Pathway · 1 proteins
Initiation and opening
DnaA, helicase and primase support replication initiation and fork formation.
How it works
- DnaA binds the replication origin and opens the duplex at an AT-rich region; the reaction needs ATP and is controlled by the nucleotide state of DnaA itself.
- A replicative helicase is loaded onto the opened strand and unwinds the duplex, while DNA primase makes the short RNA primers that a DNA polymerase requires to start.
- This module is the assembly step: helicase and primase stay at the fork as it moves. The factors are listed here; the loading order is established in model bacteria and was not re-measured for VF5.
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 |
|---|---|---|---|---|---|
| Replicative DNA helicase | 5.6.2.3 | ATP + H2O = ADP + phosphate + H(+) | Mg(2+) | 468 | 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 |
|---|---|---|---|---|---|
| Chromosomal replication initiator protein DnaAHome: Chromosome preparation | — | — | Mg(2+), ssDNA | 399 | 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 |
Origins
How does copying begin at the right place, once per cycle?
Koonin calls the origin of replication and translation the core of the origin-of-life problem, and notes that the chemistry before life lies outside biology.
Copying starts only where an initiator protein recognises the origin sequence and opens the helix there, after which the helicase is loaded. Starting once, and only once, per cell cycle keeps every daughter cell with one full copy.
From the books: Koonin, The Logic of Chance, PDF p. 226; Rana, The Cell's Design, ch. 11.
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 damage repair · DNA synthesis · Topology management · Joining and end processing · Recombination and restart · Chromosome preparation · Homologous recombination · Base excision repair · Cysteine and methionine metabolism · Not yet placed in a pathway