2FQZ

Metal-depleted Ecl18kI in complex with uncleaved DNA

Summary for 2FQZ

• Entry DOI: 10.2210/pdb2fqz/pdb
• Related: 2GB7
• Descriptor: DNA STRAND 1, DNA STRAND 2, R.Ecl18kI, ... (4 entities in total)
• Functional Keywords: ecl18ki-dna complex, type ii restriction endonuclease, nucleotide flipping, base extrusion, hydrolase-dna complex, hydrolase/dna
• Biological source: Enterobacter cloacae
• Total number of polymer chains: 8
• Total formula weight: 154704.31

Authors

Bochtler, M.,Szczepanowski, R.H.,Tamulaitis, G.,Grazulis, S.,Czapinska, H.,Manakova, E.,Siksnys, V. (deposition date: 2006-01-18, release date: 2006-06-20, Last modification date: 2024-02-14)

Primary citation

Bochtler, M.,Szczepanowski, R.H.,Tamulaitis, G.,Grazulis, S.,Czapinska, H.,Manakova, E.,Siksnys, V.
Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease
Embo J., 25:2219-2229, 2006

PubMed Abstract: 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.

PubMed: 16628220
DOI: 10.1038/sj.emboj.7601096

Experimental method

X-RAY DIFFRACTION (2 Å)