Pathway · 3 proteins
Homologous recombination
Proteins of this group that KEGG places on its “Homologous recombination” map for Aquifex aeolicus.
How it works
This map covers repair of broken DNA by copying from an intact second copy, and the restart of stalled copying. The proteins here coat single-stranded DNA, cut back broken ends, unwind DNA and help restart replication forks.
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 |
|---|---|---|---|---|---|
| Primosomal protein N | — | — | — | 678 | Unspecified |
| DNA 3'-5' helicase | 5.6.2.4 | ATP + H2O = ADP + phosphate + H(+) | — | 669 | Unspecified |
| DNA replication protein DnaC | — | — | Mg(2+) | 235 | Unspecified |
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-binding proteinHome: Homologous recombination | — | — | — | 147 | Step named |
| Probable DNA double-strand break repair Rad50 ATPaseHome: Homologous recombination | — | — | Zn(2+) | 978 | Step named |
| DNA polymerase III subunit alphaHome: DNA synthesis | 2.7.7.7 | DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate | — | 1161 | Step named |
| Probable DNA polymerase III subunit deltaHome: DNA synthesis | 2.7.7.7 | DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate | — | 350 | Step named |
| Replicative DNA helicaseHome: Initiation and opening | 5.6.2.3 | ATP + H2O = ADP + phosphate + H(+) | Mg(2+) | 468 | Step named |
| Recombination protein RecRHome: Recombination and restart | — | — | — | 211 | Step named |
| AAA+ ATPase domain-containing proteinHome: DNA synthesis | — | — | — | 305 | Step named |
| DNA polymerase III subunit gamma/tauHome: DNA synthesis | 2.7.7.7 | DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate | — | 473 | Step named |
| Beta sliding clampHome: DNA synthesis | — | — | — | 363 | Step named |
| Nuclease SbcCD subunit DHome: Homologous recombination | — | — | — | 379 | Step named |
| ATP-dependent DNA helicase RecGHome: Recombination and restart | 5.6.2.4 | Couples ATP hydrolysis with the unwinding of duplex DNA by translocating in the 3'-5' direction. | — | 792 | Step named |
| Protein RecAHome: DNA damage repair | — | — | — | 345 | Step named |
| Single-stranded-DNA-specific exonuclease RecJHome: Homologous recombination | — | — | — | 538 | Step named |
| DNA repair protein RecNHome: Homologous recombination | — | — | — | 520 | Step named |
| DNA polymerase III subunit epsilonHome: Joining and end processing | 2.7.7.7 | DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate | Mg(2+), Mn(2+) | 202 | Step named |
| DNA primaseHome: DNA replication | 2.7.7.101 | ssDNA + n NTP = ssDNA/pppN(pN)n-1 hybrid + (n-1) diphosphate. | Mg(2+), Zn(2+) | 498 | Step named |
| Polyribonucleotide nucleotidyltransferaseHome: Not yet placed in a pathway | 2.7.7.8 | RNA(n+1) + phosphate = RNA(n) + a ribonucleoside 5'-diphosphate | Mg(2+) | 775 | Step named |
Origins
How could broken DNA be repaired before recombination proteins existed?
RecA-like recombinases are found across all domains of life.
A break across both strands can be repaired accurately only by copying the missing information from a second, intact copy. That needs a protein that finds the matching sequence and exchanges strands, and five proteins in this pathway serve it.
From the books: Ribas de Pouplana (ed.), The Genetic Code and the Origin of Life, p. 158.
The wider question for this part of the cell: origins for conserved, but we cannot say what they do.
Sources
- KEGG map aae03440 (enzymes of this organism highlighted)
Other pathways in this group: tRNA charging · Nutrient and metabolic state · Biosynthesis of various nucleotide sugars · Purine metabolism · Bacterial secretion system · Glyoxylate and dicarboxylate metabolism · Starch and sucrose metabolism · Fructose and mannose metabolism · Streptomycin biosynthesis · Other carbon fixation pathways · Nicotinate and nicotinamide metabolism · Not yet placed in a pathway