NTR psilocybin biosynthetic process and associated reactions

[pgaudet]

Hello,

To annotate fungal secondary metabolites biosynthesis pathways, @marcfeuermann requested the following terms:

+[Term] +id: GO:0140380 +name: psilocybin biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of psilocybin, a psychotropic tryptamine-derived natural product." [PMID:28763571] +is_a: GO:0043386 ! mycotoxin biosynthetic process +intersection_of: GO:0009058 ! biosynthetic process +intersection_of: ends_with GO:0140381 ! 4-hydroxytryptamine 4-phosphate methyltransferase activity +intersection_of: has_intermediate CHEBI:139217 ! 4-hydroxytryptamine +intersection_of: has_intermediate CHEBI:139479 ! norbaeocystin +intersection_of: has_intermediate CHEBI:16765 ! tryptamine +intersection_of: has_part GO:0140382 ! tryptamine 4-monooxygenase activity +intersection_of: has_part GO:0140383 ! 4-hydroxytryptamine kinase activity +intersection_of: has_primary_input CHEBI:16828 ! L-tryptophan +intersection_of: has_primary_output CHEBI:8614 ! psilocybin +intersection_of: starts_with GO:0036469 ! L-tryptophan decarboxylase activity +created_by: pg +creation_date: 2019-11-20T10:03:05Z + +[Term] +id: GO:0140381 +name: 4-hydroxytryptamine 4-phosphate methyltransferase activity +namespace: molecular_function +def: "Catalysis of the reaction: 2 S-adenosyl-L-methionine (SAM) + 4-hydroxytryptamine 4-phosphate (norbaeocystin) <=> 2 S-adenosyl-L-homocysteine + psilocybin." [PMID:28763571] +synonym: "norbaeocystin methyltransferase" EXACT [] +synonym: "psilocybin synthase" EXACT [] +xref: EC 2.1.1.345 +xref: RHEA:55568 +is_a: GO:0008168 ! methyltransferase activity +created_by: pg +creation_date: 2019-11-20T10:16:28Z + +[Term] +id: GO:0140382 +name: tryptamine 4-monooxygenase activity +namespace: molecular_function +def: "Catalysis of the reaction: tryptamine + reduced acceptor + O(2) <=> 4-hydroxytryptamine + acceptor + H(2)O." [PMID:28763571] +xref: EC 1.14.99.59 +xref: RHEA:15865 +is_a: GO:0004497 ! monooxygenase activity +created_by: pg +creation_date: 2019-11-20T10:26:21Z + +[Term] +id: GO:0140383 +name: 4-hydroxytryptamine kinase activity +namespace: molecular_function +def: "Catalysis of the reaction: 4-hydroxytryptamine + ATP = 4-hydoxytryptamine 4-phosphate + ADP + H(+)." [PMID:28763571] +xref: EC:2.7.1.222 +xref: RHEA:55564 +is_a: GO:0016301 ! kinase activity +created_by: pg +creation_date: 2019-11-20T10:30:05Z

Also :

• changed EC:4.1.1.28 -> EC:4.1.1.105

[pgaudet]

@ukemi @deustp01 Can you please check the logical definition ? We added all reactions and intermediates. Let me know if this is how to do it.

Thanks, Pascale

[ukemi]

I don't know the pathway that well, but this looks ok to me. It is often not necessary to specify the intermediates unless they are required for further classification.

[pgaudet]

Should I add primary input and primary output for the MF ?

Thanks, Pascale

[ukemi]

NO. Those are restircted to metabolism terms. No need to put any participants for MFs, those will all be populated with ChEBI identifiers from Rhea at some point in time.

[deustp01]

Nothing from here, because I don't know anything about this biochemistry.

[pgaudet]

OK thanks !