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]
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]
| Recognition site | Cut results |
5' NNCCWGGNN 3' NNGGWCCNN | 5' NN CCWGGNN 3' NNGGWCC NN |
| Restriction endonuclease EcoRII, N-terminal | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 crystal structure of restriction endonuclease ecorii mutant r88a | |||||||||
| Identifiers | |||||||||
| Symbol | EcoRII-N | ||||||||
| Pfam | PF09217 | ||||||||
| Pfam clan | CL0405 | ||||||||
| InterPro | IPR015300 | ||||||||
| SCOP2 | 1na6 / SCOPe / SUPFAM | ||||||||
| |||||||||
| EcoRII C terminal | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| crystal structure of restriction endonuclease ecorii mutant r88a | |||||||||
| Identifiers | |||||||||
| Symbol | EcoRII-C | ||||||||
| Pfam | PF09019 | ||||||||
| Pfam clan | CL0236 | ||||||||
| InterPro | IPR015109 | ||||||||
| |||||||||
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.
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:
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 ).
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]
