Obsoletion request: some children of protein maturation

[pgaudet]

This replaces #29098

The following BPs represent MFs:
GO:0015680 protein maturation by copper ion transfer
GO:0097428 protein maturation by iron-sulfur cluster transfer
GO:0110147 protein maturation by nickel ion transfer
GO:0022417 protein maturation by protein folding

These terms should be obsoleted and replaced by the parent GO:0051604 protein maturation
In addition, curators should consider whether MF annotations should be added:

• GO:0015680 protein maturation by copper ion transfer >> consider copper chaperone activity
• GO:0022417 protein maturation by protein folding >> consider protein folding chaperone
• GO:0110147 protein maturation by nickel ion transfer >> NTR nickel chaperone activity (child of metallochaperone activity) : references: PMID:34530332, PMID:32133383
• GO:0097428 protein maturation by iron-sulfur cluster transfer >> consider : iron-sulfur cluster carrier activity
• To be consistent, we should rename 'iron-sulfur cluster carrier activity' > iron-sulfur cluster chaperone activity and mve it under metallochaperone activity.
• Make sure all siblings also have 'x carrier activity' as synonym.

[ValWood]

Nickel ion transfer might be a multistep process:

https://www.pombase.org/reference/PMID:24115911
In this study, we revealed the detail mechanism of how urease accessory proteins UreF, UreH, and UreG cooperate to couple GTP hydrolysis to deliver nickel to urease. UreF/UreH complex interacts with two molecules of GTPase UreG and assembles a metal binding site located at the interface between two UreG molecules. Nickel can induce GTP-dependent dimerization of UreG. This nickel-carrying UreG dimer together with UreF, UreH, and urease assemble into a protein complex. Upon stimulation of UreG GTPase activity by bicarbonate, UreG hydrolyses GTP and releases nickel into urease. Other nickel-delivering NTPases share similar properties with UreG; therefore, the nickel delivery mechanism described here is likely universally shared among these proteins.

[ValWood]

Maybe we need a term for nickel insertion, equivalent to the

GO:0044571 | [2Fe-2S] cluster assembly?

GO:0044571
[2Fe-2S] cluster assembly

[pgaudet]

Looks like the branch with the parent
GO:0031163 metallo-sulfur cluster assembly
should be moved under 'protein maturation' (and definitions improved)

@edwong57 Can you propose a reorganization of the branch? Let me know if you need help or would like to discuss these terms.

Thanks, Pascale

[edwong57]

@pgaudet, sure, I'll take a look and see if I can come up with.

[pgaudet]

I see also these related terms under a different branch:

• 'GO:0042040 metal incorporation into metallo-molybdopterin complex'
• GO:0018315 'molybdenum incorporation into molybdenum-molybdopterin complex'
• 'GO:0042042 tungsten incorporation into tungsten-molybdopterin complex'