Pathway · 3 proteins
Base excision repair
Proteins of this group that KEGG places on its “Base excision repair” map for Aquifex aeolicus.
How it works
This map shows how single damaged or wrong bases are cut out of DNA and replaced. The proteins here remove uracil and damaged bases, cut the backbone at the empty site, and prepare it for a polymerase and ligase to finish the repair.
Grouped by KEGG pathway map. The explanation above is the atlas’s own; the map itself covers more organisms than Aquifex.
Its proteins
| Protein | EC | Reaction (UniProt) | Metal or cluster | Amino acids | Certainty |
|---|---|---|---|---|---|
| Probable endonuclease 4 | 3.1.21.2 | Endonucleolytic cleavage to 5'-phosphooligonucleotide end-products. | Zn(2+) | 282 | Step named |
| Type-4 uracil-DNA glycosylase | 3.2.2.27 | Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil. | — | 195 | Step named |
| Endonuclease III | 4.2.99.18 | 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)-2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3-dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-phospho-2'-deoxyribonucleoside-DNA + H(+) | [4Fe-4S] cluster | 213 | Step named |
Also part of this pathway
These proteins are described under another pathway, but also take part here.
| Protein | EC | Reaction (UniProt) | Metal or cluster | Amino acids | Certainty |
|---|---|---|---|---|---|
| Single-stranded-DNA-specific exonuclease RecJHome: Homologous recombination | — | — | — | 538 | Step named |
| DNA ligaseHome: Joining and end processing | 6.5.1.2 | NAD(+) + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-nicotinamide D-nucleotide. | Zn(2+), Mn(2+), Mg(2+) | 720 | Step named |
Origins
How could damaged DNA letters be removed and replaced before repair enzymes existed?
The books searched describe base excision repair only in present-day cells.
DNA loses bases on its own: as many as 10,000 purines a day in a mammalian cell, and faster at high temperature; above 75 °C the uncatalysed loss of damaged purines dominates. For a cell living near 90 °C, as Aquifex does, repair is needed from the start.
Base excision repair needs at least five enzymes working in sequence.
From the books: Nelson & Cox, Lehninger Principles of Biochemistry, p. 290; Ribas de Pouplana (ed.), The Genetic Code and the Origin of Life, p. 176; Tan & Stadler, The Stairway to Life, PDF p. 112.
The wider question for this part of the cell: origins for copying and repairing the genome.
Sources
- KEGG map aae03410 (enzymes of this organism highlighted)
Other pathways in this group: DNA damage repair · DNA synthesis · Topology management · Joining and end processing · Recombination and restart · Chromosome preparation · Initiation and opening · Homologous recombination · Cysteine and methionine metabolism · Not yet placed in a pathway