Pathway · 4 proteins
Topology management
Gyrase, topoisomerases and reverse gyrase manage DNA topology.
How it works
- DNA gyrase, with an A and a B subunit (the B subunit also annotated as an ATP-hydrolysing topoisomerase), removes positive supercoils ahead of the fork at the cost of ATP.
- A type I topoisomerase relaxes supercoils without ATP, and a reverse gyrase introduces positive supercoils — the activity that stabilises duplex DNA at high temperature and is characteristic of thermophiles.
- In a hyperthermophile the reverse gyrase is not decoration: it addresses the same problem the growth temperature creates. The annotation names the enzymes; their relative contributions at 85 °C have not been measured here.
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 |
|---|---|---|---|---|---|
| Type 2 topoisomerase subunit B | 5.6.2.2 | ATP-dependent breakage, passage and rejoining of double-stranded DNA. | Mg(2+), Mn(2+), Ca(2+) | 792 | Step named |
| DNA topoisomerase 1 | 5.6.2.1 | ATP-independent breakage of single-stranded DNA, followed by passage and rejoining. | Mg(2+) | 540 | Step named |
| Reverse gyrase 1 | 5.6.2.- | ATP + H2O = ADP + phosphate + H(+) | Zn(2+), Mg(2+) | 1146 | Step named |
| Type 2 topoisomerase subunit A | 5.6.2.2 | ATP-dependent breakage, passage and rejoining of double-stranded DNA. | — | 769 | Step named |
Origins
How could DNA be unwound and untangled before topoisomerases existed?
How it was discovered
- 1976Martin Gellert and colleagues discover DNA gyrase, which uses ATP to twist DNA and relieve the tension that copying creates.Brooker, Concepts of Genetics, PDF p. 264
The books searched describe topoisomerases only in present-day cells.
Unwinding DNA to copy it builds up twisting ahead of the fork; without gyrase the fork stops. After copying, circular daughter chromosomes are interlocked and must be cut apart and resealed by a topoisomerase. Four proteins in this pathway manage both problems.
From the books: Brooker, Concepts of Genetics, PDF p. 264; 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 · 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