5YZE

Crystal structure of the [Co2+-(chromomycin A3)2]-d(CCG)3 complex

Summary for 5YZE

• Entry DOI: 10.2210/pdb5yze/pdb
• Descriptor: DNA (5'-D(*TP*CP*CP*GP*CP*CP*GP*CP*CP*GP*A)-3'), 3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose-(1-3)-(2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol-(1-3)-(2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol, 2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose-(1-3)-(2R,3R,6R)-6-hydroxy-2-methyltetrahydro-2H-pyran-3-yl acetate, ... (6 entities in total)
• Functional Keywords: drug-dna complex, chromomycin a3, ccg repeats, i-motif, flipout, dna, antibiotics-dna complex, antibiotics/dna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 9109.66

Authors

Hou, M.H.,Chen, Y.W.,Wu, P.C.,Satange, R.B. (deposition date: 2017-12-14, release date: 2018-10-17, Last modification date: 2024-03-27)

Primary citation

Chen, Y.W.,Satange, R.,Wu, P.C.,Jhan, C.R.,Chang, C.K.,Chung, K.R.,Waring, M.J.,Lin, S.W.,Hsieh, L.C.,Hou, M.H.
CoII(Chromomycin)2 Complex Induces a Conformational Change of CCG Repeats from i-Motif to Base-Extruded DNA Duplex
Int J Mol Sci, 19:-, 2018

PubMed Abstract: We have reported the propensity of a DNA sequence containing CCG repeats to form a stable i-motif tetraplex structure in the absence of ligands. Here we show that an i-motif DNA sequence may transition to a base-extruded duplex structure with a GGCC tetranucleotide tract when bound to the (Co)-mediated dimer of chromomycin A3, Co(Chro)₂. Biophysical experiments reveal that CCG trinucleotide repeats provide favorable binding sites for Co(Chro)₂. In addition, water hydration and divalent metal ion (Co) interactions also play a crucial role in the stabilization of CCG trinucleotide repeats (TNRs). Our data furnish useful structural information for the design of novel therapeutic strategies to treat neurological diseases caused by repeat expansions.

PubMed: 30227633
DOI: 10.3390/ijms19092796

Experimental method

X-RAY DIFFRACTION (1.87 Å)