Pathway · 7 proteins
DNA damage repair
DNA repair annotations identify routes distinct from protein repair.
How it works
- MutS/MutL, UvrA/UvrB/UvrC, PolX and RecA annotations connect this group to different forms of genome maintenance. Mismatches, damaged bases and broken or stalled DNA structures need different responses.
- A representative nucleotide-excision route recognizes damage and makes incisions with Uvr components, after which additional activities remove the damaged segment and restore DNA. Mismatch repair and RecA-associated recombination use other mechanisms.
- The selected genes do not constitute one complete repair pathway, and additional synthesis, processing and ligation partners may be required. Repair specificity and reaction order must be established route by route.
Grouped by the atlas’s curated pathway map. The table order is not a proven reaction order.
Its proteins
| Protein | EC | Reaction (UniProt) | Metal or cluster | Amino acids | Certainty |
|---|---|---|---|---|---|
| DNA-directed DNA polymerase | 2.7.7.7 | DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate | — | 581 | Step named |
| DNA mismatch repair protein MutL | — | — | — | 425 | Step named |
| UvrABC system protein B | — | — | — | 663 | Step named |
| UvrABC system protein C | — | — | — | 566 | Step named |
| Protein RecA | — | — | — | 345 | Step named |
| DNA mismatch repair protein MutS | — | — | — | 859 | Step named |
| UvrABC system protein A | — | — | — | 926 | Step named |
Origins
How could the first DNA have survived damage before repair enzymes existed?
The books searched describe DNA repair only in present-day cells.
Tan and Stadler point out that base excision repair needs at least five enzymes working together, and that nucleotide excision repair in E. coli needs five enzymes to replace a stretch of twelve nucleotides. Making and running these enzymes costs energy.
About a hundred kinds of repair enzymes are known in E. coli. Without repair, the information that DNA stores would decay faster than it could be copied.
From the books: Tan & Stadler, The Stairway to Life, PDF p. 112; Solomon, Berg & Martin, Biology, PDF p. 310.
The wider question for this part of the cell: origins for copying and repairing the genome.
Sources
- Atlas pathway grouping from the VF5 reference-genome system map (Deckert et al. 1998; Braakman & Smith 2014)
Other pathways in this group: DNA synthesis · Topology management · Joining and end processing · Recombination and restart · Chromosome preparation · Initiation and opening · Homologous recombination · Base excision repair · Cysteine and methionine metabolism · Not yet placed in a pathway