A domain in human EXOG converts apoptotic endonuclease to DNA-repair exonuclease

Abstract

Human EXOG (hEXOG) is a 5′-exonuclease that is crucial for mitochondrial DNA repair; the enzyme belongs to a nonspecific nuclease family that includes the apoptotic endonuclease EndoG. Here we report biochemical and structural studies of hEXOG, including structures in its apo form and in a complex with DNA at 1.81 and 1.85 Å resolution, respectively. A Wing domain, absent in other ββα-Me members, suppresses endonuclease activity, but confers on hEXOG a strong 5′-dsDNA exonuclease activity that precisely excises a dinucleotide using an intrinsic ‘tape-measure'. The symmetrical apo hEXOG homodimer becomes asymmetrical upon binding to DNA, providing a structural basis for how substrate DNA bound to one active site allosterically regulates the activity of the other. These properties of hEXOG suggest a pathway for mitochondrial BER that provides an optimal substrate for subsequent gap-filling synthesis by DNA polymerase γ.

Crystal structure of NucB, a biofilm-degrading endonuclease

“…The base of the pyramid is formed by α-helices 2 and 3 as well as the loop connecting α-helix 2 to β-strand 3, while the peak of the pyramid is formed by the C-terminus of α-helix 1. In keeping with the observed endonuclease activity of Bl NucB, the solvent-accessible surface of Bl NucB does not reveal a molecular ‘wall’ or ‘tape-measure’ ( 45 ) to confer exonuclease activity. Instead, the flat base of the pyramid contains a 15 Å deep, 10 Å wide, 20 Å long concave depression that is formed mostly by conserved amino acids (Figure 3C ).…”

Dinucleotide Degradation by REXO2 Maintains Promoter Specificity in Mammalian Mitochondria

“…ExoG releases dinucleotides as reaction products and is active upon RNA (Szymanski et al, 2017;Wu et al, 2019) and so could potentially fulfill this role. Interestingly, a very recent study of E. coli Orn has similarly revealed a stark preference for diribonucleotide substrates (Kim et al, 2019), suggesting that oligoribonucleases have a more specialized and evolutionarily conserved role than previously understood.…”

Regulations of mitochondrial DNA repair by poly(ADP-Ribose) Polymerase 1

“…To examine the biological effects of PARP1 interaction with Pol g and PARylation, we first examined Pol g activities in DNA repair on a gapped DNA substrate that mimics the DNA intermediate following hEXOG excision ( Fig. 2A) (6,7).…”

“…Pol g does not appear suitable for canonical nuclear BER because of its low-efficiency synthesis on a single-nucleotide gapped DNA and lack of strand displacement DNA synthesis ability (5), both of which are essential for singlenucleotide (SN) and long-patch (LP) BER, respectively. However, Pol g gap-filling synthesis is enhanced by the mitochondrial specific endo/exonuclease G (EXOG), which precisely excises two-nucleotides from the 5'-end of the gap of duplex DNA, thereby creating an optimal substrate for Pol g (5)(6)(7). This mtBER product resembles those from nuclear LP-BER but is produced by a different mechanism.…”