query about Lem3p-Dnf1p complex

[ValWood]

Accession GO:1990531 NameLem3p-Dnf1p complex def: A protein complex that functions as a phospholipid-translocating P-Type ATPase. Source: PMID:15090616, GOC:dph, GOC:rb

This definition does not seem to be specific enough for the term name , there are quite a few combinations of proteins that fit this definition.

Could we make a more generic "flippase" complex term?

see Coordinated Overexpression in Yeast of a P4-ATPase and Its Associated Cdc50 Subunit: The Case of the Drs2p/Cdc50p Lipid Flippase Complex. Methods Mol Biol. 2016;1377:37-55. PMID: 26695021

A high-yield co-expression system for the purification of an intact Drs2p-Cdc50p lipid flippase complex, critically dependent on and stabilized by phosphatidylinositol-4-phosphate. PLoS One. 2014 PMID: 25393116

These complexes appear to have (at least one) member from each of these families IPR006539 | P-type ATPase, subfamily IV and a IPR005045 | CDC50/LEM3 family member

Is it possible to say which way the flippase acts to refine the def? (I think this one is external to internal PM membrane but I'm not completely sure, I'm guessing because I have a flippase which is not either of these families and it seems to be internal to external)

thanks,

val

[bmeldal]

Sandra annotated it in the CP as GO:0098533 ATPase dependent transmembrane transport complex:

https://www.ebi.ac.uk/complexportal/complex/CPX-1021

There are 4 P4-ATPases in the CP, all annotated more or less the same. I guess the specific name was created after she curated the P4s...

[ValWood]

This is lipid translocation though https://www.ebi.ac.uk/QuickGO/term/GO:0034204 not transmembrane transport (Transmembrane transport requires transport of a solute across a lipid bilayer)

Here the lipid is transferred from one leaflet to another.

I think GO:0098533 is a grouping term for transmembrane transporters, by it's placement, although the definition is sub-optimal...

[bmeldal]

You are right, I will mend them. These are old entries.

[bmeldal]

Actually, before I mend ours, I propose the following updates:

-GO:1990531 Lem3p-Dnf1p complex +GO:1990531 phospholipid-translocating ATPase complex

-A protein complex that functions as a phospholipid-translocating P-Type ATPase. +A protein complex that functions has phospholipid-translocating P-Type ATPase activity.

+Synonym: Lem3p-Dnf1p complex [NARROW] +Synonym: Lem3-Dnf1 complex [NARROW] +Synonym: Dnf1-Lem3 complex [NARROW] +Synonym: Dnf2-Lem3 complex [NARROW] +Synonym: DRS2-CDC50 complex [NARROW] +Synonym: CDC50-DRS2 complex [NARROW] +Synonym: DNF3-CRF1 complex [NARROW] +Synonym: CRF1-DNF3 complex [NARROW] +Synonym: P4-ATPase complex [EXACT] +Synonym: phospholipid flippase complex [EXACT] +Synonym: aminophospholipid translocase complex [EXACT] +Synonym: APLT complex [EXACT]

Relationships: -is_a GO:1990351 transporter complex (wrong activity!)

Note to self: Change def in CP from "A membrane pump which actively transports, or flips..." to "A membrane pump which actively translocates, or flips..."

What did I miss? ;-)

[ValWood]

Sounds good!

[hdrabkin]

A protein complex that functions as a phospholipid-translocating P-Type ATPase. Why do you want the def to change to this below? The current def says the same thing?

+A protein complex that functions has phospholipid-translocating P-Type ATPase activity.

[hdrabkin]

Don't understand this: -is_a GO:1990351 transporter complex (wrong activity!) is inferred I think from the 'capable of phospholipid-translocating ATPase activity"

Have changed term name and synonyms as first pass.

[bmeldal]

A protein complex that functions as a phospholipid-translocating P-Type ATPase. Why do you want the def to change to this below? The current def says the same thing?

Just the syntax. It was standardised when we could still use TG templates to create complex terms from their activities.

-is_a GO:1990351 transporter complex (wrong activity!) is inferred I think from the 'capable of phospholipid-translocating ATPase activity"

As @ValWood mentioned above, this is a flippase that just moves a phospholipid form one membrane to another by flipping it over. It's not really transporting stuff.

Def for transport: "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein."

I'm not sure "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell..." is really capturing what's happening to these PLs. But Val and I might be wrong.

[pgaudet]

Flippases need to be fixed #14793

[bmeldal]

So, park this one til #14793 has been dealt with?

[ValWood]

Flippases are transporters, but not transmembrane transporters. Intermembrane membrane leaflet transport is not transmembrane transport because nothing crosses a lipid bilayer.

So however the flippases terms and complexes are, they should not be linked to transmembrane transport

I don't think this ticket is dependent on anything else, as long as everything points to the correct thing. I'm not in a hurry though. I just need to be able to describe a flippase complex(s) that isn't "Lem3p-Dnf1p", but is related to it

[bmeldal]

Ok, so transporter complex is correct then as is_a parent as it's defined for all types of transport.

In that case, this could be closed and I update the annotation in the CP.

[ValWood]

I still need a term to use ;)

[bmeldal]

The term's been updated to be valid for all phospholipid-translocating ATPases

GO:1990531 phospholipid-translocating ATPase complex with the specific complexes demoted to narrow synonyms.

Or do you need something more generic?

[ValWood]

Ah right Ok, if those updates are done, I'm good! I wasn't following properly!

[ValWood]

The term is not updated yet. Is it done? if I use it with the name "phospholipid-translocating ATPase complex"

[bmeldal]

updated according to QuickGO: https://www.ebi.ac.uk/QuickGO/term/GO:1990531

[ValWood]

OK!