6GHC

Modification dependent EcoKMcrA restriction endonuclease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 9829-9841

  • DOI: 10.1093/nar/gky731

  • PubMed Abstract: 
  • Escherichia coli McrA (EcoKMcrA) acts as a methylcytosine and hydroxymethylcytosine dependent restriction endonuclease. We present a biochemical characterization of EcoKMcrA that includes the first demonstration of its endonuclease activity, small an ...

    Escherichia coli McrA (EcoKMcrA) acts as a methylcytosine and hydroxymethylcytosine dependent restriction endonuclease. We present a biochemical characterization of EcoKMcrA that includes the first demonstration of its endonuclease activity, small angle X-ray scattering (SAXS) data, and a crystal structure of the enzyme in the absence of DNA. Our data indicate that EcoKMcrA dimerizes via the anticipated C-terminal HNH domains, which together form a single DNA binding site. The N-terminal domains are not homologous to SRA domains, do not interact with each other, and have separate DNA binding sites. Electrophoretic mobility shift assay (EMSA) and footprinting experiments suggest that the N-terminal domains can sense the presence and sequence context of modified cytosines. Pyrrolocytosine fluorescence data indicate no base flipping. In vitro, EcoKMcrA DNA endonuclease activity requires Mn2+ ions, is not strictly methyl dependent, and is not observed when active site variants of the enzyme are used. In cells, EcoKMcrA specifically restricts DNA that is modified in the correct sequence context. This activity is impaired by mutations of the nuclease active site, unless the enzyme is highly overexpressed.


    Organizational Affiliation

    International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5-methylcytosine-specific restriction enzyme A
A, B
287Escherichia 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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 82.045α = 90.00
b = 90.383β = 90.00
c = 95.406γ = 90.00
Software Package:
Software NamePurpose
autoSHARPphasing
REFMACrefinement
BUCCANEERmodel building
XDSdata reduction
SHELXDEphasing
DMphasing
XDSdata scaling
PARROTphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-08-22
    Type: Data collection, Database references
  • Version 1.2: 2018-10-24
    Type: Data collection, Database references