SEA-PHAGES | New function call proposal: UDP-galactopyranose mutase

Link to this post \| posted 14 Apr, 2021 16:47
kbutela	Gene 59 in Gordonia phage Madi (Cluster DG) has a nearly identical alignment (99.7% probability with 99% query coverage) in HHPred to the crystal structure of UDP-galactopyranose mutase from Mycobacterium smegmatis https://www.rcsb.org/structure/5ER9. UDP-galactopyranose mutase converts galactopyranose to galactofuranose, which is needed for cell wall biosynthesis in bacteria. Not sure why a phage would have it but cool to consider. https://pubmed.ncbi.nlm.nih.gov/24096172/. Metamorphoo gp87 is called in the official functions list as UDP-glucose dehydrogenase, which is involved in the biosynthetic pathway for hexuronic acid-containing bacterial surface glycostructures. Other phages in this cluster use the more generic term "oxioreductase." There are numerous hits for oxioreductases in the HHPred results, mostly from other proteins that match with probability greater than 90% but around 70-80% query coverage. Would we be able to make a more specific functional call for this gene? HHPred results are attached. 3.02Mb

Link to this post | posted 14 Apr, 2021 16:47

Gene 59 in Gordonia phage Madi (Cluster DG) has a nearly identical alignment (99.7% probability with 99% query coverage) in HHPred to the crystal structure of UDP-galactopyranose mutase from Mycobacterium smegmatis https://www.rcsb.org/structure/5ER9.

UDP-galactopyranose mutase converts galactopyranose to galactofuranose, which is needed for cell wall biosynthesis in bacteria. Not sure why a phage would have it but cool to consider. https://pubmed.ncbi.nlm.nih.gov/24096172/. Metamorphoo gp87 is called in the official functions list as UDP-glucose dehydrogenase, which is involved in the biosynthetic pathway for hexuronic acid-containing bacterial surface glycostructures.

Other phages in this cluster use the more generic term "oxioreductase." There are numerous hits for oxioreductases in the HHPred results, mostly from other proteins that match with probability greater than 90% but around 70-80% query coverage. Would we be able to make a more specific functional call for this gene? HHPred results are attached.

Link to this post \| posted 23 Apr, 2021 00:07
debbie	Hi Kristen, This is not a quick answer. Here is where I have gotten. The top hits seem convincing that this is a UDP-galactopyranose mutase. i am hesitant to call it because that is a very specific assignment. I am worried that this gene is ~100 aa shorter than what the crystal structures of UDP-galactopyranose mutase describe, so is it missing a domain? I was not able to dig deep enough to figure out what the C-terminus domain of a UDP-galactopyranose mutase is. (I am guessing it is the missing the mutase part.) Since this is in the oxidoreductase family, I am inclined to be more generic. If you find all of the domains of a UDP-galactopyranose mutase present, then that would settle it. I just ran out of time. What do you think? debbie

Link to this post | posted 23 Apr, 2021 00:07

debbie

Hi Kristen,
This is not a quick answer.
Here is where I have gotten.
The top hits seem convincing that this is a UDP-galactopyranose mutase. i am hesitant to call it because that is a very specific assignment. I am worried that this gene is ~100 aa shorter than what the crystal structures of UDP-galactopyranose mutase describe, so is it missing a domain? I was not able to dig deep enough to figure out what the C-terminus domain of a UDP-galactopyranose mutase is. (I am guessing it is the missing the mutase part.) Since this is in the oxidoreductase family, I am inclined to be more generic. If you find all of the domains of a UDP-galactopyranose mutase present, then that would settle it. I just ran out of time.
What do you think?
debbie

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New function call proposal: UDP-galactopyranose mutase