2C7Q image
Entry Detail
PDB ID:
2C7Q
Keywords:
Title:
HhaI DNA methyltransferase complex with oligonucleotide containing 2- aminopurine outside the recognition sequence (paired with G) and SAH
Biological Source:
PDB Version:
Deposition Date:
2005-11-27
Release Date:
2005-12-14
Method Details:
Experimental Method:
Resolution:
1.85 Å
R-Value Free:
0.21
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
H 3 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:MODIFICATION METHYLASE HHAI
Chain IDs:A
Chain Length:327
Number of Molecules:1
Biological Source:HAEMOPHILUS HAEMOLYTICUS
Polymer Type:polydeoxyribonucleotide
Description:5'-D(*T*GP*GP*(2PR)*GP*GP*(5CM)*GP*CP*TP*GP* AP*C)-3'
Chain IDs:B (auth: C)
Chain Length:13
Number of Molecules:1
Biological Source:SYNTHETIC CONSTRUCT
Polymer Type:polydeoxyribonucleotide
Description:5'-D(*T*GP*TP*CP*AP*GP*CP*GP*CP*CP*GP*CP*C)-3'
Chain IDs:C (auth: D)
Chain Length:13
Number of Molecules:1
Biological Source:SYNTHETIC CONSTRUCT
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
2PR B DG ?
5CM B DC ?
Primary Citation
Time-Resolved Fluorescence of 2-Aminopurine as a Probe of Base Flipping in M.HhaI-DNA Complexes
Nucleic Acids Res. 33 6953 ? (2005)
PMID: 16340006 DOI: 10.1093/NAR/GKI995

Abstact

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.

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Primary Citation of related structures