1L6B

CRYSTAL STRUCTURE ANALYSIS OF THE ALL DNA HOLLIDAY JUNCTION STRUCTURE OF CCGGTACM5CGG

Summary for 1L6B

• Entry DOI: 10.2210/pdb1l6b/pdb
• Descriptor: 5'-D(*CP*CP*GP*GP*TP*AP*CP*(5CM)P*GP*G)-3', CALCIUM ION (3 entities in total)
• Functional Keywords: holliday junction, dna four-way junction, cytosine methylation, dna
• Total number of polymer chains: 2
• Total formula weight: 6160.12

Authors

Vargason, J.M.,Ho, P.S. (deposition date: 2002-03-08, release date: 2002-08-07, Last modification date: 2024-02-14)

Primary citation

Vargason, J.M.,Ho, P.S.
The effect of cytosine methylation on the structure and geometry of the Holliday junction: the structure of d(CCGGTACm5CGG) at 1.5 A resolution.
J.Biol.Chem., 277:21041-21049, 2002

PubMed Abstract: The single crystal structure of the methylated sequence d(CCGGTACm(5)CGG) has been solved as an antiparallel stacked X Holliday junction to 1.5 A resolution. When compared with the parent nonmethylated d(CCGGTACCGG) structure, the duplexes are translated by 3.4 A along the helix axis and rotated by 10.8 degrees relative to each other, rendering the major grooves more accessible overall. A Ca(2+) complex is seen in the minor groove opposite the junction but is related to the B conformation of the stacked arms. At the junction itself, the hydrogen bond from the N4 nitrogen of cytosine C8 to the C7 phosphate at the crossover in the parent structure has been replaced by a water bridge. Thus, this direct interaction is not absolutely required to stabilize the junction at the previously defined ACC trinucleotide core. The more compact methylated junction forces the Na(+) of the protected central cavity of the nonmethylated junction into a solvent cluster that spans the space between the junction crossover and the stacked arms. A series of void volumes within the methylated and the nonmethylated structures suggests that small monovalent cations can fill and vacate this central cavity without the need to unfold the four-stranded Holliday junction completely.

PubMed: 11919197
DOI: 10.1074/jbc.M201357200

Experimental method

X-RAY DIFFRACTION (1.5 Å)