search

geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
Creative Commons Attribution 4.0 International
223 stars 40 forks source link

NTRs: cohesin ring activity / DNA clamp activity PMID:26687354 (types of DNA binding) #12529

Closed ValWood closed 7 years ago

ValWood commented 8 years ago

GONEW: DNA clamp activity A DNA binding activity in which a multimeric protein complex interacts selectively and non-covalently with single DNA duplex to tightly entrap the DNA

GONEW: DNA ring activity A DNA binding activity in which a multimeric protein complex interacts selectively and non-covalently with > 1 DNA duplex to entrap the DNA molecules in a loose fitting ring narrow: cohesin ring activity

These should both be both children of DNA binding and represent non-canonical DNA binding activities

ValWood commented 8 years ago

Term suggestions based on this exchange

I started trying to define cohesin as a clamp, but it clearly isn't. This is how I arrived at these 2 terms:

Frank: Hmm, I can see that it is at first sight appealing to compare PCNA and cohesin, both are ring-shaped assemblies that encircle DNA. However, the PCNA ring is about 1/10th the molecular weight of cohesin, it¹s diameter is less than 1/15th that of cohesin. PCNA is a passive ring, which needs a clamp loader ATPase to be loaded onto DNA. Cohesin, in contrast, is itself the ATPase, while the cohesin loader passively facilitates a conformational change. There is no sequence nor any other similarity between the two. Even the ATPases are from different families and the mechanisms for getting on and off DNA are unrelated. So all in all, I think it would be better to treat the two systems separately.

For PCNA the term 'clamp' is very good, as it binds tightly around DNA. Correspondingly, RFC is suitably called a 'clamp loader' ATPase

For cohesin, the term 'ring' might be better, as it is a very loose fitting ring (there will be eventually 2 or more DNAs inside the ring, which can never happen to PCNA). As mentioned, importantly, this ring itself includes the ATPase.

As far as unifying GO terms goes, it is now clear that also condensin (Cut3, Cut14, Cnd1, Cnd2, Cnd3) and the Smc5/Smc6 complex (Smc5, Smc6, Nse1, Nse2, .. Nse6) are rings that encircle DNA. So maybe the DNA ring GO term can be applied to these?

ValWood commented 8 years ago

We need MF terms for these SMC complexes for LEGO, at the moment their molecular functions are not indicating their roles in the processes.

ValWood commented 8 years ago

ring seems to be the correct terminology http://www.sciencedirect.com/science/article/pii/S0092867405007488 PMID: 16179255

ValWood commented 8 years ago

I'm not sure whether this terms should be DNA ring activity (it sounds odd) as a general term for the SMC-type ring DNA binding activities. They are usually called "cohesin ring" etc

If we go for a general term to represent this class of DNA binding, is there a better name?

ValWood commented 8 years ago

SMC ring-type DNA binding? (this sounds better than DNA ring, because its the protein complex which forms the ring which encircles the DNA) narrow synonym cohesin ring

ValWood commented 8 years ago

This is to confirm that these should be classified as DNA binding activities:

frank: yes, I would say 'DNA binding’ is still a correct term. It’s loose but very stable, with a turnover in many minutes/hours, much more stable than most other DNA binding proteins (transcription factors, heterochromatin proteins, etc., ) that all turn over much more rapidly.

ValWood commented 8 years ago

Final def DNA ring activity The DNA binding activity by which a protein complex interacts selectively and non-covalently with more than one DNA duplex to encircle the DNA molecules with a loose fitting ring.

ValWood commented 8 years ago

From Frank Uhlmann:

GO molecular function GO:0061776 ŒDNA ring activity¹, would ŒDNA topological embrace¹ be a better description? Otherwise it remains unclear what the 'ring activity' is about?

If Frank finds this name confusing, it isn't good! can we work with his new suggestion

Maybe "DNA topological encircling activity" any other suggestions? I can run these by him...

Would this need "activity" appended "DNA topological encircling" sounds better

ValWood commented 8 years ago

Frank did not get back to me on this yet. Can we go with DNA encircing, which is better than DNA ring, and closer to Frank's suggestion so we can close. If a better suggestion materialises easy to update.

ValWood commented 8 years ago

Hi David.
I didn't hear back from Frank yet on this particular question. However, from the title of this paper An In Vitro Assay for Monitoring Topological DNA Entrapment by the Chromosomal Cohesin Complex. Murayama Y, Uhlmann F. Methods Mol Biol. 2017;1515:23-35. PMID: 27797071

I vote we go with "topological DNA entrapment activity" for now as this is used in a few papers already.

ukemi commented 8 years ago

Val,

You originally requested two terms in this ticket. Do you want the clamp activity as originally stated and the ring activity to be the "topological DNA entrapment activity"?

-D

ValWood commented 8 years ago

Oh I forgot about that. Well I don't need it right now, so it could wait....will need it at some point when can probably do a better job with defs.

ukemi commented 7 years ago

Hi Val,

What do you want me to do with this request? Do you want:

GONEW:topological DNA entrapment activity The DNA binding activity by which a protein complex interacts selectively and non-covalently with more than one DNA duplex to encircle the DNA molecules with a loose fitting ring. PMID: 27797071

GONEW: DNA clamp activity A DNA binding activity in which a multimeric protein complex interacts selectively and non-covalently with single DNA duplex to tightly entrap the DNA. PMID:26687354

-D

ValWood commented 7 years ago

That will do it! I thought I had updated this ticket to this effect. I mustn't have hit the comment button!

ukemi commented 7 years ago

Actually, it looks like we already made the clamp activity and the ring activity.

http://amigo.geneontology.org/amigo/term/GO:0061777 http://amigo.geneontology.org/amigo/term/GO:0061776

but I never recorded it in this ticket. Should I just change the name of the ring activity to 'topological DNA entrapment activity'?

ValWood commented 7 years ago

Yes that's the only problem...the name...

The comment I thought I had posted was, that we should use this name

based on this: https://www.ncbi.nlm.nih.gov/pubmed/27797071 An In Vitro Assay for Monitoring Topological DNA Entrapment by the Chromosomal Cohesin Complex.

It seems to be the correct name....

ukemi commented 7 years ago

[Term] id: GO:0061776 -name: DNA ring activity +name: topological DNA entrapment activity namespace: molecular_function -def: "The DNA binding activity by which a protein complex interacts selectively and non-covalently with more than one DNA duplex to encircle the DNA molecules with a loose fitting ring." [GOC:dph, GOC:vw, PMID:16179255, PMID:26687354] +def: "The DNA binding activity by which a protein complex interacts selectively and non-covalently with more than one DNA duplex to encircle the DNA molecules with a loose fitting ring." [GOC:dph, GOC:vw, PMID:16179255, PMID:26687354, PMID:27797071] is_a: GO:0003677 ! DNA binding created_by: dph creation_date: 2016-07-13T13:10:15Z