EryCII (SACE_0725) is a cytochrome-P450-family homologue that has lost catalytic competence and instead acts as the activating partner of the desosaminyl transferase EryCIII in erythromycin biosynthesis in Saccharopolyspora erythraea. Although related to cytochrome P450s by sequence, EryCII lacks the heme-binding sites and therefore cannot perform P450 monooxygenase chemistry; it is a pseudoenzyme. Functionally, EryCII forms an elongated EryCII-EryCIII heterotetramer in which it stabilizes EryCIII and acts as an allosteric activator of the glycosyltransferase, enabling efficient transfer of TDP-D-desosamine to the macrolide scaffold (PMID:22056329, PMID:15303858). Mechanistically EryCII behaves like a conformational chaperone that templates the catalytically competent state of EryCIII, but - unlike a classical chaperone - it remains stably bound as a stoichiometric subunit and EryCIII is inactive without it, so it is best described as an activator/stabilizer subunit rather than a transient folding chaperone. EryCII is thus a clear example of domain-based over-annotation: its sequence-derived P450/heme/monooxygenase annotations do not reflect its true non-catalytic, GT-activating role.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0004497
monooxygenase activity
|
IEA
GO_REF:0000002 |
REMOVE |
Summary: InterPro-based (IEA) monooxygenase activity from the cytochrome P450 signature. EryCII is a P450 homologue that lacks the heme-binding sites and is catalytically dead; it has no monooxygenase activity. Its real role is as an allosteric activator of the EryCIII glycosyltransferase.
Reason: Demonstrably incorrect. Beyond the UniProt CAUTION ("lacks the heme-binding sites"), the structure paper shows by structure-based alignment that EryCII lacks the conserved heme-ligating cysteine and is "not an active P450 enzyme", and the 2YJN structure is apo (no heme). EryCII functions as a GT activator, not a monooxygenase. Classic domain-propagation over-annotation of a pseudoenzyme.
Supporting Evidence:
file:SACEN/eryCII/eryCII-uniprot.txt
Although related to the cytochrome P450 family, lacks the heme-binding sites.
PMID:22056329
the conserved cysteine is absent (Supplementary Fig. S5); thus, they are not active P450 enzymes
|
|
GO:0005506
iron ion binding
|
IEA
GO_REF:0000002 |
REMOVE |
Summary: IEA iron ion binding inherited from the P450 signature (P450s bind a heme iron). EryCII lacks the heme-binding sites and does not bind a catalytic iron.
Reason: Incorrect; depends on heme/iron cofactor binding that EryCII has lost. The UniProt CAUTION (lacks the heme-binding sites) and the structure (no heme; absent conserved Cys) agree.
Supporting Evidence:
file:SACEN/eryCII/eryCII-uniprot.txt
Although related to the cytochrome P450 family, lacks the heme-binding sites.
PMID:22056329
Having lost the heme group in the central core, the protein may be more conformationally dynamic
|
|
GO:0016705
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
|
IEA
GO_REF:0000002 |
REMOVE |
Summary: IEA oxidoreductase activity from the P450 signature. EryCII performs no oxygen-dependent oxidoreductase chemistry; it is a non-catalytic P450 homologue.
Reason: Incorrect catalytic MF for a heme-less, non-catalytic P450 homologue (UniProt CAUTION plus the apo structure / absent conserved Cys).
Supporting Evidence:
file:SACEN/eryCII/eryCII-uniprot.txt
Although related to the cytochrome P450 family, lacks the heme-binding sites.
PMID:22056329
the conserved cysteine is absent (Supplementary Fig. S5); thus, they are not active P450 enzymes
|
|
GO:0020037
heme binding
|
IEA
GO_REF:0000002 |
REMOVE |
Summary: IEA heme binding from the P450 signature. EryCII explicitly lacks the heme-binding sites, so it does not bind heme.
Reason: Both the UniProt CAUTION ("lacks the heme-binding sites") and primary structural data agree: the conserved heme-ligating cysteine is absent and EryCII has "lost the heme group in the central core" (PMID:22056329); the 2YJN structure contains no heme ligand. The most clearly incorrect of the inherited P450 terms.
Supporting Evidence:
file:SACEN/eryCII/eryCII-uniprot.txt
Although related to the cytochrome P450 family, lacks the heme-binding sites.
PMID:22056329
Having lost the heme group in the central core, the protein may be more conformationally dynamic
|
|
GO:0008047
enzyme activator activity
|
IDA
PMID:22056329 Structure of the glycosyltransferase EryCIII in complex with... |
NEW |
Summary: Proposed NEW annotation capturing EryCII's actual molecular function: it allosterically activates the glycosyltransferase EryCIII (EryCIII is inactive on its own; activity is restored by EryCII). Not present in GOA, which carries only the inherited (incorrect) P450 catalytic terms.
