Pathway · 5 proteins
Protein turnover
ATP-dependent proteases and peptidases remove selected proteins.
How it works
- The selected proteolytic systems include Clp-associated ATPases and ClpP, HslU/HslV and membrane-associated FtsH. Each recognizes particular substrates in an appropriate cellular location.
- ATP-dependent substrate handling can expose and feed a protein chain into a proteolytic chamber or active site. Peptide-bond cleavage then produces shorter fragments that other peptidases can further process.
- These are alternative protease systems, not successive stages through every listed enzyme. Substrate selection, degradation signals and the fate of each protein require system-specific evidence.
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 |
|---|---|---|---|---|---|
| ATP-dependent Clp protease | — | — | — | 810 | System only |
| ATP-dependent Clp protease ATP-binding subunit ClpX | — | — | Zn(2+) | 412 | Step named |
| ATP-dependent protease ATPase subunit HslU | — | — | — | 450 | Step named |
| ATP-dependent Clp protease proteolytic subunit | 3.4.21.92 | Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. alpha-casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec, and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs). | — | 201 | Step named |
| ATP-dependent protease subunit HslV | 3.4.25.2 | ATP-dependent cleavage of peptide bonds with broad specificity. | Na(+) | 176 | 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 |
|---|---|---|---|---|---|
| ATP-dependent zinc metalloprotease FtsHHome: Damaged-protein turnover | 3.4.24.- | — | Zn(2+) | 634 | Step named |
Origins
When did a cell first need to break proteins down as well as make them?
The books searched discuss protein breakdown only in present-day cells. Alberts raises the central paradox of the origins question: nucleic acids are needed to make proteins and proteins are needed to make nucleic acids, and the RNA world is proposed to escape it.
A cell that makes proteins must also remove the faulty and unneeded ones and recycle their amino acids. Making and unmaking have to be balanced from the beginning, or the cell fills with useless protein.
From the books: Alberts et al., Molecular Biology of the Cell, p. 389.
The wider question for this part of the cell: origins for building proteins and folding them.
Sources
- Atlas pathway grouping from the VF5 reference-genome system map (Deckert et al. 1998; Braakman & Smith 2014)
Other pathways in this group: Ribosomal subunits · Translation interface · RNA maturation · Translation cycle · Protein translocation · Folding and stabilization · Recycling and rescue · Early folding support · Protein targeting · Ribosome · Protein export · Not yet placed in a pathway