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.[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 | |||||||||
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![]() crystal structure of restriction endonuclease ecorii mutant r88a | |||||||||
Identifiers | |||||||||
Symbol | EcoRII-N | ||||||||
Pfam | PF09217 | ||||||||
Pfam clan | CL0405 | ||||||||
InterPro | IPR015300 | ||||||||
SCOP2 | 1na6 / SCOPe / SUPFAM | ||||||||
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EcoRII C terminal | |||||||||
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![]() crystal structure of restriction endonuclease ecorii mutant r88a | |||||||||
Identifiers | |||||||||
Symbol | EcoRII-C | ||||||||
Pfam | PF09019 | ||||||||
Pfam clan | CL0236 | ||||||||
InterPro | IPR015109 | ||||||||
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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]