot: 
Entries for UniProt/Swiss-Prot: Q03708
Entries for UniProt/Swiss-Prot: Q47112
Entries for EC: 3.1.-.-
Other Databases:
PDB entry: 1znv
PDBsum entry: 1znv
UniProt/Swiss-Prot: 
UniProt/Swiss-Prot: Q03708
UniProt/Swiss-Prot: Q47112
IntEnz entry: 3.1.-.-
Literature Report:
Introduction:
The ColE7 endonuclease from Escherichia coli binds nucleic acids and hydrolyzes a phosphodiester bond. It contains the His-metal finger motif and may function with a range of metals, although the physiological metal is thought to be Zn(II).
Mechanism:
1) A water nucleophile is polarised by His 545, which acts as a general base to generate hydroxide.

2) An non-bridging oxygen of the scissile phosphodiester group coordinates to Zn(II), making the phosphorus more electrophilic.

3) Hydroxide attacks the scissile phosphodiester bond.

4) Zn(II) stabilises the charge build-up in the pentacovalent transition state.

5) The transition state collapses, with Zn(II) stabilising the charge on the terminal 3' hydroxyl cleavage product.
Sites:

Click to Display Catalytic Site (Get help with this section)
Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
GLUB 545 545Sidechain
Acid/baseWater
His 545 acts as the general base catalyst, deprotonating water as it attacks as a nucleophile.
Evidence from paper Evidence concerns Evidence type
PubMed ID 16434744 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 16434744 Current protein Conservation of residue
PubMed ID 16434744 Current protein Mutagenesis of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
NIB 580 0
ElectrostaticTransition state
ElectrostaticSubstrate
The divalent metal ion (Zn(II) in the native enzyme) coordinates the scissile phosphate group via a non-bridging oxygen atom. This has up to three effects: 1) Increases the electrophilicity of the scissile phosphodiester bond 2) Acts as an oxyanion hole, stabilising the charge build-up in the transition state. 3) Stabilises the charge on the 3' terminal hydroxy cleavage product.
Evidence from paper Evidence concerns Evidence type
PubMed ID 16434744 Current protein Ligand is essential for catalysis
PubMed ID 16434744 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 16434744 Current protein Structural similarity to homologue of known mechanism
Notes:
The literature does not state if His 545 is the acid that protonates the 3' hydroxy cleavage product.
References:
1
Which EBI biological databases are available and how do I access them? EBI Site Map