R.EcoRII
Restriction enzyme
From Wikipedia, the free encyclopedia
EcoRII (pronounced 'eco R two') is an Restriction endonuclease enzyme (REase) of the 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.[1]
Mode of action
EcoRII is a bacterial Type IIE[2] REase that interacts with two[3] or three[4] 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 cuts the target DNA sequence CCWGG, generating sticky ends.[5]
Cut diagram
| Recognition site | Cut results |
5' NNCCWGGNN 3' NNGGWCCNN |
5' NN CCWGGNN 3' NNGGWCC NN |
Structure
The apo crystal structure of EcoRII mutant R88A (PDB: 1NA6)[6] 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)[7]
- C-terminal domain of restriction endonuclease BfiI[8] (PDB: 2C1L)[9]
Catalytic domain
The C-terminal catalytic domain has a typical[10] 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.[6]
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
