SEA-PHAGES | C1 RNA ligase or phosphoesterase

Link to this post \| posted 18 Apr, 2018 16:24
kaylafast	In our C1 phage Cane17 we are seeing about equal support for the functions RNA ligase and phosphoesterase. There are several members of C1 that support each function. Any suggestions of which to choose or how to choose? Our evidence for each function is below. F: RNA ligase SIF-BLAST: RNA ligase, phagesDB & NCBI, Yucca gp 95 (10 others), AOZ62967.1, 1:1, 95%, e-102 SIF-HHPred: RNA ligase LigT, HHPred, d1iuha_, 57.9%, 99.57% SIF-Syn: RNA ligase; Lukilu & Phox F: phosphoesterase SIF-BLAST: phosphoesterase, phagesDB & NCBI, Pleione gp98 (5 others), AEN79717.1, 1:1, 95%, -102 SIF-HHPred: 2H phosphoesterase/ligase, HHPred, 5LDQ_C, 81.1%, 99.5% SIF-Syn: phosphoesterase; ZaigoTaiga Cane17 gp89 MEFVADDRIPPGYHIPSSWMLRSADAEQAKQTGGMVALYPSTESAQKIVVPGGEPIDDLHLTVTYFGQDVTGQDPTELVDFLYYLAPQFPPIEANIFGTAVFNSTGEDPCIVYLVGNSPHLTPLFQQLKRFALEHYPGAAEQHDPWIPHITAAYGSGAMIDYEGPVVFDRIGIRWPGADQDFNLZ

Link to this post | posted 18 Apr, 2018 16:24

In our C1 phage Cane17 we are seeing about equal support for the functions RNA ligase and phosphoesterase. There are several members of C1 that support each function. Any suggestions of which to choose or how to choose? Our evidence for each function is below.

F: RNA ligase SIF-BLAST: RNA ligase, phagesDB & NCBI, Yucca gp 95 (10 others), AOZ62967.1, 1:1, 95%, e-102 SIF-HHPred: RNA ligase LigT, HHPred, d1iuha_, 57.9%, 99.57% SIF-Syn: RNA ligase; Lukilu & Phox
F: phosphoesterase SIF-BLAST: phosphoesterase, phagesDB & NCBI, Pleione gp98 (5 others), AEN79717.1, 1:1, 95%, -102 SIF-HHPred: 2H phosphoesterase/ligase, HHPred, 5LDQ_C, 81.1%, 99.5% SIF-Syn: phosphoesterase; ZaigoTaiga

Cane17 gp89
MEFVADDRIPPGYHIPSSWMLRSADAEQAKQTGGMVALYPSTESAQKIVVPGGEPIDDLHLTVTYFGQDVTGQDPTELVDFLYYLAPQFPPIEANIFGTAVFNSTGEDPCIVYLVGNSPHLTPLFQQLKRFALEHYPGAAEQHDPWIPHITAAYGSGAMIDYEGPVVFDRIGIRWPGADQDFNLZ

Link to this post \| posted 19 Apr, 2018 05:32
cdshaffer	I must say I really like this gene cluster. I use it as a great didactic opportunity to have students think carefully about biochemistry and the nature of enzymes. I remind them that all an enzyme can do is speed up the reaction rate, it cannot control "the direction" of the reaction. The direction depends on which substrates are in excess. This is especially an issue when enzymes are purified and studied in vitro where substrate concentrations can be orders of magnitude different than intracellular levels. This leads to confusion when trying to functionally annotate and this cluster is a great example. The top hit from hhpred is called an RNA Ligase on the short text but when you dig into the enzyme it all makes sense. The pdb entry for this RNA Ligase is 1IUH. Here is the link: https://www.rcsb.org/structure/1iUH If you go to the page and click on the "annotations" tab you will see down in the "molecular function" section that this one enzyme lists both an RNA ligase and a 2' 3' Cyclic Nucleotide 3' Phosphodiesterase activity are listed. This is because experimenters can detect both activities in vitro. Some labs put in the cyclic nucleotide and see breakage of the phosphate to carbon bond (phosphodiesterase). A different set of substrates and you can drive the reaction the other way and create a phosphate to carbon bond (ligase). As for annotation, of the available approved terms, I feel like RNA ligase is the best available term since phosphodiesterase is not available. Phosphoesterase just feels too generic since there are many phosphoesterases that are not phosphodiesterases.

Link to this post | posted 19 Apr, 2018 05:32

cdshaffer

I must say I really like this gene cluster. I use it as a great didactic opportunity to have students think carefully about biochemistry and the nature of enzymes. I remind them that all an enzyme can do is speed up the reaction rate, it cannot control "the direction" of the reaction. The direction depends on which substrates are in excess. This is especially an issue when enzymes are purified and studied in vitro where substrate concentrations can be orders of magnitude different than intracellular levels.

This leads to confusion when trying to functionally annotate and this cluster is a great example. The top hit from hhpred is called an RNA Ligase on the short text but when you dig into the enzyme it all makes sense. The pdb entry for this RNA Ligase is 1IUH. Here is the link:

https://www.rcsb.org/structure/1iUH

If you go to the page and click on the "annotations" tab you will see down in the "molecular function" section that this one enzyme lists both an RNA ligase and a 2' 3' Cyclic Nucleotide 3' Phosphodiesterase activity are listed. This is because experimenters can detect both activities in vitro. Some labs put in the cyclic nucleotide and see breakage of the phosphate to carbon bond (phosphodiesterase). A different set of substrates and you can drive the reaction the other way and create a phosphate to carbon bond (ligase).

As for annotation, of the available approved terms, I feel like RNA ligase is the best available term since phosphodiesterase is not available. Phosphoesterase just feels too generic since there are many phosphoesterases that are not phosphodiesterases.

Link to this post \| posted 19 Apr, 2018 15:34
kaylafast	Thanks!

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C1 RNA ligase or phosphoesterase