4DNB

METHYLATION OF THE ECORI RECOGNITION SITE DOES NOT ALTER DNA CONFORMATION. THE CRYSTAL STRUCTURE OF D(CGCGAM6ATTCGCG) AT 2.0 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Methylation of the EcoRI recognition site does not alter DNA conformation: the crystal structure of d(CGCGAm6ATTCGCG) at 2.0-A resolution.

Frederick, C.A.Quigley, G.J.van der Marel, G.A.van Boom, J.H.Wang, A.H.Rich, A.

(1988) J.Biol.Chem. 263: 17872-17879


  • PubMed Abstract: 
  • Methylation of nucleic acid bases is known to prevent the cleavage of DNA by restriction endonucleases. The effect on the conformation of the DNA molecule itself and hence its interactions with other DNA binding proteins has been a subject of general ...

    Methylation of nucleic acid bases is known to prevent the cleavage of DNA by restriction endonucleases. The effect on the conformation of the DNA molecule itself and hence its interactions with other DNA binding proteins has been a subject of general interest. To help address this question, we have solved the crystal structure at 2.0 A of the methylated dodecamer, d(CGCGAm6ATTCGCG), which contains the EcoRI recognition sequence and have compared the conformation of the methylated molecule with that of its nonmethylated counterpart. This methylation produces a bulky hydrophobic patch on the floor of the major groove of B-DNA which plays an important role in the mechanism of inhibition of EcoRI restriction activity. However, with the exception of small perturbations in the immediate vicinity of the methyl groups, the structure is virtually unchanged. Given the lack of a conformational change upon methylation, we have extended this thesis of the recognition process to other types of restriction systems and found that different restriction enzymes seem to have their own characteristic protein-DNA interactions. The relative spatial orientations of methylation sites and cleavage sites must play a major role in ordering protein secondary structure elements as well as subunit-subunit interactions along the DNA strand.


    Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*GP*AP*(6MA)P*TP*TP*CP*GP*CP*G)-3')A,B12N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
6MA
Query on 6MA
A, B
DNA LINKINGC11 H16 N5 O6 PA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 25.620α = 90.00
b = 40.390β = 90.00
c = 67.320γ = 90.00
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1989-01-09
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance