4B21

Unprecedented sculpting of DNA at abasic sites by DNA glycosylase homolog Mag2

Summary for 4B21

• Entry DOI: 10.2210/pdb4b21/pdb
• Related: 4B22 4B23 4B24
• Descriptor: PROBABLE DNA-3-METHYLADENINE GLYCOSYLASE 2, 5'-D(*GP*CP*TP*AP*CP*3DRP*GP*AP*TP*CP*GP)-3', 5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP)-3', ... (6 entities in total)
• Functional Keywords: hydrolase-dna complex, helix-hairpin-helix, hydrolase/dna
• Biological source: SCHIZOSACCHAROMYCES POMBE; More
• Total number of polymer chains: 3
• Total formula weight: 33137.31

Authors

Dalhus, B.,Nilsen, L.,Korvald, H.,Huffman, J.,Forstrom, R.J.,McMurray, C.T.,Alseth, I.,Tainer, J.A.,Bjoras, M. (deposition date: 2012-07-12, release date: 2013-01-09, Last modification date: 2024-05-08)

Primary citation

Dalhus, B.,Nilsen, L.,Korvald, H.,Huffman, J.,Forstrom, R.J.,Mcmurray, C.T.,Alseth, I.,Tainer, J.A.,Bjoras, M.
Sculpting of DNA at Abasic Sites by DNA Glycosylase Homolog Mag2.
Structure, 21:154-, 2013

PubMed Abstract: Modifications and loss of bases are frequent types of DNA lesions, often handled by the base excision repair (BER) pathway. BER is initiated by DNA glycosylases, generating abasic (AP) sites that are subsequently cleaved by AP endonucleases, which further pass on nicked DNA to downstream DNA polymerases and ligases. The coordinated handover of cytotoxic intermediates between different BER enzymes is most likely facilitated by the DNA conformation. Here, we present the atomic structure of Schizosaccharomyces pombe Mag2 in complex with DNA to reveal an unexpected structural basis for nonenzymatic AP site recognition with an unflipped AP site. Two surface-exposed loops intercalate and widen the DNA minor groove to generate a DNA conformation previously only found in the mismatch repair MutS-DNA complex. Consequently, the molecular role of Mag2 appears to be AP site recognition and protection, while possibly facilitating damage signaling by structurally sculpting the DNA substrate.

PubMed: 23245849
DOI: 10.1016/J.STR.2012.11.004

Experimental method

X-RAY DIFFRACTION (1.45 Å)