8XP8

Crystal structure of d(ACGmCCGT/ACGGCGT) in complex with Echinomycin

Summary for 8XP8

• Entry DOI: 10.2210/pdb8xp8/pdb
• Related PRD ID: PRD_000491
• Descriptor: DNA (5'-D(P*AP*CP*GP*GP*CP*GP*T)-3'), DNA (5'-D(P*AP*CP*GP*(5CM)P*CP*GP*T)-3'), Echinomycin, ... (6 entities in total)
• Functional Keywords: dna-ligand complex, dna, antibiotic, dna-antibiotic complex, dna/antibiotic
• Biological source: Streptomyces echinatus.; More
• Total number of polymer chains: 4
• Total formula weight: 6730.30

Authors

Hou, M.H.,Lin, S.M.,Neidle, H. (deposition date: 2024-01-03, release date: 2024-05-29, Last modification date: 2024-08-28)

Primary citation

Lin, S.M.,Huang, H.T.,Fang, P.J.,Chang, C.F.,Satange, R.,Chang, C.K.,Chou, S.H.,Neidle, S.,Hou, M.H.
Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation.
Nucleic Acids Res., 52:8566-8579, 2024

PubMed Abstract: 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.

PubMed: 38989613
DOI: 10.1093/nar/gkae594

Experimental method

X-RAY DIFFRACTION (1.64 Å)