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: 1.7 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.196 

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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:  

  • 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, i ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MODIFICATION METHYLASE HHAI
A
327Haemophilus parahaemolyticusMutation(s): 0 
Gene Names: hhaIM
EC: 2.1.1.37
Find proteins for P05102 (Haemophilus parahaemolyticus)
Go to UniProtKB:  P05102
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*G*GP*AP*TP*GP*(5CM*2PR)*CP*TP*GP*AP*C)-3'C12synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*G*TP*CP*AP*GP*CP*GP*CP*AP*TP*CP*C)-3'D12synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE
Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT
Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4
Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
SAH
Query on SAH
Download SDF File 
Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
C
DNA LINKINGC10 H16 N3 O7 PDC
2PR
Query on 2PR
C
DNA LINKINGC10 H14 N5 O6 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.196 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 94.845α = 90.00
b = 94.845β = 90.00
c = 313.030γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
CNSrefinement
AMoREphasing
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

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