2C7P

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

Summary for 2C7P

• Entry DOI: 10.2210/pdb2c7p/pdb
• Related: 10MH 1FJX 1HMY 1M0E 1MHT 1SKM 1SVU 2C7O 2C7Q 2C7R 2HMY 3MHT 4MHT 5MHT 6MHT 7MHT 8MHT 9MHT
• Descriptor: MODIFICATION METHYLASE HHAI, 5'-D(*G*GP*AP*TP*GP*(5CM*2PR)*CP*TP*GP*AP*C)-3', 5'-D(*G*TP*CP*AP*GP*CP*GP*CP*AP*TP*CP*C)-3', ... (8 entities in total)
• Functional Keywords: base flipping, restriction system, transferase-dna complex, transferase/dna
• Biological source: HAEMOPHILUS HAEMOLYTICUS; More
• Total number of polymer chains: 3
• Total formula weight: 45662.17

Authors

Neely, R.K.,Daujotyte, D.,Grazulis, S.,Magennis, S.W.,Dryden, D.T.F.,Klimasauskas, S.,Jones, A.C. (deposition date: 2005-11-25, release date: 2005-12-14, Last modification date: 2023-12-13)

Primary citation

Neely, R.K.,Daujotyte, D.,Grazulis, S.,Magennis, S.W.,Dryden, D.T.F.,Klimasauskas, S.,Jones, A.C.
Time-Resolved Fluorescence of 2-Aminopurine as a Probe of Base Flipping in M.HhaI-DNA Complexes.
Nucleic Acids Res., 33:6953-, 2005

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. 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.

PubMed: 16340006
DOI: 10.1093/NAR/GKI995

Experimental method

X-RAY DIFFRACTION (1.7 Å)