4BE7

MUTANT (K220R) OF THE HSDR SUBUNIT OF THE ECOR124I RESTRICTION ENZYME IN COMPLEX WITH ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.744 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Functional Coupling of Duplex Translocation to DNA Cleavage in a Type I Restriction Enzyme.

Csefalvay, E.Lapkouski, M.Guzanova, A.Csefalvay, L.Baikova, T.Shevelev, I.Bialevich, V.Shamayeva, K.Janscak, P.Kuta Smatanova, I.Panjikar, S.Carey, J.Weiserova, M.Ettrich, R.

(2015) Plos One 10: 28700

  • DOI: 10.1371/journal.pone.0128700
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Type I restriction-modification enzymes are multifunctional heteromeric complexes with DNA cleavage and ATP-dependent DNA translocation activities located on motor subunit HsdR. Functional coupling of DNA cleavage and translocation is a hallmark of t ...

    Type I restriction-modification enzymes are multifunctional heteromeric complexes with DNA cleavage and ATP-dependent DNA translocation activities located on motor subunit HsdR. Functional coupling of DNA cleavage and translocation is a hallmark of the Type I restriction systems that is consistent with their proposed role in horizontal gene transfer. DNA cleavage occurs at nonspecific sites distant from the cognate recognition sequence, apparently triggered by stalled translocation. The X-ray crystal structure of the complete HsdR subunit from E. coli plasmid R124 suggested that the triggering mechanism involves interdomain contacts mediated by ATP. In the present work, in vivo and in vitro activity assays and crystal structures of three mutants of EcoR124I HsdR designed to probe this mechanism are reported. The results indicate that interdomain engagement via ATP is indeed responsible for signal transmission between the endonuclease and helicase domains of the motor subunit. A previously identified sequence motif that is shared by the RecB nucleases and some Type I endonucleases is implicated in signaling.


    Organizational Affiliation

    Center for Nanobiology and Structural Biology, Institute of Microbiology and Global Change Research Center, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33 Nove Hrady, Czech Republic.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TYPE I RESTRICTION ENZYME ECOR124II R PROTEIN
B, D
1038Escherichia coliMutation(s): 1 
Gene Names: hsdR (hsr)
EC: 3.1.21.3
Find proteins for P10486 (Escherichia coli)
Go to UniProtKB:  P10486
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
B, D
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
B, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.744 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.249 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 87.045α = 90.00
b = 124.354β = 108.86
c = 128.012γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
PHENIXrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-26
    Type: Initial release
  • Version 1.1: 2015-06-17
    Type: Database references
  • Version 1.2: 2019-03-06
    Type: Data collection, Experimental preparation, Other