sctN (YscN, P40290) — Yersinia enterocolitica Ysc injectisome ATPase — curation notes

Identity

UniProt P40290, gene sctN (synonym yscN), first gene of the virB locus on the pYV virulence plasmid
PMID:8132449.
UniProt RecName is "Type 3 secretion system ATPase", EC 7.4.2.8 (protein-exporting ATPase) — not an
ATP-synthase EC. This contrasts with several flagellar FliI entries, which UniProt still calls
"Flagellum-specific ATP synthase" with EC 7.1.2.2. So for this gene the protein name/EC is already correct and
the synthase-flavoured GO rows come purely from PANTHER/InterPro pipelines.
Do not confuse with YsaN, the ATPase of the chromosomal Ysa–Ysp T3SS of the same organism. YsaN
biochemistry (Mg2+ dependence, YsaL inhibition) is a different protein and is not evidence for P40290
(flagged in sctN-deep-research-falcon.md, "Critical ambiguity resolved: SctN/YscN is not YsaN").

Family placement (relevant to the ATP-synthase GO rows)

PANTHER PTHR15184 "ATP SYNTHASE"; P40290 is in subfamily PTHR15184:SF9 (SPI-1 type 3 secretion system
ATPase), i.e. the T3SS/FliI export-ATPase branch, not the F1-beta branch (SF51/SF74/SF75/SF76/SF80/SF82/
SF83/SF85).
interpro/panther/PTHR15184/PTHR15184-paint.tsv: the GO:0046933 IBD sits at PTN008558586, seeded by
PomBase SPAC222.12c, SGD S000003882, UniProtKB:P06576 (human ATP5F1B), UniProtKB:P0ABB4 (E. coli AtpD) —
all genuine F1-beta subunits.
projects/TREEGRAFTER/rotary_atpase/node_placement.tsv: PTN001807733 (the WITH/FROM on this gene's
GO:0046933 row) is a TreeGrafter graft node in clade PTN000390097, the eubacterial sister clade of the
F1-beta clade PTN008558588 under the same IBD node. PTN000390097 contains exactly the export-ATPase
subfamilies SF9 / SF62 / SF81. So the graft sits under an IBD node whose function arose in (and is
experimentally grounded only in) the F1-beta sister clade — a paralog over-propagation across a duplication
node, not an inheritance the target shares.

Experimental evidence on this protein

ATPase, cooperative, YscL-regulated. Purified HisYscN is an ATPase; activity is inhibited by HisYscL
PMID:16672607. The paper frames the system as
["The bacterial energy source for secretion is ATP, which is consumed by an ATPase that couples ATP hydrolysis
to the unfolding of secreted proteins and the dissociation of their chaperones just prior to secretion"].
Inhibition is non-competitive/allosteric.
Required for Yop secretion; Walker-A dependent. A pYV mutant lacking box A is secretion-defective and
complementable PMID:8132449; the Walker-box point mutant is likewise non-functional
PMID:20453832.
Substrate/secretion-signal recognition. YopR (encoded by yscH, UniProtKB:Q01249) hybrids capture YscN in
vivo and purified HisYscN binds YopR-GST but not signal-deleted YopR
PMID:17050689. This is the IPI row's
experiment: it is substrate-signal recognition by the export ATPase, not generic protein binding.
Cytosolic sorting platform. EGFP-YscN localizes to injectisome foci; its assembly requires YscC, YscJ,
YscK, YscL and YscQ, and YscN is in turn needed for C-ring formation — structurally, not catalytically, since
YscN K175E still supports C-ring formation PMID:20453832. YscN is also part of stable cytosolic K/Q/L/N
complexes PMID:28653671, and is fully cytosolic when YscQ_C is absent PMID:25591178.
Hexamer. PMID:20453832. Blaylock et al. could not observe hexamers with
refolded recombinant protein.
Localization. Cytoplasm (UniProt SUBCELLULAR LOCATION from PMID:16672607); peripheral, at the cytoplasmic
face of the injectisome basal body.

Energetics — why the proton terms are wrong for this protein

Yersinia type III secretion needs the PMF, but the dependency is a property of the machine, not of YscN:
PMID:15213145
In the homologous flagellar system the proton flux is carried by the membrane export gate, not by the soluble
ATPase [PMID:21934659 "the export gate complex by itself is a proton-protein antiporter";
PMID:29946050 "FlhA has an ion channel activity, and the FlhA-FliJ interaction enables effective utilization
of PMF for protein export"].
The homologous FliI ATPase is insensitive to F-, V- and P-type ATPase inhibitors
PMID:8943245, i.e. it is not
an F-type enzyme despite the fold.
The rotary-like architecture is real (SctO/YscO is the gamma-stalk analogue
PMID:25591178; FliJ binds the centre of the FliI hexamer
PMID:21278755),
but there is no Fo-like proton channel partner and no ATP synthesis. Structural rotary homology is not
proton-transporting ATPase activity.

Mechanism (ortholog support)

Chaperone release and substrate unfolding are shown for the Salmonella SPI-1 ortholog InvC
PMID:16208377; the same role is assumed for SctN/YscN [PMID:25591178, PMID:28653671]. Note the
flagellar-system caveat that export can proceed without ATPase activity under some conditions — for Yersinia,
however, YscN catalytic activity is required for secretion (K175E is secretion-null).

Annotation decisions (summary)

Term	Evid	Source	Action
GO:0046933 ATP synthase activity, rotational	IEA	GO_REF:0000118, PTN001807733	REMOVE
GO:0015986 PMF-driven ATP synthesis	IEA	GO_REF:0000108 from GO:0046933	REMOVE
GO:0046961 proton-transporting ATPase, rotational	IEA	GO_REF:0000002, IPR013380	REMOVE
GO:1902600 proton transmembrane transport	IEA	GO_REF:0000002, IPR004100	REMOVE
GO:0006754 ATP biosynthetic process	IEA	GO_REF:0000002, IPR013380	REMOVE
GO:0046034 ATP metabolic process	IEA	GO_REF:0000002, IPR004100	MARK_AS_OVER_ANNOTATED
GO:0008564 protein-exporting ATPase activity	IEA	GO_REF:0000003, EC:7.4.2.8	ACCEPT (core MF)
GO:0016887 ATP hydrolysis activity	IEA	GO_REF:0000002	ACCEPT
GO:0005524 ATP binding	IEA	GO_REF:0000002	ACCEPT
GO:0030254 protein secretion by T3SS	IEA	GO_REF:0000002	ACCEPT
GO:0030257 T3SS complex	IEA	GO_REF:0000002	ACCEPT
GO:0005737 cytoplasm (EXP + IEA)	EXP/IEA	PMID:16672607 / GO_REF:0000120	ACCEPT
GO:0005515 protein binding	IPI	PMID:17050689, Q01249	MODIFY → GO:0008564

IPR013380 (T3SS ATPase SctN) is the InterPro entry that carries both GO:0046961 and GO:0006754 — a
T3SS-specific signature mapped to rotary-ATP-synthase terms. That mapping is wrong at source and affects every
SctN protein, so it is raised as a suggested question.