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InterPro2GO: Tubulin/FtsZ, GTPase domain (IPR003008) #3619

Closed sjm41 closed 3 years ago

sjm41 commented 3 years ago

This domain is associated with all tubulins (alpha, beta and gamma), at least in Drosophila.

It is associated with the GO MF "GTPase activity (GO:0003924)" and has this def: This entry represents a GTPase domain found in all tubulin chains, such as tubulin alpha, beta and gamma chains, and some bacterial FtsZ proteins [1]. These proteins are involved in polymer formation. Tubulin is the major component of microtubules, while FtsZ is the polymer-forming protein of bacterial cell division, it is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells [2, 3]. FtsZ and tubulin are GTPases, this entry is the GTPase domain. FtsZ can polymerise into tubes, sheets, and rings invitro and isubiquitous in bacteria and archaea.

alpha-beta tubulin dimers do have GTPase activity, though I can't work out whether it's just the beta subunit or the alpha-beta interface that is implicated in GTPase activity. (good review: https://www.frontiersin.org/articles/10.3389/fpls.2014.00511/full)

But Reference 1 in the def and the review given above don't mention gamma tubulin - it's not a GTPase as far as I can tell - any one else know?

So I'm wondering if 'GTPase activity' should be removed from this InterPro entry. Perhaps replace with 'GTP binding'? Thoughts?

@sarach06 @EBI-Hsinyu

sarach06 commented 3 years ago

Hi, Thank you for this. I agree with you that 'GTPase activity' should be removed. I agree with you, that gamma tubulin binds GTP and doesn't have GTPase activity (https://www.nature.com/articles/ncb2863, https://www.nature.com/articles/s42003-018-0037-3, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6214090/). I will replace the term for GTP binding.

Best regards, Sara

sjm41 commented 3 years ago

Thanks Sara!

sjm41 commented 2 years ago

Hi @sarach06 I notice that 'GTPase activity' is still associated with IPR003008 as of InterPro release 87. Did this removal get missed?

sarach06 commented 2 years ago

Hi Steven, Thank you for pointing this and my apologies (I probably forgot to remove the term when adding the other one, my bad). It is now removed. Best regards, Sara

sjm41 commented 2 years ago

OK, thanks @sarach06 !