NTR: [N]MP 5' nucleotidase activities

[ValWood]

Please provide as much information as you can:

• Suggested term label:

AMP 5' nucleotidase activity Rhea 29375
CMP 5' nucleotidase activity Rhea 29367
UMP 5' nucleotidase activity Rhea 29359

• Definition (free text)

AMP 5' nucleotidase activity
Catalysis of the reaction: 5'-AMP + H2O = adenosine + phosphate.

CMP 5' nucleotidase activity
Catalysis of the reaction: 5'-CMP + H2O = cytosine + phosphate.

UMP 5' nucleotidase activity
Catalysis of the reaction: 5'-UMP + H2O = uridine + phosphate.

• Reference, in format PMID:#######

PMID:39660919

• Gene product name and ID to be annotated to this term

https://www.pombase.org/gene/SPBPB2B2.06c
https://www.pombase.org/gene/SPAC1039.02

• Parent term(s)

GO:0008253 5'-nucleotidase activity

• Children terms (if applicable) Should any existing terms that should be moved underneath this new proposed term?

• Synonyms (please specify, EXACT, BROAD, NARROW or RELATED)

• Cross-references

• For enzymes, please provide RHEA and/or EC numbers.

• Can also provide MetaCyc, KEGG, Wikipedia, and other links.

• Any other information

[pgaudet]

For nucleotides, usually enzymes are not specific for individual nucleotides. This is why we map to the more general reaction from 5'-nucleotidase activity to https://www.rhea-db.org/rhea/12484

Unless there is a good justification, we would not create this.
In GO-CAM we would use the broader reaction and 'has input'.

Does that work ?

Thanks, Pascale

[ValWood]

Yes I can do it this way (not soon because the GO CAM for this process is a little way off)

(although it's currently inconsistent , some terms exist. I was able to use GMP 5' nucleotidase activity, if we are doing it this way should we remove this inconsistency?)

[ValWood]

i.e.

GO:0050484 GMP 5'-nucleotidase activity is_a
GO:0050483 IMP 5'-nucleotidase activity is_a
GO:0050340 thymidylate 5'-phosphatase activity is_a
GO:1990224 NMN phosphatase activity is_a
GO:0106411 XMP 5'-nucleosidase activity is_a

[pgaudet]

Looks like these may need to be obsoleted

@raymond91125 Can you please look into that ?

@sjm41 have you come across these?

[raymond91125]

PMID:18404470 Recent advances in structure and function of cytosolic IMP-GMP specific 5′nucleotidase II (cN-II)
PMID:6260203 "The enzyme had markedly higher affinities for IMP, dIMP, GMP and dGMP than the other 5'-mononucleotides, although V values for all the substrates tested were in the same order of magnitude."
It seems that there is usually an ordered preference of substrates but not exclusivity. I think it makes sense to obsolete the specific terms and merge into the parent GO:0008253 5'-nucleotidase activity.

[pgaudet]

Sounds good