PDBsum entry 384d

DNA

PDB id: 384d

Contents

DNA/RNA

Metals

_MG

Waters ×88

PDB id:

384d

Name:

DNA

Title:

Hydration and recognition of methylated cpg steps in DNA

Structure:

5'-d( Cp (5Cm)p Gp Cp (5Cm)p Gp Gp (5Cm)p Gp G)-3'. Chain: a, b. Engineered: yes

Source:

Synthetic: yes

Biol. unit:

Dimer (from PQS)

Resolution:

2.15Å R-factor: 0.166

Authors:

C.Mayer-Jung,D.Moras,Y.Timsit

Key ref:

C.Mayer-Jung et al. (1998). Hydration and recognition of methylated CpG steps in DNA. Embo J, 17, 2709-2718. PubMed id: 9564052 DOI: 10.1093/emboj/17.9.2709

Date:

02-Mar-98 Release date: 10-Mar-98

DNA/RNA chains

C-5CM-G-C-5CM-G-G-5CM-G-G 10 bases

C-5CM-G-C-5CM-G-G-5CM-G-G 10 bases

DOI no: 10.1093/emboj/17.9.2709

Embo J 17:2709-2718 (1998)

PubMed id: 9564052

Hydration and recognition of methylated CpG steps in DNA.

C.Mayer-Jung, D.Moras, Y.Timsit.

ABSTRACT

The analysis of the hydration pattern around methylated CpG steps in three high resolution (1.7, 2.15 and 2.2 A) crystal structures of A-DNA decamers reveals that the methyl groups of cytosine residues are well hydrated. In comparing the native structure with two structurally distinct forms of the decamer d(CCGCCGGCGG) fully methylated at its CpG steps, this study shows also that in certain structural and sequence contexts, the methylated cytosine base can be more hydrated that the unmodified one. These water molecules seem to be stabilized in front of the methyl group through the formation C-H...O interactions. In addition, these structures provide the first observation of magnesium cations bound to the major groove of A-DNA and reveal two distinct modes of metal binding in methylated and native duplexes. These findings suggest that methylated cytosine bases could be recognized by protein or DNA polar residues through their tightly bound water molecules.

Selected figure(s)

Figure 1.
Figure 1 Comparison of the overall major groove and backbone hydration patterns of the native and methylated A-DNA decamers. Frontal stereo view of the native decamer (A), the methylated orthorhombic decamer (B) and the methylated hexagonal decamer (C). Water molecules are indicated in light blue and hexacoordinated magnesium ions in cyan. Hydrogen bonds are represented by red dashed lines.

Figure 3.
Figure 3 New hydration sites in the methylated structures. The methylated CpG steps 2 -3 (A) and 5 -6 (B) of the hexagonal methylated decamer and 5 -6 of the orthorhombic decamer (C). Additional water molecules are named wA' and wB' depending on their proximity to the wA and wB sites.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: Embo J (1998, 17, 2709-2718) copyright 1998.

Figures were selected by an automated process.