6T22

N-terminal domain of EcoKMcrA restriction endonuclease (NEco) in complex with T5hmCGA target sequence


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the EcoKMcrA N-terminal domain (NEco): recognition of modified cytosine bases without flipping.

Slyvka, A.Zagorskaite, E.Czapinska, H.Sasnauskas, G.Bochtler, M.

(2019) Nucleic Acids Res. --: --

  • DOI: 10.1093/nar/gkz1017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • EcoKMcrA from Escherichia coli restricts CpG methylated or hydroxymethylated DNA, and may act as a barrier against host DNA. The enzyme consists of a novel N-terminal specificity domain that we term NEco, and a C-terminal catalytic HNH domain. Here, ...

    EcoKMcrA from Escherichia coli restricts CpG methylated or hydroxymethylated DNA, and may act as a barrier against host DNA. The enzyme consists of a novel N-terminal specificity domain that we term NEco, and a C-terminal catalytic HNH domain. Here, we report that NEco and full-length EcoKMcrA specificities are consistent. NEco affinity to DNA increases more from hemi- to full-methylation than from non- to hemi-methylation, indicating cooperative binding of the methyl groups. We determined the crystal structures of NEco in complex with fully modified DNA containing three variants of the Y5mCGR EcoKMcrA target sequence: C5mCGG, T5mCGA and T5hmCGA. The structures explain the specificity for the two central base pairs and one of the flanking pairs. As predicted based on earlier biochemical experiments, NEco does not flip any DNA bases. The proximal and distal methyl groups are accommodated in separate pockets. Changes to either pocket reduce DNA binding by NEco and restriction by EcoKMcrA, confirming the relevance of the crystallographically observed binding mode in solution.


    Related Citations: 
    • Activity and structure of EcoKMcrA.
      Czapinska, H.,Kowalska, M.,Zagorskaite, E.,Manakova, E.,Slyvka, A.,Xu, S.Y.,Siksnys, V.,Sasnauskas, G.,Bochtler, M.
      (2018) Nucleic Acids Res. 46: 9829


    Organizational Affiliation

    Institute of Biotechnology, Vilnius University, SaulÄ—tekio av. 7, 10257 Vilnius, Lithuania.,International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.,Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EcoKMcrA modification dependent restriction endonuclease
A, B
152Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: mcrA (rglA)
EC: 3.1.21.-
Find proteins for P24200 (Escherichia coli (strain K12))
Go to UniProtKB:  P24200
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*AP*TP*(5HC)P*GP*AP*TP*TP*C)-3')C,E10synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*AP*TP*(5HC)P*GP*AP*TP*GP*A)-3')D,F10synthetic construct
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5HC
Query on 5HC
C, D, E, F
DNA LINKINGC10 H16 N3 O8 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.157 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 113.417α = 90.00
b = 113.417β = 90.00
c = 156.367γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
MOLREPphasing
ARP/wARPmodel building
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-10-30
    Type: Initial release
  • Version 1.1: 2019-11-27
    Type: Database references