Reason: Replaces the removed P450 catalytic terms with EryCII's true, experimentally supported activator role.
Supporting Evidence:
PMID:22056329
EryCII stabilizes EryCIII and also functions as an allosteric activator of the GT
|
Q: Would a dedicated "glycosyltransferase activator activity" term (child of GO:0008047) better capture the role of EryCII and analogous P450-homologue GT activators (e.g. in other deoxysugar pathways)?
Experiment: Confirm absence of heme binding and monooxygenase activity for purified EryCII, and quantify EryCIII GT stimulation as a function of EryCII, to formally retire the P450 catalytic annotations.
Part of the BGC exemplar curation project (projects/BGC.md). MIBiG BGC0000055
(Saccharopolyspora erythraea, erythromycin PKS). GenBank CAM00066.1 β UniProt
A4F7P2 (ERYC2_SACEN), gene eryCII / SACE_0725. Also relevant to
projects/PSEUDOENZYMES.md.
EryCII is a cytochrome-P450-family homologue that has lost catalytic competence
and instead serves as the activating partner of the desosaminyl transferase
EryCIII in erythromycin biosynthesis.
So the no-heme / no-catalysis conclusion rests on (1) the absent conserved Cys in a
structure-based alignment, and (2) an apo crystal structure β not merely UniProt.
- UniProt FUNCTION: "Involved in the erythromycin biosynthesis pathway. Acts by
forming a complex and stabilizing the desosaminyl transferase EryCIII."
(ECO:0000269|PubMed:22056329); SUBUNIT: "Heterotetramer composed of EryCII and EryCIII."
- Structure (PDB 2YJN): "EryCIII, in concert with its partner EryCII, attaches a
nucleotide-activated sugar to the macrolide scaffold... a heterotetramer...
EryCII stabilizes EryCIII and also functions as an allosteric activator of the GT."
PMID:22056329
- EryCII is required for EryCIII catalysis (not merely an enhancer): purified
EryCIII "was inactive under all conditions tried"; combining EryCIII + EryCII
extracts "restored" GT activity [PMID:22056329 full text]. Stoichiometry is
Ξ±2Ξ²2 (dimer of heterodimers, ~188 kDa); activation is allosteric via EryCII's
N-terminal Aβ³ helix, which contacts EryCIII's acceptor domain.
All four GOA molecular-function terms are IEA from the P450 sequence signature and are
incorrect for this catalytically dead homologue:
Accurate roles to assert instead: GO:0008047 enzyme activator activity (allosteric
activator of EryCIII; added as a NEW annotation), GO:0050821 protein stabilization
(stabilizes EryCIII's fold/quaternary structure), GO:1901115 erythromycin
biosynthetic process (BP), GO:0032991 protein-containing complex (EryCII-EryCIII
heterotetramer).
Mechanistically EryCII templates/stabilizes the catalytically competent conformation of
EryCIII, which is chaperone-like. But it is not annotated as a protein folding
chaperone (GO:0044183): a chaperone acts transiently and is released, and its client
stays active afterwards; EryCII is a stably bound stoichiometric subunit and EryCIII
is inactive without it (PMID:22056329). So the stabilizing aspect is captured by
protein stabilization (GO:0050821) and the activating aspect by enzyme activator
activity (GO:0008047) - not a chaperone MF. (The older fold-and-release / "does not
bind tightly" model, ref 13, was superseded by the stable-complex structure.)
A "NEW NOT" (negated: true + action: NEW) can only be used for a term NOT already in
GOA. Here the erroneous P450 functions (monooxygenase, heme binding, iron binding,
oxidoreductase) are already present in GOA, so they are handled by REMOVE; there is no
review action to convert an existing positive annotation into a NOT.
Moriwaki et al. (bioRxiv 2025.10.26.684697) predict the EryCII-EryCIII interaction
(BGC0000055; CAM00066.1/CAM00067.1) at ipTM 0.92, matching PDB 2YJN (hetero 4-mer).
id: A4F7P2
gene_symbol: eryCII
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:405948
label: Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC
13426 / NCIMB 8594 / NRRL 2338)
description: >-
EryCII (SACE_0725) is a cytochrome-P450-family homologue that has lost catalytic
competence and instead acts as the activating partner of the desosaminyl
transferase EryCIII in erythromycin biosynthesis in Saccharopolyspora erythraea.
