SEA-PHAGES | IrrE or metallopeptidase

Link to this post \| posted 28 Apr, 2022 14:49
smolloy123	Hi All, I am calling a gene in a singleton phage Finkle (gp42 on Phamerator and and between integrase and Immunity repressor). I noted that in AY cluster specific tips Debbie states that the gene that hits IrrE only aligns to the HTH DNA binding domain and therefore call it such. The gene I am looking at is found in a long list of phage across both Gordonia clusters and prophage clusters (CY, CZ, DN, F, MabA, P). But this protein in HHpred has high quality alignment to IrrE and includes the peptidase region (with the HEXXH motif) and the HTH DNA binding domain. Given its location between the integrase and immunity repressor my guess is that this is something like the ImmA antirepressor. But since we can't use guesses for function assignment what do we call this? metallopeptidase helix-turn-helix DNA binding protein? That is too long a name. Please send suggestions. Also the HHpred data is attached!

Link to this post | posted 28 Apr, 2022 14:49

Hi All,
I am calling a gene in a singleton phage Finkle (gp42 on Phamerator and and between integrase and Immunity repressor). I noted that in AY cluster specific tips Debbie states that the gene that hits IrrE only aligns to the HTH DNA binding domain and therefore call it such. The gene I am looking at is found in a long list of phage across both Gordonia clusters and prophage clusters (CY, CZ, DN, F, MabA, P). But this protein in HHpred has high quality alignment to IrrE and includes the peptidase region (with the HEXXH motif) and the HTH DNA binding domain. Given its location between the integrase and immunity repressor my guess is that this is something like the ImmA antirepressor. But since we can't use guesses for function assignment what do we call this? metallopeptidase helix-turn-helix DNA binding protein? That is too long a name.

Please send suggestions. Also the HHpred data is attached!

Link to this post \| posted 28 Apr, 2022 14:52
smolloy123	I am going to answer my own post and suggest simply metallopeptidase. There are five different functions (DNA binding protein. HTH DNA binding domain, metalloprotease, metallopeptidase, peptidase) assigned to this homolog in phagesdb and it would be good if we could settle on one!

Link to this post \| posted 28 Apr, 2022 14:52
smolloy123	I am going to answer my own post and suggest simply metallopeptidase. There are five different functions (DNA binding protein. HTH DNA binding domain, metalloprotease, metallopeptidase, peptidase) assigned to this homolog in phagesdb and it would be good if we could settle on one!

Link to this post \| posted 28 Apr, 2022 16:46
pia1@pitt.edu	HI, This is Ping at University of Pittsburgh. I may have a similar case with gp39 of phage Nettuno in cluster CZ2. There is a mix of metalloprotease and HTH DNA binding domain calls in BLAST hits. The top HHpred hit for gp39 is 3DTE_A (IrrE) with 99.7% probability and 81% coverage. The alignment is gp39 aa9-128 and IrrE aa53-187. The IrrE crystal structure reveals that this protein is folded into three distinct domains: an N-terminal domain (residues 8–125) that consists of five α-helices and a three-stranded antiparallel β-sheet; a middle helix-turn-helix (HTH)-containing domain (residues 126–167); and a C-terminal domain (residues 168–263) folded into a highly twisted six-stranded antiparallel β-sheet with a short α-helix. The alignment between gp39 (aa 9-12 and IrrE (aa 53-187) corresponds to part of the metalloprotease domain, which contains a HEXXH motif and an E (glutamate) 20-30aa downstream of the HEXXH. The key motif HEXXH and the downstream E for the metalloprotease activity are indeed conserved in gp39; the alignment between gp39 and IrrE also covers the complete HTH DNA binding domain. Taken together, gp39 of Nettuno really seems to have both the metalloprotease function and HTH DNA binding domain. I'm not entirely sure which is the better function call because neither reflects the whole picture. See link to the reference below, https://www.sciencedirect.com/science/article/abs/pii/S0022283608015970?via%3Dihub

Link to this post | posted 28 Apr, 2022 16:46

pia1@pitt.edu

HI,

This is Ping at University of Pittsburgh.
I may have a similar case with gp39 of phage Nettuno in cluster CZ2. There is a mix of metalloprotease and HTH DNA binding domain calls in BLAST hits. The top HHpred hit for gp39 is 3DTE_A (IrrE) with 99.7% probability and 81% coverage. The alignment is gp39 aa9-128 and IrrE aa53-187. The IrrE crystal structure reveals that this protein is folded into three distinct domains: an N-terminal domain (residues 8–125) that consists of five α-helices and a three-stranded antiparallel β-sheet; a middle helix-turn-helix (HTH)-containing domain (residues 126–167); and a C-terminal domain (residues 168–263) folded into a highly twisted six-stranded antiparallel β-sheet with a short α-helix. The alignment between gp39 (aa 9-12 smile

and IrrE (aa 53-187) corresponds to part of the metalloprotease domain, which contains a HEXXH motif and an E (glutamate) 20-30aa downstream of the HEXXH. The key motif HEXXH and the downstream E for the metalloprotease activity are indeed conserved in gp39; the alignment between gp39 and IrrE also covers the complete HTH DNA binding domain. Taken together, gp39 of Nettuno really seems to have both the metalloprotease function and HTH DNA binding domain. I'm not entirely sure which is the better function call because neither reflects the whole picture.
See link to the reference below, https://www.sciencedirect.com/science/article/abs/pii/S0022283608015970?via%3Dihub

Link to this post \| posted 28 Apr, 2022 16:48
pia1@pitt.edu	I have no idea where the emoji came from but it seems to be in the place for )…

Link to this post \| posted 28 Apr, 2022 17:06
balish	There's no reason a protein can't do more than one thing, and even among our many phage genes we have other examples of genes encoding fusion proteins. It sounds to me like you have a DNA-binding protease, and it will be fascinating to learn what it does! -Mitch Edited 28 Apr, 2022 17:07

Link to this post \| posted 28 Apr, 2022 17:57
debbie	We keep bumping into the IrrE protein. I have added "IrrE-like protein" to the Approved Function List. Will that work? debbie

Link to this post \| posted 28 Apr, 2022 18:08
pia1@pitt.edu	Would it help to add in the notes that this type of protein (IrrE-like protein) has both a metelloprotease domain and a HTH DNA binding domain?

Link to this post \| posted 28 Apr, 2022 19:17
debbie	Great idea! I just added that! debbie

Link to this post \| posted 28 Apr, 2022 23:40
smolloy123	Wow wonderful ideas and thanks for the speedy responses! I like the idea of adding a note that specifies that both domains must be included in the alignment. Thanks everyone!!!

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IrrE or metallopeptidase