4KYW

Restriction endonuclease DPNI in complex with two DNA molecules


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis of the methylation specificity of R.DpnI.

Mierzejewska, K.Siwek, W.Czapinska, H.Kaus-Drobek, M.Radlinska, M.Skowronek, K.Bujnicki, J.M.Dadlez, M.Bochtler, M.

(2014) Nucleic Acids Res. 42: 8745-8754

  • DOI: 10.1093/nar/gku546

  • PubMed Abstract: 
  • R.DpnI consists of N-terminal catalytic and C-terminal winged helix domains that are separately specific for the Gm6ATC sequences in Dam-methylated DNA. Here we present a crystal structure of R.DpnI with oligoduplexes bound to the catalytic and winge ...

    R.DpnI consists of N-terminal catalytic and C-terminal winged helix domains that are separately specific for the Gm6ATC sequences in Dam-methylated DNA. Here we present a crystal structure of R.DpnI with oligoduplexes bound to the catalytic and winged helix domains and identify the catalytic domain residues that are involved in interactions with the substrate methyl groups. We show that these methyl groups in the Gm6ATC target sequence are positioned very close to each other. We further show that the presence of the two methyl groups requires a deviation from B-DNA conformation to avoid steric conflict. The methylation compatible DNA conformation is complementary with binding sites of both R.DpnI domains. This indirect readout of methylation adds to the specificity mediated by direct favorable interactions with the methyl groups and solvation/desolvation effects. We also present hydrogen/deuterium exchange data that support 'crosstalk' between the two domains in the identification of methylated DNA, which should further enhance R.DpnI methylation specificity.


    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
Type-2 restriction enzyme DpnI
A
257Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)Gene Names: dpnC
EC: 3.1.21.4
Find proteins for P0A459 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Go to UniProtKB:  P0A459
Entity ID: 2
MoleculeChainsLengthOrganism
5'-(*DC*DTP*DGP*DGP*6MAP*DTP*DCP*DCP*DAP*DG)-3'C,D,E,F10N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
6MA
Query on 6MA
C, D, E, F
DNA LINKINGC11 H16 N5 O6 PA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.201 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 95.700α = 90.00
b = 101.050β = 90.00
c = 114.850γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
ARP/wARPmodel building
MOLREPphasing
XSCALEdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-04
    Type: Initial release
  • Version 1.1: 2014-07-02
    Type: Database references
  • Version 1.2: 2014-07-09
    Type: Database references
  • Version 1.3: 2014-08-20
    Type: Database references