[annotation] pseudouridine synthase vs. pseudouridylate synthase

[Petra Fey]

Hello,

I'm curating the Dicty ortholog of human RPUSD2 (RNA pseudouridylate  
synthase domain containing 2), and like the human protein, it has the  
InterPro hits to IPR006145, IPR006224, IPR006225 with the following  
GO annotations
IPR006145 Pseudouridine synthase: GO:0009982 pseudouridine synthase  
activity
IPR006224 Pseudouridine synthase, Rlu: GO:0004730 pseudouridylate  
synthase activity
IPR006225 Pseudouridine synthase, Rlu: GO:0004730 pseudouridylate  
synthase activity

When checking GO:
GO:0009982 Catalysis of the reaction: RNA uridine = RNA  
pseudouridine. Note that this term should not be confused with  
'pseudouridylate synthase activity ; GO:0004730', which refers to the  
formation of free pseudouridine from uracil and ribose-5-phosphate.
GO:0004730 Catalysis of the reaction: uracil + D-ribose 5-phosphate =  
pseudouridine 5'-phosphate + H2O. Note that this term should not be  
confused with 'pseudouridine synthase activity ; GO:0009982', which  
refers to the intramolecular isomerization of uridine to pseudouridine.

I just submitted this SF item
https://sourceforge.net/tracker/? 
func=detail&atid=605890&aid=1756470&group_id=36855

However, there seems to be a larger issue:
Why are the human and mouse proteins called 'RNA pseudouridylate  
synthase'? What complicates this further, PF00849, on which IPR006145  
(!) is based on, also calls it 'RNA pseudouridylate synthase'.
http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00849

Is this all a consequence of the easy confusion the GO note alerts to?

Thanks,

Petra
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