phzM (PA4209, Q9HWH2) notes

Identity

Phenazine-1-carboxylate N-methyltransferase, EC 2.1.1.327, 334 aa. Class I
SAM-dependent methyltransferase of the cation-independent
O-methyltransferase (COMT-like, Pfam Methyltransf_2 + Dimerisation) family;
PANTHER PTHR43712:SF2. PE 1; crystal structure 2IP2 (1.8 A, unliganded).
UniProt: [file:PSEAE/phzM/phzM-uniprot.txt "Converts phenazine-1-carboxylate (PCA) to 5-methylphenazine-1-carboxylate (5- methyl-PCA)."] (ECO:0000269 PMID:17253782); "In vitro, requires PhzS for activity."

PMID:17253782
PMID:17253782
PMID:17253782
PMID:17253782 So SAM binding is not seen directly; it is implied by the SAM requirement and the motif.
PMID:17253782
Methylation is at N5 of PCA, unlike the O-methylation done by its plant homologues (IOMT): PMID:17253782.
Transient PhzM-PhzS interaction inferred from dialysis and filtration experiments; no stable complex seen.
Genetics: PMID:11591691 (abstract only)
Crystallization: PMID:16946471 (abstract only).
Regulation (not annotated here): Crc binds phzM mRNA (PMID:22562990); temperature-dependent phzM expression in strain M18 (PMID:19717631).

GO:0008757 IDA (PseudoCAP, PMID:17253782) and IBA: ACCEPT, core. GO:0102168 (the specific reaction) is is_a GO:0008168 only in current GO, not GO:0008757 or GO:0008170, so GO:0008757 is not entailed by the specific term; ontology gap raised as a question.
GO:0102168 IDA and IEA: ACCEPT, core.
GO:0106220 pyocyanine biosynthetic process IDA: ACCEPT.
GO:0008168 methyltransferase activity IEA: MODIFY to GO:0102168.
GO:0008171 O-methyltransferase activity IEA (InterPro COMT_C): REMOVE; PhzM is an N-methyltransferase, so the family-level InterPro2GO mapping is wrong for this member.
GO:0046983 protein dimerization activity IEA and GO:0042802 identical protein binding IDA (x2): MODIFY to GO:0042803.
GO:0042803 protein homodimerization activity IDA (x2): KEEP_AS_NON_CORE.
GO:1904047 S-adenosyl-L-methionine binding IDA: KEEP_AS_NON_CORE (true, but structural evidence is an unliganded structure; support is the SAM requirement and the motif).
GO:0005515 protein binding IPI (PhzS): REMOVE per policy.

Tree analysis: phzM-bioinformatics/RESULTS.md.

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN002463933	GO:0008757 S-adenosylmethionine-dependent methyltransferase activity	1 (sole seed)	80 (16 taxa); 64 GOA rows	GO:0008757 SAM-dependent methyltransferase activity, IDA, PMID:17253782 (PseudoCAP)	SOUND	Purified PhzM with PhzS converts PCA to pyocyanin only when SAM is present, and PhzM has the DVGGGXG SAM motif and a class I methyltransferase fold; the methyl transfer is PhzM's step, so the IDA is direct enough (PhzM alone is inactive, which is an activation requirement, not a missing activity). The node is the LUCA root of PTHR43712, mostly fungal and animal O-methyltransferases plus bacterial PhzM-like proteins; GO:0008757 is the right level because the clade mixes O- and N-methylation, so O-methyltransferase activity or the PhzM reaction would each be wrong for part of it. Flag: two fungal cluster coactivators (tpcD Q4WQZ4, mdpA C8VQ72) inherit the IBA; their catalytic status is unchecked.

How does PhzS activate PhzM? Is the 5-methyl-PCA intermediate channelled?
Should GO:0102168 be placed under GO:0008757 and GO:0008170 N-methyltransferase activity?
Are tpcD and mdpA catalytically dead PTHR43712 members (candidates for NOT annotations at their leaves)?