SEA-PHAGES | Methyl transferase, Reductase or ?

Link to this post \| posted 10 Aug, 2017 19:29
delesall	In reviewing the annotation of Demsculpinboyz (an F2),the protein of ORF 82 (start 43366, stop 44214) has blast matches to tRNA methyl transferase, PAPs reductase, and ribonucleotide reductase! There is no CDD hits but a number of good HHPred matches (Prob 99%, coverage greater than 65%, low E-values)to 1) phosphoadenosine phosphosulfate sulfurtransferase, 2) Adenine nucleotide alpha hydrolases superfamily, and 3) adenosine 5'-phosphosulfate reductase. All this suggests that going with ribonucleotide reductase is safest bet. What does the forum think?

Link to this post | posted 10 Aug, 2017 19:29

In reviewing the annotation of Demsculpinboyz (an F2),the protein of ORF 82 (start 43366, stop 44214) has blast matches to tRNA methyl transferase, PAPs reductase, and ribonucleotide reductase! There is no CDD hits but a number of good HHPred matches (Prob 99%, coverage greater than 65%, low E-values)to 1) phosphoadenosine phosphosulfate sulfurtransferase, 2) Adenine nucleotide alpha hydrolases superfamily, and 3) adenosine 5'-phosphosulfate reductase. All this suggests that going with ribonucleotide reductase is safest bet. What does the forum think?

Link to this post \| posted 15 Aug, 2017 18:29
kklyczek	Hi Veronique, This is the same pham I was investigating in cluster J phages, where it has been called as PAPS reductase. This pham (2324 currently) is found in A1, F1, F2, and J. It looks like it generally has not been assigned a function in the As and Fs. But as you say, there are good HHPred hits. For Klein_172 the top several hit are PAPS (phosphoadenosine phosphosulfate) reductase, https://toolkit.tuebingen.mpg.de/#/jobs/8893012, and I was leaning toward that call, though it is not yet on the approved function list. Phyre2 returned PAPS reductase with 100% confidence, but at 63% coverage: http://www.sbg.bio.ic.ac.uk/phyre2/phyre2_output/5a596153e1c66682/summary.html Adenine nucleotide alpha hydrolase would be a more general call - enzymes in this family share a ribonucleotide binding domain which is probably what is generating the various HHPred hits. But PAPS reductase seems like a common phage function - it's been called in several other clusters (in other phams, e.g. 2991 in cluster B3 Chandler_4) and is found in phages from other hosts. I am not sure what it's function is in phage multiplication, but it uses thioredoxin as an electron donor to reduce inorganic sulfate to form organic thiols (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2064068/). I don't think ribonucleotide reductase is the best call. The example gene on the approved function list, RedRock_53, looks quite different from this pham, and hits several ribonucleotide reductases full length: https://toolkit.tuebingen.mpg.de/#/jobs/3357242. This enzyme reduces ribonucleotides to deoxyribonucleotides. Karen Edited 15 Aug, 2017 18:30

Link to this post | posted 15 Aug, 2017 18:29

kklyczek

Hi Veronique,

This is the same pham I was investigating in cluster J phages, where it has been called as PAPS reductase. This pham (2324 currently) is found in A1, F1, F2, and J. It looks like it generally has not been assigned a function in the As and Fs. But as you say, there are good HHPred hits. For Klein_172 the top several hit are PAPS (phosphoadenosine phosphosulfate) reductase, https://toolkit.tuebingen.mpg.de/#/jobs/8893012, and I was leaning toward that call, though it is not yet on the approved function list. Phyre2 returned PAPS reductase with 100% confidence, but at 63% coverage: http://www.sbg.bio.ic.ac.uk/phyre2/phyre2_output/5a596153e1c66682/summary.html

Adenine nucleotide alpha hydrolase would be a more general call - enzymes in this family share a ribonucleotide binding domain which is probably what is generating the various HHPred hits. But PAPS reductase seems like a common phage function - it's been called in several other clusters (in other phams, e.g. 2991 in cluster B3 Chandler_4) and is found in phages from other hosts. I am not sure what it's function is in phage multiplication, but it uses thioredoxin as an electron donor to reduce inorganic sulfate to form organic thiols (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2064068/).

I don't think ribonucleotide reductase is the best call. The example gene on the approved function list, RedRock_53, looks quite different from this pham, and hits several ribonucleotide reductases full length: https://toolkit.tuebingen.mpg.de/#/jobs/3357242. This enzyme reduces ribonucleotides to deoxyribonucleotides.

Karen

Edited 15 Aug, 2017 18:30

Link to this post \| posted 15 Aug, 2017 19:47
dbolliva	Hi Veronique and Karen, Just to muddy the waters a bit about ribonucleotide reductases is that are two classes that are found in bacteriophages (Ribonucleotide reductases: essential enzymes for bacterial life Eduard Torrents in Frontiers in Cellular and Infection Microbiology) One does not care if oxygen is around and uses B12 (adenosylcobalamin)(class II) at the active site and the other one is considered anaerobic and uses Adenosylmethionine at the active site (class III). There are also two other subclasses (Ia and Ib) of ribonucleotide reductases found in the eubacteria that have not yet been associated with bacteriophages. The three main classes do not really have any sequence similarity. The hits for the Redrock_53 protein are all to class II RNR's. The one BLAST hit I see for RNR is from a phage and I don't see any HHPred results for RNR's. The HHPred really seems to argue for the PAPS reductase PAPS reductase seems like the better call based on all the information together. Dave

Link to this post | posted 15 Aug, 2017 19:47

dbolliva

Hi Veronique and Karen,

Just to muddy the waters a bit about ribonucleotide reductases is that are two classes that are found in bacteriophages (Ribonucleotide reductases: essential enzymes for bacterial life
Eduard Torrents in Frontiers in Cellular and Infection Microbiology) One does not care if oxygen is around and uses B12 (adenosylcobalamin)(class II) at the active site and the other one is considered anaerobic and uses Adenosylmethionine at the active site (class III). There are also two other subclasses (Ia and Ib) of ribonucleotide reductases found in the eubacteria that have not yet been associated with bacteriophages. The three main classes do not really have any sequence similarity. The hits for the Redrock_53 protein are all to class II RNR's. The one BLAST hit I see for RNR is from a phage and I don't see any HHPred results for RNR's.

The HHPred really seems to argue for the PAPS reductase PAPS reductase seems like the better call based on all the information together.

Dave

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Methyl transferase, Reductase or ?