SEA-PHAGES | acyltransferase and SGNH domains

Link to this post \| posted 04 May, 2021 16:28
rlb6	Hi I'm looking for the best function assignment for a Gordonia gene LonelyBoi_31. This gene has strong hhpred and blast hits to acyltransferase and SGNH domains. Many transmembrane helices are also predicted. I don't see any appropriate function on the Official function list This is the amino acid sequence starting at nucleotide 29456 which seems to align best with the start of top hits: LRLDIQGLRAVAVILVILDHLFEWPKAGFIGVDVFFVISGFVITAGLQRGYGRTGTISFGDFYRKRARRI IPASTLVLVATCAAAAYAFYSSRFHETLIDAVWAFFFASNWRFAFQGTNYLTAEGPVSPLQHYWSLGIEE QFYVVWPLLMLGVFTLAASRGLHAHSERIAAAAIGLVIAVSFSWAMIQTATHAEFAYFSTFTRVWELGIG AMLALLAVEWKKIPDAARPFLAWVGLLGILVSAFIVSSESGFPAPWAALPVLATALVIAAGTGGERKHLY PLTNPVASYIGDISYSLYLWHFPVIVILAAMMPSGWRYHFLCLALMSILSVLSYHILEDPVRKSTWLEPK AVREDRRRLRRGASTTTLADSVGSAKWKIISLTAVLLVALAVVADGRGSDMSSVPDFTAAGQVSDNGAPT SPLQAGLVEGVEATKWPANLSPSLEELGDISFPTADANGCAPATPRGRDCTIAGVDPSRLAVVVGDSISV AWLPAIRAALEPKGWTVAALPYIGCPFVDGATENADATVVRTCPAHKQEVVDIINRAKPALVIGSSTNNI RSARGESPENGARALSDQVAKIDAAAGRYVQLSPPPSGDNPQECATRFSSPRECLGGLPSNYTASVEAQK AVMAGPGRQFVDTSDWFCTPEGDCPILNGSTLIRRDTSHITPQYAKVIAPQLASALLTTG Beckie Bortz 82Kb

Link to this post | posted 04 May, 2021 16:28

Hi I'm looking for the best function assignment for a Gordonia gene LonelyBoi_31. This gene has strong hhpred and blast hits to acyltransferase and SGNH domains. Many transmembrane helices are also predicted. I don't see any appropriate function on the Official function list
This is the amino acid sequence starting at nucleotide 29456 which seems to align best with the start of top hits:
LRLDIQGLRAVAVILVILDHLFEWPKAGFIGVDVFFVISGFVITAGLQRGYGRTGTISFGDFYRKRARRI
IPASTLVLVATCAAAAYAFYSSRFHETLIDAVWAFFFASNWRFAFQGTNYLTAEGPVSPLQHYWSLGIEE
QFYVVWPLLMLGVFTLAASRGLHAHSERIAAAAIGLVIAVSFSWAMIQTATHAEFAYFSTFTRVWELGIG
AMLALLAVEWKKIPDAARPFLAWVGLLGILVSAFIVSSESGFPAPWAALPVLATALVIAAGTGGERKHLY
PLTNPVASYIGDISYSLYLWHFPVIVILAAMMPSGWRYHFLCLALMSILSVLSYHILEDPVRKSTWLEPK
AVREDRRRLRRGASTTTLADSVGSAKWKIISLTAVLLVALAVVADGRGSDMSSVPDFTAAGQVSDNGAPT
SPLQAGLVEGVEATKWPANLSPSLEELGDISFPTADANGCAPATPRGRDCTIAGVDPSRLAVVVGDSISV
AWLPAIRAALEPKGWTVAALPYIGCPFVDGATENADATVVRTCPAHKQEVVDIINRAKPALVIGSSTNNI
RSARGESPENGARALSDQVAKIDAAAGRYVQLSPPPSGDNPQECATRFSSPRECLGGLPSNYTASVEAQK
AVMAGPGRQFVDTSDWFCTPEGDCPILNGSTLIRRDTSHITPQYAKVIAPQLASALLTTG

Beckie Bortz

Link to this post \| posted 04 May, 2021 20:09
cdshaffer	Wow, so cool. Never heard of a SGNH domain. It appears to be a specific subtype of acytltransferase. I have not had time to do a suitable in depth on this but here is the paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7448272/ That paper on the crystal is only 10 months old so not surprising it has not come up before. My brief survey suggests a good general annotation here might be "carbohydrate acetyltransferase" but that would need more work to provide more evidence to have the term added to the approved list. Since both domains in this protein appear to both be related to acetyltransferases of two different types I would think "acetyltransferase" is a good match from the options on the current approved terms list.

Link to this post | posted 04 May, 2021 20:09

cdshaffer

Wow, so cool. Never heard of a SGNH domain. It appears to be a specific subtype of acytltransferase. I have not had time to do a suitable in depth on this but here is the paper:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7448272/

That paper on the crystal is only 10 months old so not surprising it has not come up before. My brief survey suggests a good general annotation here might be "carbohydrate acetyltransferase" but that would need more work to provide more evidence to have the term added to the approved list. Since both domains in this protein appear to both be related to acetyltransferases of two different types I would think "acetyltransferase" is a good match from the options on the current approved terms list.

