7SVB

APE1 exonuclease substrate complex with 8oxoG opposite C

Summary for 7SVB

• Entry DOI: 10.2210/pdb7svb/pdb
• Descriptor: DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG))-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... (5 entities in total)
• Functional Keywords: nuclease, dna repair protein, dna binding protein, hydrolase, hydrolase-dna complex, hydrolase/dna
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 5
• Total formula weight: 75169.36

Authors

Whitaker, A.W.,Freudenthal, B.D. (deposition date: 2021-11-18, release date: 2022-09-07, Last modification date: 2023-10-18)

Primary citation

Whitaker, A.M.,Stark, W.J.,Freudenthal, B.D.
Processing oxidatively damaged bases at DNA strand breaks by APE1.
Nucleic Acids Res., 50:9521-9533, 2022

PubMed Abstract: Reactive oxygen species attack the structure of DNA, thus altering its base-pairing properties. Consequently, oxidative stress-associated DNA lesions are a major source of the mutation load that gives rise to cancer and other diseases. Base excision repair (BER) is the pathway primarily tasked with repairing DNA base damage, with apurinic/apyrimidinic endonuclease (APE1) having both AP-endonuclease and 3' to 5' exonuclease (exo) DNA cleavage functions. The lesion 8-oxo-7,8-dihydroguanine (8-oxoG) can enter the genome as either a product of direct damage to the DNA, or through polymerase insertion at the 3'-end of a DNA strand during replication or repair. Importantly, 3'-8-oxoG impairs the ligation step of BER and therefore must be removed by the exo activity of a surrogate enzyme to prevent double stranded breaks and cell death. In the present study, we use X-ray crystallography to characterize the exo activity of APE1 on 3'-8-oxoG substrates. These structures support a unified APE1 exo mechanism that differs from its more canonical AP-endonuclease activity. In addition, through complementation of the structural data with enzyme kinetics and binding studies employing both wild-type and rationally designed APE1 mutants, we were able to identify and characterize unique protein: DNA contacts that specifically mediate 8-oxoG removal by APE1.

PubMed: 36018803
DOI: 10.1093/nar/gkac695

Experimental method

X-RAY DIFFRACTION (2.24 Å)