nirJ (G3XD10, PA0511) notes

Review session 2026-10-28 (PseudoCAP IBA-seed protocol, worklist rank 71)

No deep-research provider was available; these notes are my own reading of the UniProt record, the
PseudoCAP-cited paper (PMID:8982003, abstract only; the PubMed MCP returned no PMC body text for PMC178684)
and three NirJ biochemistry papers found by PubMed search and cached with just fetch-pmid
(PMID:20420837 and 29076625 abstract-only; PMID:40318205 full text).

Identity

PAO1 PA0511, UniProtKB G3XD10 (unreviewed), 387 aa. Radical SAM core (PS51918, residues 20-239) with the
CxxxCxxC SAM-cluster cysteines (Cys37, Cys41, Cys44), followed by a SPASM-type C-terminal region.
NCBIfam TIGR04051 rSAM_NirJ; InterPro IPR023992 Pre-heme d1 synthase NirJ; SFLD heme_D1_biosynthesis
(NirJ-like); PANTHER PTHR11228:SF7.
Encoded in the nirSMCFDLGHJEN cluster for cytochrome cd1 nitrite reductase and its heme d1 cofactor.
The UniProt FUNCTION text and name are ARBA predictions and are not used as evidence here.

Literature

Genetics in P. aeruginosa: PMID:8982003. Polarity on the downstream
nirE is a concern for an insertion in an operon, but complementation was performed (details not visible
in the abstract).
Radical SAM nature: PMID:20420837
Activity (ortholog, abstract does not name the organism): PMID:29076625; substrate
PMID:29076625.
Mechanism (Dinoroseobacter shibae NirJ): auxiliary [4Fe-4S] cluster and acrylate byproduct
PMID:40318205; PMID:40318205. NirJ is related to AhbC of the
siroheme-dependent (alternative) heme b pathway, which acts on the same substrate PMID:40318205.

Is heme d1 'heme' in GO?

GO:0006783 heme biosynthetic process is defined for "heme, any compound of iron complexed in a porphyrin
(tetrapyrrole) ring". Heme d1 is an iron dioxo-isobacteriochlorin, not a porphyrin in the strict sense, but
GO already places GO:0019354 siroheme biosynthetic process (also an iron isobacteriochlorin) under
GO:0006783, so heme d1 synthesis falls within the term as GO uses it. There is no heme d1-specific GO term;
GO:0006783 is the most precise available, and it says nothing wrong about NirJ. A "heme d1 biosynthetic
process" NTR (is_a GO:0006783) would make the annotation informative and would separate it from protoheme
synthesis. The term must not be read as protoheme (heme b) synthesis for NirJ.

The node PTN000132400

QuickGO (2026-10-28): 15 GO:0006783 IBA leaves, 6 taxa. Apart from NirJ, all are archaeal SPASM-domain
radical SAM proteins: Korarchaeum cryptofilum (B1L4Z0, B1L5P2, B1L7M3), Methanosarcina acetivorans
(Q8THT9, Q8TIJ8, Q8TL56, Q8TLK1, Q8TR79, Q8TU98), Pyrobaculum aerophilum (Q8ZYW8), Sulfolobus
solfataricus (Q97WC3, Q97XA7, Q97XS7) and Halobacterium salinarum (Q9HQF7). UniProt/InterPro
(2026-10-28) classify only Q8TLK1 as a heme-pathway enzyme (TIGR04546 12,18-didecarboxysiroheme
deacetylase, i.e. AhbC; IPR030894). The others carry generic SPASM signatures (TIGR04085), TIGR03961
PTO1314 family, TIGR04347 pseudo-SAM/SPASM (Q9HQF7, despite its "Heme biosynthesis protein" name), or names
such as "tungsten-containing aldehyde ferredoxin oxidoreductase cofactor modifying protein" (Q8TR79). The
node is therefore a broad archaeal SPASM radical SAM clade in which heme (or heme d1) synthesis is
established for at most two lineages (NirJ, AhbC). The IBD over-generalises one gene's pathway.

Annotation decisions

GO:0006783 heme biosynthetic process (IMP PseudoCAP; IBA): ACCEPT for NirJ (most precise GO term;
heme d1 synthesis), with a GO_CENTRAL defect on the node placement.
GO:0003824 catalytic activity (IEA InterPro): MODIFY to an NTR for the NirJ reaction (no GO term exists).
GO:0046872 metal ion binding, GO:0051536 iron-sulfur cluster binding (IEA): MODIFY to GO:0051539.
GO:0051539 4 iron, 4 sulfur cluster binding (IEA): ACCEPT (radical SAM cluster motif; ortholog
spectroscopy shows two [4Fe-4S] clusters).

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN000132400	GO:0006783 heme biosynthetic process	1 (sole)	15 (6 taxa)	GO:0006783, IMP, PMID:8982003 (PseudoCAP)	OVER-SPECIFIC	For NirJ the seed is sound: insertion plus complementation shows nirJ is needed for heme d1, and ortholog biochemistry shows NirJ performs a step (propionate removal from 12,18-didecarboxysiroheme). Heme d1 counts as heme in GO (siroheme biosynthesis is_a GO:0006783), though it is not protoheme. The node, however, is a broad archaeal SPASM radical SAM clade; of 14 other leaves only Q8TLK1 (AhbC) is a heme-pathway enzyme. The IBD should be withdrawn or moved to a NirJ (TIGR04051) node.