5HNF

Crystal structure of pyrene- and phenanthrene-modified DNA in complex with the BpuJ1 endonuclease binding domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.546 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI endonuclease.

Probst, M.Aeschimann, W.Chau, T.T.Langenegger, S.M.Stocker, A.Haner, R.

(2016) Nucleic Acids Res. 44: 7079-7089

  • DOI: 10.1093/nar/gkw644
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The use of the DNA duplex as a supramolecular scaffold is an established approach for the assembly of chromophore aggregates. In the absence of detailed structural insight, the characterization of thus assembled oligochromophores is, today, largely b ...

    The use of the DNA duplex as a supramolecular scaffold is an established approach for the assembly of chromophore aggregates. In the absence of detailed structural insight, the characterization of thus assembled oligochromophores is, today, largely based on solution-phase spectroscopy. Here, we describe the crystal structures of three DNA-organized chromophore aggregates. DNA hybrids containing non-nucleosidic pyrene and phenanthrene building blocks were co-crystallized with the recently described binding domain of the restriction enzyme BpuJI. Crystal structures of these complexes were determined at 2.7, 1.9 and 1.6 Å resolutions. The structures reveal aromatic stacking interactions between pyrene and/or phenanthrene units within the framework of the B-DNA duplex. In hybrids containing a single modification in each DNA strand near the end of the duplex, the two polyaromatic hydrocarbons are engaged in a face-to-face stacking orientation. Due to crystal packing and steric effects, the terminal GC base pair is disrupted in all three crystal structures, which results in a non-perfect stacking arrangement of the aromatic chromophores in two of the structures. In a hybrid containing a total of three pyrenes, crystal lattice induced end-to-end stacking of individual DNA duplexes leads to the formation of an extended aromatic π-stack containing four co-axially arranged pyrenes. The aromatic planes of the stacked pyrenes are oriented in a parallel way. The study demonstrates the value of co-crystallization of chemically modified DNA with the recombinant binding domain of the restriction enzyme BpuJI for obtaining detailed structural insight into DNA-assembled oligochromophores.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Restriction endonuclease R.BpuJI
A
288Bacillus pumilusMutation(s): 0 
Gene Names: bpuJIR
Find proteins for A3FMN7 (Bacillus pumilus)
Go to UniProtKB:  A3FMN7
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*(YPE)P*AP*CP*CP*CP*GP*TP*GP*GP*A)-3')L11synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*CP*AP*CP*GP*GP*GP*TP*(YPF)P*C)-3')M11synthetic construct
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
YPE
Query on YPE
L
NON-POLYMERC24 H19 O5 P

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YPF
Query on YPF
M
NON-POLYMERC22 H19 O5 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.546 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.171 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 165.723α = 90.00
b = 59.278β = 94.20
c = 44.048γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2016-09-14
    Type: Database references