Nucleotide flips determine the specificity of the Ecl18kI restriction endonucleaseBochtler, M., Szczepanowski, R.H., Tamulaitis, G., Grazulis, S., Czapinska, H., Manakova, E., Siksnys, V.
(2006) Embo J. 25: 2219-2229
- PubMed: 16628220
- DOI: 10.1038/sj.emboj.7601096
- Primary Citation of Related Structures:
- PubMed Abstract:
- The Ecl18kI restriction-modification system: cloning, expression, properties of the purified enzymes.
Denjmukhametov, M.M.,Brevnov, M.G.,Zakharova, M.V.,Repyk, A.V.,Solonin, A.S.,Petrauskene, O.V.,Gromova, E.S.
(1998) FEBS Lett. 433: 233
- Alternative arrangements of catalytic residues at the active sites of restriction enzymes.
Tamulaitis, G.,Solonin, A.S.,Siksnys, V.
(2002) FEBS Lett. 518: 17
Restricion endonuclease Ecl18kI is specific for the sequence /CCNGG and cleaves it before the outer C to generate 5 nt 5'-overhangs. It has been suggested that Ecl18kI is evolutionarily related to NgoMIV, a 6-bp cutter that cleaves the sequence G/CCG ...
Restricion endonuclease Ecl18kI is specific for the sequence /CCNGG and cleaves it before the outer C to generate 5 nt 5'-overhangs. It has been suggested that Ecl18kI is evolutionarily related to NgoMIV, a 6-bp cutter that cleaves the sequence G/CCGGC and leaves 4 nt 5'-overhangs. Here, we report the crystal structure of the Ecl18kI-DNA complex at 1.7 A resolution and compare it with the known structure of the NgoMIV-DNA complex. We find that Ecl18kI flips both central nucleotides within the CCNGG sequence and buries the extruded bases in pockets within the protein. Nucleotide flipping disrupts Watson-Crick base pairing, induces a kink in the DNA and shifts the DNA register by 1 bp, making the distances between scissile phosphates in the Ecl18kI and NgoMIV cocrystal structures nearly identical. Therefore, the two enzymes can use a conserved DNA recognition module, yet recognize different sequences, and form superimposable dimers, yet generate different cleavage patterns. Hence, Ecl18kI is the first example of a restriction endonuclease that flips nucleotides to achieve specificity for its recognition site.
International Institute of Molecular and Cell Biology, Warsaw, Poland. MBochtler@iimcb.gov.pl