Link to this post \| posted 04 May, 2021 20:35
kbutela	Hi Beckie- The HHPred hits support your observations of an acetyltransferase domain linked via a series of transmembrane domains to the SGNH domains. I found an article (https://mbio.asm.org/content/11/4/e01364-20)"Acetylation of Surface Carbohydrates in Bacterial Pathogens Requires Coordinated Action of a Two-Domain Membrane-Bound Acyltransferase" describing AT3, and one class seems to fit what you described here: "Among bacterial AT3 carbohydrate acetyltransferases, there are two known domain architectures, proteins consisting of an AT3 domain only (AT3-only) and an N-terminal AT3 domain linked to an extracytoplasmic domain, commonly an SGNH domain (AT3-SGNH fused). The SGNH domain is fused through addition of an 11th TMH and linking region." There is a conserved motif (GG-F/Y-XGV-D/P/V) found in a diverse set of these proteins from Gram pos and neg bacteria within the AT3 domain. I downloaded the same sequences that contained both domains from the paper and repeated their T-coffee alignment (attached. LonelyBoi does contain this motif, but the first letter is A not G. Otherwise it is identical to the rest of the group. Other conserved residues based on OafA (WP_000639473.1) are S112, N113, and Y122. LonelyBoi does contain these conserved residues based on the alignment to OafA. In the SGNH domain, the following residues are conserved using OafA as the reference: G409, D 410, S411. LonelyBoi contains these residues in the same area in the alignment. Essential catalytic residues experimentally determined in OatA (WP_000379821) G502, T503, and N504 (not conserved across the entire group of sequences) are found in LonelyBoi at the corresponding alignment area with the exception of LonelyBoi having S corresponding to the G502 residue. I used Figure S3 as a reference to map out how LonelyBoi compares to other sequences in terms of catalytic residues, and it appears that LonelyBoi has all of the highly conserved residues but not on the less conserved residues. Based on this information, I propose a new function: Membrane bound acyltransferase-3 (AT3) domain-containing protein. This is a more generic family level call, but I don't think we have enough wet bench evidence to further narrow down the function as to what this particular enzyme is doing. A quick article search suggests that phages carry this gene to modify cell surface peptidoglycans and lipopolysaccharides. 25Kb

Link to this post | posted 04 May, 2021 20:35

kbutela

Hi Beckie-

The HHPred hits support your observations of an acetyltransferase domain linked via a series of transmembrane domains to the SGNH domains. I found an article (https://mbio.asm.org/content/11/4/e01364-20)"Acetylation of Surface Carbohydrates in Bacterial Pathogens Requires Coordinated Action of a Two-Domain Membrane-Bound Acyltransferase" describing AT3, and one class seems to fit what you described here: "Among bacterial AT3 carbohydrate acetyltransferases, there are two known domain architectures, proteins consisting of an AT3 domain only (AT3-only) and an N-terminal AT3 domain linked to an extracytoplasmic domain, commonly an SGNH domain (AT3-SGNH fused). The SGNH domain is fused through addition of an 11th TMH and linking region."

There is a conserved motif (GG-F/Y-XGV-D/P/V) found in a diverse set of these proteins from Gram pos and neg bacteria within the AT3 domain. I downloaded the same sequences that contained both domains from the paper and repeated their T-coffee alignment (attached. LonelyBoi does contain this motif, but the first letter is A not G. Otherwise it is identical to the rest of the group. Other conserved residues based on OafA (WP_000639473.1) are S112, N113, and Y122. LonelyBoi does contain these conserved residues based on the alignment to OafA.

In the SGNH domain, the following residues are conserved using OafA as the reference: G409, D 410, S411. LonelyBoi contains these residues in the same area in the alignment.

Essential catalytic residues experimentally determined in OatA (WP_000379821) G502, T503, and N504 (not conserved across the entire group of sequences) are found in LonelyBoi at the corresponding alignment area with the exception of LonelyBoi having S corresponding to the G502 residue. I used Figure S3 as a reference to map out how LonelyBoi compares to other sequences in terms of catalytic residues, and it appears that LonelyBoi has all of the highly conserved residues but not on the less conserved residues.

Based on this information, I propose a new function: Membrane bound acyltransferase-3 (AT3) domain-containing protein. This is a more generic family level call, but I don't think we have enough wet bench evidence to further narrow down the function as to what this particular enzyme is doing. A quick article search suggests that phages carry this gene to modify cell surface peptidoglycans and lipopolysaccharides.

Link to this post \| posted 04 May, 2021 20:47
debbie	Becky, I wrote this way before Chris posted. So to muddle this a bit. Hi. I think I would like to call this O-acetyltransferase A. I have attached an article that describes this gene as having 2 domains, which I believe I see in LonelyBoi_31, namely an acetyltransferase and a SGNH hydrolase fold. Let me know what you think, debbie https://www.sciencedirect.com/science/article/pii/S0021925817494105?via%3Dihub Edited 04 May, 2021 20:48

Link to this post | posted 04 May, 2021 20:47

debbie

Becky,
I wrote this way before Chris posted. So to muddle this a bit.

Hi. I think I would like to call this O-acetyltransferase A. I have attached an article that describes this gene as having 2 domains, which I believe I see in LonelyBoi_31, namely an acetyltransferase and a SGNH hydrolase fold.

Let me know what you think,
debbie

https://www.sciencedirect.com/science/article/pii/S0021925817494105?via%3Dihub

Edited 04 May, 2021 20:48

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acyltransferase and SGNH domains