2Y7C

Atomic model of the Ocr-bound methylase complex from the Type I restriction-modification enzyme EcoKI (M2S1). Based on fitting into EM map 1534.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Structure of M.Ecoki Type I DNA Methyltransferase with a DNA Mimic Antirestriction Protein.

Kennaway, C.K.Obarska-Kosinska, A.White, J.H.Tuszynska, I.Cooper, L.P.Bujnicki, J.M.Trinick, J.Dryden, D.T.F.

(2009) Nucleic Acids Res. 37: 762

  • DOI: 10.1093/nar/gkn988
  • Primary Citation of Related Structures:  2Y7H

  • PubMed 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 me ...

    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.


    Organizational Affiliation

    Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN
A
464Escherichia coli (strain K12)Gene Names: hsdS (hss)
Find proteins for P05719 (Escherichia coli (strain K12))
Go to UniProtKB:  P05719
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TYPE I RESTRICTION ENZYME ECOKI M PROTEIN
B, C
529Escherichia coli (strain K12)Gene Names: hsdM (hsm)
EC: 2.1.1.72
Find proteins for P08957 (Escherichia coli (strain K12))
Go to UniProtKB:  P08957
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
GENE 0.3 PROTEIN
D, E
116Enterobacteria phage T7N/A
Find proteins for P03775 (Enterobacteria phage T7)
Go to UniProtKB:  P03775
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-09
    Type: Initial release
  • Version 1.1: 2013-03-20
    Type: Other, Refinement description, Version format compliance
  • Version 1.2: 2017-08-30
    Type: Data collection