OTR: DBD domain binding

[lpalbou]

I was looking at DBD domain binding and there is a relation to Protein binding but not to DNA binding, is that on purpose ? I may misunderstand something but the DBD does bind DNA and not other protein, so could it be a misclassification ?

I found that one in the "other" category with the ribbon and was surprised not to see it under DNA binding:

In addition, I was looking at the definition ("The DNA binding domain of the vitamin D receptor, one of a family of receptors with the DBD..") and it seems to be very VDR oriented whereas to my knowledge every nuclear receptor has a DBD, including GCRs.

[cmungall]

A gene product may bind to the protein domain without binding to DNA?

On Wed, Oct 23, 2019, 15:17 lpalbou notifications@github.com wrote:

I was looking at DBD domain binding http://amigo.geneontology.org/amigo/term/GO:0050692 and there is a relation to Protein binding http://amigo.geneontology.org/amigo/term/GO:0005515 but not to DNA binding http://amigo.geneontology.org/amigo/term/GO:0003677, is that on purpose ? I may misunderstand something but the DBD does bind DNA and not other protein, so could it be a misclassification ?

In addition, I was looking at the definition ("The DNA binding domain of the vitamin D receptor, one of a family of receptors with the DBD..") and it seems to be very VDR oriented whereas to my knowledge every nuclear receptor has a DBD, including GCRs.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/geneontology/go-ontology/issues/18047?email_source=notifications&email_token=AAAMMOPUA6M47HVFZKJDVEDQQDEOPA5CNFSM4JELUSU2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HT6M6FA, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMMOMPJ7M7GND3ATTDTJDQQDEOPANCNFSM4JELUSUQ .

[lpalbou]

I am unsure I understand your question: the dimerization process of nuclear receptors is driven by the LBD, not the DBD, but yes in the dimer, the DBDs of both subunit interacts to shape a binding site able to bind DNA. In that sense you could say there are some protein-protein interactions but the primary/biological role of a DBD is to bind and regulate DNA transcription, not to bind protein.. hence my surprise and why I would first describe a DBD domain as a "DNA binding" rather than a "Protein binding".

[srengel]

right. the DBD domain itself is DNA binding, but something that is 'DBD-domain binding' is binding the DBD domain, which is within a protein, so 'protein binding'.

[bmeldal]

While I agree that @lpalbou mixed up the DNA- and protein-binding aspects (see @srengel comment) I do agree that the definition is odd with the specific description of the Vitamin D receptor DBD details. Should that section be removed or added as a comment?

Come to think of, the term name should also be "DBD binding" (= DNA binding domain binding) as "DBD domain binding" = DNA binding domain domain binding.

New ticket or change title?

[krchristie]

While I agree that @lpalbou mixed up the DNA- and protein-binding aspects (see @srengel comment) I do agree that the definition is odd with the specific description of the Vitamin D receptor DBD details. Should that section be removed or added as a comment?

It seems to me that the Vitamin D receptor details should just be removed.

Come to think of, the term name should also be "DBD binding" (= DNA binding domain binding) as "DBD domain binding" = DNA binding domain domain binding.

Perhaps the title should be spelled out as "DNA binding domain binding", with "DBD binding" as a synonym?

New ticket or change title?

I think we could just change the title.

[bmeldal]

Go ahead, @krchristie :)

[krchristie]

@ukemi - Since I happened to read through this ticket and it seemed very simple, I just took it to save anyone else the time of reading through it.

[lpalbou]

Thanks for the clarification !