Link to this post | posted 15 Apr, 2018 21:51

smolloy123

Hi All, I found a Phosphoribosylpyrophosphate synthetase match for gene 82 in Neville (an unclustered Gordonia). The phagesdb matches have this gene called all over the board from less specific phosporibosyl transferase (Oneup_100), phosphoribosylphosphatase (thibault_115). There is also a gene called ribose-phosphate pyrophosphokinase (Snenia_73) which is the same thing as a Phosphoribosylpyrophosphate synthetase. Phosphoribosyl transferase is the only approved function call. I looked at the alignment of Neville_82 to the Bacillus subtillus PPRP synthetase (which is crystalized) and found that it had nearly all of the conserved residues and many of the less conserved residues. It has the conserved residues necessary for the pyrophosphate binding domain, for the ribose-5phosphate binding domain and the mADP binding and active site. (see attachment). Is it best just to call this a phosphoribosyl transferase or do you want the specificity of PPRP synthetase? Thanks Sally 1.31Mb

Link to this post | posted 16 Apr, 2018 16:05
welkin	sounds like you are making a strong case for including the more specific one. Which way are you leaning on this?

Link to this post | posted 16 Apr, 2018 18:50
smolloy123	Hi Welkin, I was thinking that this gene is for sure a PRPP synthetase and that we should add it to the function list. I guess I was worried about clouding the waters by throwing another name in for that one pham. Thanks Welkin!

Link to this post | posted 31 May, 2018 20:32
smolloy123	Just for the record, I am calling gp83 of Neville as the Phosphoribosylpyrophophate synthetase.

Link to this post | posted 22 Jan, 2021 02:33

smolloy123

Ok, I just searched phosphoribosylpyrophosphate synthetase and found my own entry! I am looking at Rose_5 (Cluster L1) gene stop 49111 and it has been called a phosphoribosyl transferase. The hits are again to phosphoribosyl pyrophosphate synthetase. Looking at the accepted functions list I found hosphoribosyl pyrophosphate transferase with example gene Loadrie_73. I also found function name phosphoribosyl transferase on the accepted function list with Bantam_3 as the example gene. but Bantam_3 and Loadrie_73 are in the same Pham. And just for the record (again) Phosphoribosylpyrophosphage synthetase is not on the accepted functions list… Does anyone know about these enzymes and have a suggestion about how we should be calling these genes?

Link to this post | posted 23 Jan, 2021 17:57
smolloy123	Maybe these all should be pyrophosphate kinases or phosphoribosylpyrophosphate synthetase but phosphoribosyl transferase doesn't make sense if in fact it is a kinase reaction

Link to this post | posted 23 Jan, 2021 19:33

cdshaffer

When it comes to enzyme naming issues I prefer the KEGG and exapasy "Enzyme" databases. For example here is the info on this enzyme at Expasy: https://enzyme.expasy.org/EC/2.7.6.1 The preferred name is Ribose-phosphate diphosphokinase, so they agree with your preference for "kinase". I also note that one of the mentioned synonyms also uses kinase. I have always been pretty agnostic on which term we should put on our approved function list but once it is there I think it makes all our work better if we all try to use that particular term as it creates a more consistent data set across all the SEA phages. phosphoribosyl transferase appears to be a general term as it hits to about 25 different enzymes in the Expasy database, the vast marjority of which are glycosyltransferases.

Link to this post | posted 23 Jan, 2021 23:00
smolloy123	Thanks Chris, that is helpful. I think we will go with either pyrophosphate kinase or your diphosphate kinase…I'll let Deb decide. Who says diphosphate instead of pyrophosphate? Either way, we need to pick one name and go with it as you suggest