2LZV

DNA duplex containing mispair-aligned O4U-heptylene-O4U interstrand cross-link

Summary for 2LZV

• Entry DOI: 10.2210/pdb2lzv/pdb
• Related: 1N4B 1S37 1XCI 2LZW
• NMR Information: BMRB: 18780
• Descriptor: DNA (5'-D(*CP*GP*AP*AP*AP*UP*TP*TP*TP*CP*G)-3'), HEPTANE (2 entities in total)
• Functional Keywords: interstrand cross-link, dna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 6768.57

Authors

Denisov, A.Y.,McManus, F.P.,Noronha, A.M.,Wilds, C.J. (deposition date: 2012-10-11, release date: 2013-10-16, Last modification date: 2024-05-15)

Primary citation

Denisov, A.Y.,McManus, F.P.,O'Flaherty, D.K.,Noronha, A.M.,Wilds, C.J.
Structural basis of interstrand cross-link repair by O 6 -alkylguanine DNA alkyltransferase.
Org.Biomol.Chem., 15:8361-8370, 2017

PubMed Abstract: DNA interstrand cross-links (ICL) are among the most cytotoxic lesions found in biological systems. O-Alkylguanine DNA alkyltransferases (AGTs) are capable of removing alkylation damage from the O-atom of 2'-deoxyguanosine and the O-atom of thymidine. Human AGT (hAGT) has demonstrated the ability to repair an interstrand cross-linked duplex where two O-atoms of 2'-deoxyguanosine were tethered by a butylene (XLGG4) or heptylene (XLGG7) linkage. However, the analogous ICL between the O-atoms of thymidine was found to evade repair. ICL duplexes connecting the O-atoms of 2'-deoxyuridine by a butylene (XLUU4) or heptylene (XLUU7) linkage have been prepared to examine the influence of the C5-methyl group on AGT-mediated repair. Both XLUU4 and XLUU7 were refractory to repair by human and E. coli (OGT and Ada-C) AGTs with comparably low μM dissociation constants for 2 : 1 or 4 : 1 AGT/DNA stoichiometries. The solution structures of two heptylene linked DNA duplexes (CGAAAYTTTCG), XLUU7 (Y = dU) and XLGG7 (Y = dG), were solved and the global structures were virtually identical with a RMSD of 1.22 Å. The ICL was found to reside in the major groove for both duplexes. The linkage adopts an E conformation about the C4-O bond for XLUU7 whereas a Z conformation about the C6-O bond was observed for XLGG7. This E versus Z conformation may partially account for hAGTs discrimination towards the repair of these ICL, supported by the crystal structures of hAGT with various substrates which have been observed to adopt a Z conformation. In addition, a higher mobility at the ICL site for XLUU7 is observed relative to XLGG7 that may play a role in repair by hAGT. Taken together, these findings provide insights on the AGT-mediated repair of cytotoxic ICL in terms of its processing capability and substrate specificity.

PubMed: 28937154
DOI: 10.1039/c7ob02093g

Experimental method

SOLUTION NMR