Pathway · 3 proteins
DNA replication
Proteins of this group that KEGG places on its “DNA replication” map for Aquifex aeolicus.
How it works
This map covers the proteins that copy the chromosome. The three on this page deal with RNA in DNA: primase makes the short RNA starts that DNA polymerase needs, and two RNase H enzymes remove them afterwards.
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 |
|---|---|---|---|---|---|
| DNA primase | 2.7.7.101 | ssDNA + n NTP = ssDNA/pppN(pN)n-1 hybrid + (n-1) diphosphate. | Mg(2+), Zn(2+) | 498 | Step named |
| Ribonuclease HIII | 3.1.26.4 | Endonucleolytic cleavage to 5'-phosphomonoester. | Mn(2+), Mg(2+) | 257 | Step named |
| Ribonuclease HII | 3.1.26.4 | Endonucleolytic cleavage to 5'-phosphomonoester. | Mn(2+), Mg(2+) | 196 | 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-binding proteinHome: Homologous recombination | — | — | — | 147 | 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 |
| 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 |
| 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 |
| 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 |
Origins
How could a DNA genome be copied before the replication machinery existed?
Koonin notes a puzzle: transcription machinery is shared by all cells, while key DNA replication proteins of bacteria and archaea are not related to each other. He describes a proposed retrovirus-like copying cycle as a speculative scheme.
Copying DNA starts with short RNA primers made by primase, which must later be removed and replaced with DNA. DNA copying therefore depends on RNA-making and RNA-removing enzymes; three of them sit in this pathway.
From the books: Koonin, The Logic of Chance, PDF p. 216; Koonin, The Origins of Cellular Life, PDF p. 5.
The wider question for this part of the cell: origins for reading genes into rna.
Sources
- KEGG map aae03030 (enzymes of this organism highlighted)
Other pathways in this group: Transcription · RNA processing and turnover · Not yet placed in a pathway