SNAP output for PDB entry 2y7h [SNAP web server]

PDB-id

2y7h; SNAP-derived features in text and JSON formats; DNAproDB

Class

transferase-DNA

Method

cryo-EM (18.0 Å)

Summary

Atomic model of the DNA-bound methylase complex from the type i restriction-modification enzyme ecoki (m2s1). based on fitting into em map 1534.

Reference

Kennaway CK, Obarska-Kosinska A, White JH, Tuszynska I, Cooper LP, Bujnicki JM, Trinick J, Dryden DTF (2009): "The Structure of M.Ecoki Type I DNA Methyltransferase with a DNA Mimic Antirestriction Protein." Nucleic Acids Res., 37, 762. doi: 10.1093/NAR/GKN988.

Abstract

Type-I DNA restriction-modification (R/M) systems are important agents in limiting the transmission of mobile genetic elements responsible for spreading bacterial resistance to antibiotics. EcoKI, a Type I R/M enzyme from Escherichia coli, acts by methylation- and sequence-specific recognition, leading to either methylation of DNA or translocation and cutting at a random site, often hundreds of base pairs away. Consisting of one specificity subunit, two modification subunits, and two DNA translocase/endonuclease subunits, EcoKI is inhibited by the T7 phage antirestriction protein ocr, a DNA mimic. We present a 3D density map generated by negative-stain electron microscopy and single particle analysis of the central core of the restriction complex, the M.EcoKI M(2)S(1) methyltransferase, bound to ocr. We also present complete atomic models of M.EcoKI in complex with ocr and its cognate DNA giving a clear picture of the overall clamp-like operation of the enzyme. The model is consistent with a large body of experimental data on EcoKI published over 40 years.