Pathway · 5 proteins
DNA synthesis
Polymerase, clamp and loader subunits support processive replication.
How it works
- DNA polymerase III alpha is the catalytic subunit. The beta subunit is the sliding clamp that keeps the polymerase on the template, and the delta subunit is part of the clamp loader.
- The gamma/tau subunits belong to the same clamp-loader complex and couple ATP hydrolysis to opening and closing the clamp, which is what makes synthesis processive rather than distributive.
- VF5 lists further DNA polymerase III subunits as well, so the replicative apparatus is assembled from separate proteins rather than a single polypeptide.
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 polymerase III subunit alpha | 2.7.7.7 | DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate | — | 1161 | Step named |
| Probable DNA polymerase III subunit delta | 2.7.7.7 | DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate | — | 350 | Step named |
| AAA+ ATPase domain-containing protein | — | — | — | 305 | Step named |
| DNA polymerase III subunit gamma/tau | 2.7.7.7 | DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate | — | 473 | Step named |
| Beta sliding clamp | — | — | — | 363 | Step named |
Origins
How could DNA be copied before DNA polymerase and its helpers existed?
How it was discovered
- 1956Arthur Kornberg discovers DNA polymerase, the enzyme that builds new DNA on a template.Kornberg et al., Biochimica et Biophysica Acta 21:197–198 (1956)
Enzymes that copy RNA, found in RNA viruses, are cited as having implications for self-replicating molecules that may have existed before cells.
Copying DNA takes an ensemble: a helicase to open the helix, single-strand binding proteins, a primase to start each strand, polymerases, a proofreading exonuclease, a ligase to seal the pieces and gyrase to relieve the twisting. Five proteins in this pathway alone are needed to build new strands.
From the books: Nelson & Cox, Lehninger Principles of Biochemistry, p. 1050; 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 · 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