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: 18.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    2Y7C, 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 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEINA464Escherichia coliMutation(s): 0 
EC: 3.1.21.3
UniProt
Find proteins for P05719 (Escherichia coli (strain K12))
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Go to UniProtKB:  P05719
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UniProt GroupP05719
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TYPE I RESTRICTION ENZYME ECOKI M PROTEINB, C529Escherichia coliMutation(s): 0 
EC: 3.1.21.3 (PDB Primary Data), 2.1.1.72 (PDB Primary Data)
UniProt
Find proteins for P08957 (Escherichia coli (strain K12))
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UniProt GroupP08957
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
GENE 0.3 PROTEIND, E116Escherichia phage T7Mutation(s): 0 
Gene Names: 0.3
UniProt
Find proteins for P03775 (Escherichia phage T7)
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Go to UniProtKB:  P03775
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UniProt GroupP03775
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 18.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-09
    Type: Initial release
  • Version 1.1: 2013-03-20
    Changes: Other, Refinement description, Version format compliance
  • Version 1.2: 2017-08-30
    Changes: Data collection
  • Version 1.3: 2019-10-23
    Changes: Data collection, Other