R.EcoRII

File:Eco RII 1NA6.png

Eco RII dimer based on PDB ID 1NA6

Restriction endonuclease (REase) EcoRII (pronounced "eco R two") is an enzyme of restriction modification system (RM) naturally found in Escherichia coli, a Gram-negative bacteria. Its molecular mass is 45.2 kDa, being composed of 402 amino acids.

Mode of action

EcoRII is a bacterial Type IIE REase that interacts with two or three copies of the pseudopalindromic DNA recognition sequence 5'-CCWGG-3' (W = A or T), one being the actual target of cleavage, the other(s) serving as the allosteric activator(s). EcoRII cut target DNA sequence CCWGG generating sticky ends.

Cut diagram

Recognition site	Cut results
5' NNCCWGGNN 3' NNGGWCCNN	5' NN CCWGGNN 3' NNGGWCC NN

Structure

Restriction endonuclease EcoRII, N-terminal
File:PDB 1na6 EBI.jpg crystal structure of restriction endonuclease ecorii mutant r88a
Identifiers
Symbol	EcoRII-N
Pfam	PF09217
Pfam clan	CL0405
InterPro	IPR015300
SCOP	1na6
SUPERFAMILY	1na6
Available protein structures: Pfam structures PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

EcoRII C terminal
File:PDB 1na6 EBI.jpg crystal structure of restriction endonuclease ecorii mutant r88a
Identifiers
Symbol	EcoRII-C
Pfam	PF09019
Pfam clan	CL0236
InterPro	IPR015109
Available protein structures: Pfam structures PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

The apo crystal structure of EcoRII mutant R88A (PDB: 1NA6​) has been solved at 2.1 Å resolution. The EcoRII monomer has two domains, N-terminal and C-terminal, linked through a hinge loop.

Effector-binding domain

The N-terminal effector-binding domain has an archetypal DNA-binding pseudobarrel fold (SCOP 101936) with a prominent cleft. Structural superposition showed it is evolutionarily related to:

• B3 DNA binding domain (SCOP 117343) from the transcription factors in higher plants (PDB: 1WID​)
• C-terminal domain of restriction endonuclease BfiI (PDB: 2C1L​)

Catalytic domain

The C-terminal catalytic domain has a typical restriction endonuclease-like fold (SCOP 52979) and belongs to the large (more than 30 members) restriction endonuclease superfamily (SCOP 52980).

Autoinhibition/activation mechanism

Structure-based sequence alignment and site-directed mutagenesis identified the putative PD..D/EXK active sites of the EcoRII catalytic domain dimer that in apo structure are spatially blocked by the N-terminal domains.

See also

• EcoRI, another nuclease enzyme from Escherichia coli.
• EcoRV, another nuclease enzyme from Escherichia coli.
• B3 DNA binding domain from higher plants is evolutionary related to EcoRII
• FokI, another nuclease enzyme from Flavobacterium okeanokoites

External links

• EcoRII in Restriction Enzyme Database REBASE