Crystal structure of the HsdR subunit of the EcoR124I restriction enzyme with the C-terminal domain

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

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Re-refinement Note

This entry reflects an alternative modeling of the original data in: 2w00 5j3n


Crystal structure of a novel domain of the motor subunit of the Type I restriction enzyme EcoR124 involved in complex assembly and DNA binding.

Grinkevich, P.Sinha, D.Iermak, I.Guzanova, A.Weiserova, M.Ludwig, J.Mesters, J.R.Ettrich, R.H.

(2018) J Biol Chem 293: 15043-15054

  • DOI: https://doi.org/10.1074/jbc.RA118.003978
  • Primary Citation of Related Structures:  
    5J3N, 6H2J

  • PubMed Abstract: 

    Although EcoR124 is one of the better-studied Type I restriction-modification enzymes, it still presents many challenges to detailed analyses because of its structural and functional complexity and missing structural information. In all available structures of its motor subunit HsdR, responsible for DNA translocation and cleavage, a large part of the HsdR C terminus remains unresolved. The crystal structure of the C terminus of HsdR, obtained with a crystallization chaperone in the form of pHluorin fusion and refined to 2.45 Å, revealed that this part of the protein forms an independent domain with its own hydrophobic core and displays a unique α-helical fold. The full-length HsdR model, based on the WT structure and the C-terminal domain determined here, disclosed a proposed DNA-binding groove lined by positively charged residues. In vivo and in vitro assays with a C-terminal deletion mutant of HsdR supported the idea that this domain is involved in complex assembly and DNA binding. Conserved residues identified through sequence analysis of the C-terminal domain may play a key role in protein-protein and protein-DNA interactions. We conclude that the motor subunit of EcoR124 comprises five structural and functional domains, with the fifth, the C-terminal domain, revealing a unique fold characterized by four conserved motifs in the IC subfamily of Type I restriction-modification systems. In summary, the structural and biochemical results reported here support a model in which the C-terminal domain of the motor subunit HsdR of the endonuclease EcoR124 is involved in complex assembly and DNA binding.

  • Organizational Affiliation

    From the Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zamek 136, 373 33 Nove Hrady, Czech Republic.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Type I restriction enzyme R Protein
A, B
1,038Escherichia coliMutation(s): 0 
Gene Names: hsdR
Find proteins for P10486 (Escherichia coli)
Explore P10486 
Go to UniProtKB:  P10486
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10486
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.91α = 90
b = 129.922β = 90
c = 161.01γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Czech Science FoundationCzech RepublicP207/12/2323

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-10-10
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-10
    Changes: Data collection
  • Version 1.3: 2019-07-17
    Changes: Data collection
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description