8XPB image
Entry Detail
PDB ID:
8XPB
Keywords:
Title:
Crystal structure of d(ACGCCGT/ACGGCGT) in complex with Echinomycin
Biological Source:
PDB Version:
Deposition Date:
2024-01-03
Release Date:
2024-05-29
Method Details:
Experimental Method:
Resolution:
2.00 Å
R-Value Free:
0.21
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 31 1 2
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(P*AP*CP*GP*GP*CP*GP*T)-3')
Chain IDs:A
Chain Length:7
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(P*AP*CP*GP*CP*CP*GP*T)-3')
Chain IDs:B
Chain Length:7
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polypeptide(L)
Description:Echinomycin
Chain IDs:C (auth: D), D (auth: E)
Chain Length:8
Number of Molecules:2
Biological Source:Streptomyces echinatus.
Peptide-like Molecules
PRD_000491
Primary Citation
Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation.
Nucleic Acids Res. 52 8566 8579 (2024)
PMID: 38989613 DOI: 10.1093/nar/gkae594

Abstact

Non-CpG methylation is associated with several cellular processes, especially neuronal development and cancer, while its effect on DNA structure remains unclear. We have determined the crystal structures of DNA duplexes containing -CGCCG- regions as CCG repeat motifs that comprise a non-CpG site with or without cytosine methylation. Crystal structure analyses have revealed that the mC:G base-pair can simultaneously form two alternative conformations arising from non-CpG methylation, including a unique water-mediated cis Watson-Crick/Hoogsteen, (w)cWH, and Watson-Crick (WC) geometries, with partial occupancies of 0.1 and 0.9, respectively. NMR studies showed that an alternative conformation of methylated mC:G base-pair at non-CpG step exhibits characteristics of cWH with a syn-guanosine conformation in solution. DNA duplexes complexed with the DNA binding drug echinomycin result in increased occupancy of the (w)cWH geometry in the methylated base-pair (from 0.1 to 0.3). Our structural results demonstrated that cytosine methylation at a non-CpG step leads to an anti→syntransition of its complementary guanosine residue toward the (w)cWH geometry as a partial population of WC, in both drug-bound and naked mC:G base pairs. This particular geometry is specific to non-CpG methylated dinucleotide sites in B-form DNA. Overall, the current study provides new insights into DNA conformation during epigenetic regulation.

Legend

Protein

Chemical

Disease

Primary Citation of related structures