ribosome binding

[gocentral]

Hi Jane,

Just come across an entry where I need this term.

I am annotating eIF2A...which binds 40S and 80S ribosomes.

So I need:

ribosomal complex binding

and ribosome small subunit binding and ribosome large subunit binding

I also need as child of cytoplasm: eukaryotic translation initiation factor 2A complex:

Possible Def: Complex of three heterogeneous polypeptide chains, that form a ternary complex with initiator methionyl-tRNA and GTP (via eIF5B). This ternary complex binds to free 40S subunit or 80S ribosome, which subsequently binds the 5' end of mRNA.

For Q8NFM1 PMID 12133843

cheers Evelyn

Reported by: ecamon

Original Ticket: "geneontology/ontology-requests/1170":https://sourceforge.net/p/geneontology/ontology-requests/1170

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Do you want these as a process (binding??) or activity (function)? I think it should be function. And, we should be careful to not make them eukaryote specific; however, should they go under binding, OR, also make a term "RNP binding" (def: the activity of binding to a complex or RNA and protein) under binding, and then child "ribosome binding" and its sibs: "small and large subunit binding". If small and large are children of ribsome binding, it would imply that a protein binds the small (or large) subunit AND the ribosome (which is not always the case);

Original comment by: hdrabkin

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I was thinking of the function ontology. I guess the GO-GO gals will get back to us. BTW doesn't the above definition for eukaryotic translation initiation factor 2A complex include interacting proteins. Not sure that is a good idea given recent decisions not to use complex Component terms for annotating interacting proteins. cheers Evelyn

Original comment by: ecamon

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• priority: 5 --> 9

Original comment by: jl242

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• assigned_to: nobody --> jenclark

Original comment by: jenclark

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"Ribosome binding" should certainly be ok, as would be large ribosomal subunit binding and small ribosomal subunit binding as sibs (because there are proteins that bind small subunit and are released upon joining of the large subunit)... There are gene products that definitely bind one or the other. These would just be children of "binding" rather than protein binding (since these are RNP's.. ) I notice that "SnoRNP binding" is a child of protein binding. However, because it is a complex or RNA and protein, one doesn't know what something is binding to necessarily. Perhaps we also need "RNP binding" under binding.

Original comment by: jenclark

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Harold - the def of protein binding is:

Interacting selectively with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).

so that would surely include all RNPs wouldn't it?

I suggest the following structure and defs:

protein binding ; GO:0005515 ---%RNP binding ; GO:new ------%snoRNP binding ; GO:0030519 ------%ribosome binding ; GO:new ---------%ribosomal large subunit binding ; GO:new ---------%ribosomal small subunit binding ; GO:new

RNP binding Intracting selectively with any complex of RNA and protein.

ribosome binding Interacting selectively with any part of a ribosome or one of its subunits.

ribosomal large subunit binding Interacting selectively with any part of the larger ribosomal subunit.

ribosomal small subunit binding Interacting selectively with any part of the small ribosomal subunit.

?

Original comment by: jl242

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Original comment by: jl242

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Hi Jane bu unless an experiment is done to the contrary, if something binds to the ribosome, or any other RNP for that matter, how does one know that it is binding to the protein part and not the RNA part? So, these terms shouldn't be assumed to be a child of protein binding.

Original comment by: hdrabkin

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Hmmm - I guess that's true. That means there's a problem with a couple of other children of 'protein binding' too:

hemoglobin binding lipoprotein binding

can you think of a suitable grouping term that would include these and RNP binding?

Original comment by: jl242

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Jane, you're right. In all cases, the non-protein component could be directly contributing to the binding site. The two you cited are really "complexes". And an RNP can be a simple thing like RNase P (one protein and one RNA). A homoenzyme indicates "a catalytically active complex comprising the protein part of an enzyme (apoenzyme) combinded with the appropriate cofactor or cofactors."

So, (and I see Oxford has this) homoprotein: the functional form of a protein containing a protein part (apopprotein) together with any appropriate ligand or ligands.

So, a term: homoprotein binding might be an appropirate thing, where we define it along the lindes of the homoprotein, and designate the ligand part as being either covalently or non-covalently attached (like the lipid part of a lipoprotein vs the RNA part of many RNPs).

Original comment by: hdrabkin

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I don't think people will know what 'homoprotein' means - I know I'd never heard it before! And I think calling the lipid moiety of a lipoprotein a ligand would also throw people.

The only other solutions I can think of are

1/ 'protein-containing complex binding' which is ugly

2/ Add 'RNP binding' directly under binding and move the other two to be direct children of binding too.

I'd probably opt for the latter. What do you think?

binding ; GO:0005488 ---%RNP binding ; GO:new ------%snoRNP binding ; GO:0030519 ------%ribosome binding ; GO:new ---------%ribosomal large subunit binding ; GO:new ---------%ribosomal small subunit binding ; GO:new ---%hemoglobin binding ---%lipoprotein binding

RNP binding Intracting selectively with any complex of RNA and protein.

ribosome binding Interacting selectively with any part of a ribosome or one of its subunits.

ribosomal large subunit binding Interacting selectively with any part of the larger ribosomal subunit.

ribosomal small subunit binding Interacting selectively with any part of the small ribosomal subunit.

Original comment by: jl242

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2/ Add 'RNP binding' directly under binding and move the other two to be direct children of binding too. Yes; that would do for ribosome binding and its two sibs (Small subunit and Large subunit). As for lipoprotein binding, etc., I guess we could leave them where they are for now, but there is a potential for a true path violation there.

I didn't know about the "holoprotein" either except I suspected it was there in the Oxford because of "holoenzyme" being there.

Original comment by: hdrabkin

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Added new terms:

GO:0043021 JL ribonucleoprotein binding GO:0043022 JL ribosome binding GO:0043023 JL ribosomal large subunit binding GO:0043024 JL ribosomal small subunit binding

and moved terms:

---%hemoglobin binding ---%lipoprotein binding

to be direct children of binding ; GO:0005488

Original comment by: jl242

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• status: open --> closed-accepted

Original comment by: jl242

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• priority: 9 --> 5

Original comment by: mah11