NOV1 (Saro_0802, Q2GA76_NOVAD) — review notes

Identity and function

Saro_0802 = NOV1, a resveratrol-cleaving dioxygenase / stilbene cleavage oxygenase (SCO) of
Novosphingobium aromaticivorans (DSM 12444). It is a bacterial member of the same enzyme class as
Neurospora CAO-1 and the Sphingomonas lignostilbene α,β-dioxygenases (LSDs); the CCO/RPE65 superfamily
(PANTHER PTHR10543). EC 1.13.11.-; non-heme Fe(II).

Reaction: cleaves the central (interphenyl) Cα–Cβ double bond of stilbenes → two aromatic
aldehydes. Structurally characterized with resveratrol (substrate) and vanillin (product).
PMID:27911781
Fold/cofactor: PMID:27911781; seven-bladed
β-propeller. Dioxygen binds side-on to the iron.
Mechanism (why the 4′-OH matters): the reaction proceeds by a ferric-superoxide reacting with
substrate PMID:27911781.
So the 4′-OH is catalytically essential (the deprotonation/activation site), not merely a binding
determinant. Correspondingly PMID:27911781.
Biotech: NOV1 has been engineered to convert lignin-derived isoeugenol to vanillin
(PMID:35687874) — a lignin-valorization application.

The annotation problem: carotenoid over-annotation, via TreeGrafter (IEA)

All three GOA annotations for NOV1 are IEA:
- GO:0010436 carotenoid dioxygenase activity — GO_REF:0000118 (TreeGrafter)
- GO:0016121 carotene catabolic process — GO_REF:0000118 (TreeGrafter)
- GO:0016702 oxidoreductase (dioxygenase) — GO_REF:0000002 (InterPro2GO)

This is the same substrate-class over-annotation as cao-1 (carotenoid terms on a stilbene cleaver),
but propagated by TreeGrafter (automated phylogenetic grafting onto the PANTHER tree) rather than
manual PAINT/IBA — so the fungal IBA case and this bacterial IEA case are two propagation mechanisms
making the identical error, because the CCO family mixes carotenoid- and stilbene-cleaving members. NOV1
is a stilbene cleavage oxygenase, not a carotenoid enzyme.

Review decisions

GO term	Evidence	Decision	Rationale
GO:0010436 carotenoid dioxygenase activity	IEA (TreeGrafter)	REMOVE	NOV1 cleaves stilbenes (resveratrol, isoeugenol), not carotenoids; TreeGrafter over-propagation. Correct specific term is GO:7770086 resveratrol dioxygenase activity (go-ontology #32332, merged 2026-07-17).
GO:0016121 carotene catabolic process	IEA (TreeGrafter)	MODIFY → GO:0046272 stilbene catabolic process	Wrong substrate class; NOV1 acts in stilbene/lignin-derived compound catabolism.
GO:0016702 oxidoreductase (2 O atoms)	IEA (InterPro2GO)	ACCEPT	Correct general dioxygenase MF.

Core function: resveratrol/stilbene cleavage dioxygenase (best specific term GO:7770086, added by
go-ontology #32332 merged 2026-07-17; parent
GO:0016702), non-heme four-His Fe(II), in stilbene catabolic process. Flag the TreeGrafter rule
(GO_REF:0000118) that assigns carotenoid activity to the SCO clade for correction (cf. the TreeGrafter
and IBA_REVIEW projects).

Cross-family point (vs cao-1)

NOV1 shows the 4′-OH requirement is mechanistic (phenol deprotonation activates catalysis) and is
comparatively permissive (cleaves a wide range of 4′-OH stilbenes). CAO-1 is more restrictive,
requiring additional free hydroxyls for its two-ring binding anchors (see
genes/NEUCR/cao-1/cao-1-bioinformatics/RESULTS.md). Shared catalytic logic (4′-OH activation),
different binding-pocket stringency.