SEA-PHAGES | ClpP-like protease or CMP?

Link to this post \| posted 14 May, 2022 16:54
kcornely	Greetings, all! We are finishing up Langerak and checking our functions. gp4 has hits to the capsid maturation protease as well as ClpP-like proteases. On the SEA PHAGES official function list, we are told that sometimes the capsid maturation proteases has hits to ClpP-like proteases and in the notes, we are told "sometimes the CMP hits to ClpP proteases. If so, look for a serine-type endopeptidase activity". gp4 in Langerak does have hits to serine-type endopeptidase activity. To me, the directions aren't clear: If there are hits to endopeptidase activity does that mean that it is a ClpP-like protease? Or is it not a ClpP-like protease and we should assign "capsid maturation protease" instead? Thanks for help! Kathleen

Link to this post | posted 14 May, 2022 16:54

Greetings, all! We are finishing up Langerak and checking our functions. gp4 has hits to the capsid maturation protease as well as ClpP-like proteases. On the SEA PHAGES official function list, we are told that sometimes the capsid maturation proteases has hits to ClpP-like proteases and in the notes, we are told "sometimes the CMP hits to ClpP proteases. If so, look for a serine-type endopeptidase activity". gp4 in Langerak does have hits to serine-type endopeptidase activity. To me, the directions aren't clear: If there are hits to endopeptidase activity does that mean that it is a ClpP-like protease? Or is it not a ClpP-like protease and we should assign "capsid maturation protease" instead?
Thanks for help!
Kathleen

Link to this post \| posted 14 May, 2022 17:14
balish	I think the idea is that the capsid maturation protease is sufficiently similar to the ClpP family of proteases that it will sometimes get a hit with ClpP in its name. But if the other signs are there that it's a capsid maturation protease, it should be called that, and not ClpP-like. Given that ClpP is also a serine protease, I'm not sure that there would ever be a case when it doesn't hit something with that activity. So that's confusing and seems possibly extraneous - unless my interpretation is incorrect. I would expect that the presence of a ClpP-like or capsid maturation protease gene at the left end of the phage genome amid all the other capsid genes is likely to be sufficient to warrant calling it a capsid maturation protease in most cases. -Mitch

Link to this post | posted 14 May, 2022 17:14

balish

I think the idea is that the capsid maturation protease is sufficiently similar to the ClpP family of proteases that it will sometimes get a hit with ClpP in its name. But if the other signs are there that it's a capsid maturation protease, it should be called that, and not ClpP-like. Given that ClpP is also a serine protease, I'm not sure that there would ever be a case when it doesn't hit something with that activity. So that's confusing and seems possibly extraneous - unless my interpretation is incorrect. I would expect that the presence of a ClpP-like or capsid maturation protease gene at the left end of the phage genome amid all the other capsid genes is likely to be sufficient to warrant calling it a capsid maturation protease in most cases.

-Mitch

Link to this post \| posted 14 May, 2022 17:35
kcornely	Thanks for the speedy reply, Mitch!

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ClpP-like protease or CMP?