2C7P: Hhai Dna Methyltransferase Complex With Oligonucleotide Containing 2-aminopurine Opposite To The Target Base (gcgc:gmpc) And Sah

Citation:
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.
PDB ID: 2C7PDownload
MMDB ID: 86915
PDB Deposition Date: 2005/11/25
Updated in MMDB: 2010/12
Experimental Method:
x-ray diffraction
Resolution: 1.7  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 2C7P: trimeric; determined by author and by software (PISA)
Molecular Components in 2C7P
Label Count Molecule
Protein (1 molecule)
1
Modification Methylase Hhai
Molecule annotation
Nucleotides(2 molecules)
1
5'-d(*g*gp*ap*tp*gp*(5cm*2pr)*cp*tp*gp*ap*c)-3'
Molecule annotation
1
5'-d(*g*tp*cp*ap*gp*cp*gp*cp*ap*tp*cp*c)-3'
Molecule annotation
Chemicals (8 molecules)
1
1
2
5
3
1
4
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
.