7BTR

EcoR124I-ArdA in the Restriction-Alleviation State


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into assembly, operation and inhibition of a type I restriction-modification system.

Gao, Y.Cao, D.Zhu, J.Feng, H.Luo, X.Liu, S.Yan, X.X.Zhang, X.Gao, P.

(2020) Nat Microbiol 

  • DOI: 10.1038/s41564-020-0731-z
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Type I restriction-modification (R-M) systems are widespread in prokaryotic genomes and provide robust protection against foreign DNA. They are multisubunit enzymes with methyltransferase, endonuclease and translocase activities. Despite extensive st ...

    Type I restriction-modification (R-M) systems are widespread in prokaryotic genomes and provide robust protection against foreign DNA. They are multisubunit enzymes with methyltransferase, endonuclease and translocase activities. Despite extensive studies over the past five decades, little is known about the molecular mechanisms of these sophisticated machines. Here, we report the cryo-electron microscopy structures of the representative EcoR124I R-M system in different assemblies (R 2 M 2 S 1 , R 1 M 2 S 1 and M 2 S 1 ) bound to target DNA and the phage and mobile genetic element-encoded anti-restriction proteins Ocr and ArdA. EcoR124I can precisely regulate different enzymatic activities by adopting distinct conformations. The marked conformational transitions of EcoR124I are dependent on the intrinsic flexibility at both the individual-subunit and assembled-complex levels. Moreover, Ocr and ArdA use a DNA-mimicry strategy to inhibit multiple activities, but do not block the conformational transitions of the complexes. These structural findings, complemented by mutational studies of key intermolecular contacts, provide insights into assembly, operation and inhibition mechanisms of type I R-M systems.


    Organizational Affiliation

    CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. gaopu@ibp.ac.cn.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antirestriction protein ArdA
B, F
165Enterococcus faecalis EnGen0302Mutation(s): 0 
Gene Names: UMC_02545
Find proteins for A0A0M2A928 (Enterococcus faecalis EnGen0302)
Go to UniProtKB:  A0A0M2A928

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Type I restriction enzyme R Protein
C
1038Escherichia coliMutation(s): 0 
Gene Names: hsdR
EC: 3.1.21.3
Find proteins for Q304R3 (Escherichia coli)
Go to UniProtKB:  Q304R3

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Type I restriction enzyme EcoR124II M protein
A, D
520Escherichia coliMutation(s): 0 
Gene Names: hsdMhsm
EC: 2.1.1.72
Find proteins for P10484 (Escherichia coli)
Go to UniProtKB:  P10484

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Type-1 restriction enzyme EcoR124II specificity protein
E
404Escherichia coliMutation(s): 0 
Gene Names: hsdShss
Find proteins for P10485 (Escherichia coli)
Go to UniProtKB:  P10485
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2020-04-02 
  • Released Date: 2020-05-27 
  • Deposition Author(s): Gao, Y., Gao, P.

Revision History 

  • Version 1.0: 2020-05-27
    Type: Initial release
  • Version 1.1: 2020-06-24
    Changes: Database references