Query acyl carrier protein

[gocentral]

Shold "acyl carrier proteins" be defined as transporters? (they are currently) http://en.wikipedia.org/wiki/Acyl\_carrier\_protein

It seems they are not involved in directed movement (maybe localization?)

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/9207

[gocentral]

No, not a transporter in the sense that a membrane channel is or in the sense that an extracellular protein that binds another molecule to solubilize it or direct it to a target is. During fatty acid biosynthesis, ACP holds the growing entity that is acted on to make the fatty acid. If you like factory analogies, the enzymes that catalyze the steps of each round of 2-carbon addition form one; ACP is a combination vise-truck that moves the growing substrate from site to site, so there's motion but more nearly in the sense of conformational change or the swinging of a flexible arm. Peter

Original comment by: deustp01

[gocentral]

I was thinking about this some more.. I have convinced myself it isn't a "transporter" in the GO transport sense because the movement isn't "directed". Its analogous to a protein which is anchored by another protein, which makes the anchored protein accessible to other proteins which it is proximal to. There may be movement, (i.e its movement is constrained by the 'reach' of the linker molecule), but not transport. The molecule is free to move anywhere in the vicinity (but is constrained by the linker). Peter do you agree?

Original comment by: ValWood

[gocentral]

Yes, exactly.

Original comment by: deustp01

[gocentral]

Becky and I been discussing this, and we think that although ACP is different to most of the other transporter activities we have, we think it does still belong under transporter activity. The 'directed' in the definition of transporter just means not random, and to specific sites which fits for ACP:

http://web.ethlife.ethz.ch/e/articles/sciencelife/fasscban.html

It could definitely use a better def though, and it should be part of the process of fatty acid biosynthesis.

Original comment by: jl242

[gocentral]

But then every enzyme complex that features some sort of swinging-arm mechanism whereby a tethered substrate is moved from place to place within the complex as the overall reaction proceeds should be annotated with a transport activity, e.g., all 2-oxoacid dehydrogenase complexes like pyruvate dehydrogenase - see the section "Active site coupling mechanism" starting at the bottom of page 8972 in PMID 2188967. Is that intended?

Original comment by: deustp01

[gocentral]

I agree with Peter. I don't think this should be classed as transporter (it isn't one) In effect the movement is random, but restricted....

If the arm was physically and mechanistically "directing" the movement of the substrate from A-B it would be, but it isn't ,so it mustn't be transport

Original comment by: ValWood

[gocentral]

• assigned_to: nobody --> jl242

Original comment by: rebeccafoulger

[gocentral]

'acyl carrier activity ; GO:0000036' currently only has parentage under transporter...what would you suggest it was re-classified as? Some sub-type of binding maybe?

Original comment by: jl242

[gocentral]

how about something like

phosphopantetheine chain linker binding

(the def of the esisting term will change though so might need to be obsoleted)

Original comment by: ValWood

[gocentral]

Or how about 'phosphopantetheine chain linker binding involved in fatty acid biosynthesis' and then we can make it part of 'fatty acid biosynthesis'?

I don't think we'll need to obsolete - looking at the annotations they're all ACP so we can just move it and redefine.

Original comment by: jl242

[gocentral]

I think it needs a parent though this could be a child. Not all of the 'phosphopantetheine chain linker binding are involved in fatty acid biosynthesis, it is used in other contexts

Val

Original comment by: ValWood

[gocentral]

Yep - it would have generic 'phosphopantetheine chain linker binding' as a parent, but the existing term 'acyl carrier activity ; GO:0000036' would become the 'phosphopantetheine chain linker binding involved in fatty acid biosynthesis'

Jane

Original comment by: jl242

[gocentral]

Sorry, yes, being dim, that sounds fine val

Original comment by: ValWood

[gocentral]

Okay, so I'm confused now. The phosphopantetheine is the prosthetic group of the ACP, so isn't phosphopantetheine part of ACP?

Original comment by: jl242

[gocentral]

Yes, the phosphopantetheine moiety is part_of ACP. It is covalently attached to a serine side chain, as described in psiMOD http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MOD (so it has John Garavalli's blessing, and I suspect he would concede that this is even an instance of a post-translational covalent modification)

Original comment by: deustp01

[gocentral]

Yep the moiety being bound (E.g. Coenzyme A) attaches to thephosphopantetheine attachment site which is attached to the ACP.

Would it be better to say "ACP phosphopantetheine attachment binding" "ACP phosphopantetheine attachment binding Acetyl CoA" etc?

Original comment by: ValWood

[gocentral]

Okay, so how about

ACP phosphopantetheine attachment site binding (GO:new) Interacting selectively with the attachment site of the phosphopantetheine prosthetic group of an acyl carrier protein (ACP).

and then we'll also have as a child:

ACP phosphopantetheine attachment site binding involved in fatty acid biosynthetic process (GO:0000036) Interacting selectively with the attachment site of the phosphopantetheine prosthetic group of an acyl carrier protein (ACP) as part of the process of fatty acid biosynthesis. exact synonym: acyl carrier activity

Original comment by: jl242

[gocentral]

Sounds good, as long as it moves from under transport;)

Original comment by: ValWood

[gocentral]

Added:

ACP phosphopantetheine attachment site binding ; GO:0044620

Changed name of GO:0000036 from "acyl carrier activity" to "ACP phosphopantetheine attachment site binding involved in fatty acid biosynthetic process"

Changed definition of GO:0000036 from "Enables the directed movement of acyl groups into, out of, within or between cells." to "Interacting selectively with the attachment site of the phosphopantetheine prosthetic group of an acyl carrier protein (ACP) as part of the process of fatty acid biosynthesis."

Moved ACP phosphopantetheine attachment site binding involved in fatty acid biosynthetic process (GO:0000036) (as OBO_REL:is_a), to prosthetic group binding (GO:0051192) from binding (GO:0005488)

Original comment by: jl242

[gocentral]

• milestone: --> PomBase
• status: open --> closed-works-for-me

Original comment by: jl242