2C7P

HhaI DNA methyltransferase complex with oligonucleotide containing 2- aminopurine opposite to the target base (GCGC:GMPC) and SAH

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Time-Resolved Fluorescence of 2-Aminopurine as a Probe of Base Flipping in M.HhaI-DNA Complexes.

Neely, R.K., Daujotyte, D., Grazulis, S., Magennis, S.W., Dryden, D.T.F., Klimasauskas, S., Jones, A.C.

(2005) Nucleic Acids Res 33: 6953

  • DOI: 10.1093/nar/gki995
  • Primary Citation of Related Structures:  
    2C7R, 2C7Q, 2C7P, 2C7O

  • PubMed Abstract: 

    • DNA base flipping is an important mechanism in molecular enzymology, but its study is limited by the lack of an accessible and reliable diagnostic technique. A series of crystalline complexes of a DNA methyltransferase, M.HhaI, and its cognate DNA, in which a fluorescent nucleobase analogue, 2-aminopurine (AP), occupies defined positions with respect the target flipped base, have been prepared and their structures determined at higher than 2 A resolution ...

    DNA base flipping is an important mechanism in molecular enzymology, but its study is limited by the lack of an accessible and reliable diagnostic technique. A series of crystalline complexes of a DNA methyltransferase, M.HhaI, and its cognate DNA, in which a fluorescent nucleobase analogue, 2-aminopurine (AP), occupies defined positions with respect the target flipped base, have been prepared and their structures determined at higher than 2 A resolution. From time-resolved fluorescence measurements of these single crystals, we have established that the fluorescence decay function of AP shows a pronounced, characteristic response to base flipping: the loss of the very short (approximately 100 ps) decay component and the large increase in the amplitude of the long (approximately 10 ns) component. When AP is positioned at sites other than the target site, this response is not seen. Most significantly, we have shown that the same clear response is apparent when M.HhaI complexes with DNA in solution, giving an unambiguous signal of base flipping. Analysis of the AP fluorescence decay function reveals conformational heterogeneity in the DNA-enzyme complexes that cannot be discerned from the present X-ray structures.

    Organizational Affiliation: 

    School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK.



Macromolecules

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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MODIFICATION METHYLASE HHAIA327Haemophilus haemolyticusMutation(s): 0 
EC: 2.1.1.37
Find proteins for P05102 (Haemophilus parahaemolyticus)
Explore P05102 
Go to UniProtKB:  P05102
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*G*GP*AP*TP*GP*(5CM*2PR)*CP*TP*GP*AP*C)-3'B [auth C]12synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*G*TP*CP*AP*GP*CP*GP*CP*AP*TP*CP*C)-3'C [auth D]12synthetic construct
      Small Molecules
      Ligands 4 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      SAH
      Query on SAH
      Download Ideal Coordinates CCD File 
      		 D [auth A]S-ADENOSYL-L-HOMOCYSTEINE
      C14 H20 N6 O5 S
      ZJUKTBDSGOFHSH-WFMPWKQPSA-N      		 Ligand Interaction
      EPE
      Query on EPE
      Download Ideal Coordinates CCD File 
      		 J [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
      C8 H18 N2 O4 S
      JKMHFZQWWAIEOD-UHFFFAOYSA-N      		 Ligand Interaction
      CIT
      Query on CIT
      Download Ideal Coordinates CCD File 
      		 K [auth A]CITRIC ACID
      C6 H8 O7
      KRKNYBCHXYNGOX-UHFFFAOYSA-N      		 Ligand Interaction
      SO4
      Query on SO4
      Download Ideal Coordinates CCD File 
      		 E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]SULFATE ION
      O4 S
      QAOWNCQODCNURD-UHFFFAOYSA-L      		 Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.70 Å
      • R-Value Free: 0.220 
      • R-Value Work: 0.196 
      • R-Value Observed: 0.196 
      • Space Group: H 3 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 94.845α = 90
      b = 94.845β = 90
      c = 313.03γ = 120
      Software Package:
      Software NamePurpose
      CNSrefinement
      MOSFLMdata reduction
      SCALAdata scaling
      AMoREphasing

      Structure Validation

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      View more in-depth experimental data

      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2005-12-14
        Type: Initial release
      • Version 1.1: 2014-01-29
        Changes: Atomic model, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
      • Version 1.2: 2019-07-24
        Changes: Data collection, Derived calculations