Although related to cytochrome P450s by sequence, EryCII lacks the heme-binding
sites and therefore cannot perform P450 monooxygenase chemistry; it is a
pseudoenzyme. Functionally, EryCII forms an elongated EryCII-EryCIII heterotetramer
in which it stabilizes EryCIII and acts as an allosteric activator of the
glycosyltransferase, enabling efficient transfer of TDP-D-desosamine to the
macrolide scaffold (PMID:22056329, PMID:15303858). Mechanistically EryCII behaves
like a conformational chaperone that templates the catalytically competent state of
EryCIII, but - unlike a classical chaperone - it remains stably bound as a
stoichiometric subunit and EryCIII is inactive without it, so it is best described as
an activator/stabilizer subunit rather than a transient folding chaperone. EryCII is
thus a clear example of domain-based over-annotation: its sequence-derived
P450/heme/monooxygenase annotations do not reflect its true non-catalytic,
GT-activating role.
references:
- id: PMID:22056329
title: Structure of the glycosyltransferase EryCIII in complex with its activating
P450 homologue EryCII.
findings:
- statement: >-
EryCII forms a heterotetramer with EryCIII, stabilizes it, and acts as an
allosteric activator of the glycosyltransferase.
supporting_text: >-
Our biophysical and enzymatic data support a model in which EryCII stabilizes
EryCIII and also functions as an allosteric activator of the GT.
- statement: >-
The EryCIII-EryCII complex is a heterotetramer.
supporting_text: >-
The structure reveals a heterotetramer with a distinctive, elongated quaternary
organization.
- statement: >-
EryCII lacks the conserved heme-ligating cysteine of P450s and has no heme; it is
not an active P450 enzyme (structure-based alignment, apo structure).
supporting_text: >-
As expected for EryCIIβand indeed the macrolide auxiliary proteins generallyβthe
conserved cysteine is absent (Supplementary Fig. S5); thus, they are not active
P450 enzymes.
- statement: >-
EryCII has lost the heme group from the central core of the P450-like fold.
supporting_text: >-
Having lost the heme group in the central core, the protein may be more
conformationally dynamic
- statement: >-
EryCIII is inactive on its own; EryCII is required to restore its
glycosyltransferase activity.
supporting_text: >-
When separate EryCIII- and EryCII-containing extracts were combined, the GT
activity of EryCIII was restored, confirming as expected that EryCII is required
by EryCIII.
- statement: >-
The complex is an alpha2-beta2 heterotetramer (dimer of EryCIII-EryCII
heterodimers); EryCII activates allosterically via its N-terminal A'' helix, which
contacts EryCIII's acceptor domain without touching the active site directly.
supporting_text: >-
Binding of EryCII to the N-terminal acceptor domain of EryCIII (Fig. 6) may
likewise trigger a closer association with the C-terminal sugar-nucleotide binding
domain and the correct juxtaposition of the acceptor and donor sites of EryCIII.
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
PubMed-verified; PDB 2YJN. Beyond the UniProt CAUTION (ECO:0000305), the full text
provides primary evidence that EryCII lacks the conserved heme-ligating cysteine
and the heme group ("not active P450 enzymes"); the 2YJN coordinates contain no
heme ligand (apo structure).
- id: PMID:15303858
title: 'Reconstitution and characterization of a new desosaminyl transferase, EryCIII,
from the erythromycin biosynthetic pathway.'
findings:
- statement: >-
EryCIII transfers TDP-D-desosamine to alpha-mycarosyl erythronolide B to form
erythromycin D; EryCII is its biosynthetic partner.
supporting_text: >-
EryCIII converts alpha-mycarosyl erythronolide B into erythromycin D using
TDP-d-desosamine as the glycosyl donor.
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: >-
Characterizes the partner GT EryCIII; supports the erythromycin-biosynthesis role
of the EryCII/EryCIII system.
- id: file:SACEN/eryCII/eryCII-notes.md
title: eryCII review notes (BGC project); pseudoenzyme over-annotation analysis
- id: file:SACEN/eryCII/eryCII-uniprot.txt
title: UniProtKB A4F7P2 (ERYC2_SACEN) record
findings:
- statement: >-
UniProt flags that EryCII, though related to the cytochrome P450 family, lacks
the heme-binding sites.
supporting_text: >-
Although related to the cytochrome P450 family, lacks the heme-binding sites.
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
The CAUTION is an ECO:0000305 curator inference; it carries real weight as an
expert assessment and is independently corroborated by the structure (absent
conserved Cys; apo 2YJN). Both lines of evidence are cited together.
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO terms
existing_annotations:
- term:
id: GO:0004497
label: monooxygenase activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: >-
InterPro-based (IEA) monooxygenase activity from the cytochrome P450 signature.
EryCII is a P450 homologue that lacks the heme-binding sites and is catalytically
dead; it has no monooxygenase activity. Its real role is as an allosteric
activator of the EryCIII glycosyltransferase.
action: REMOVE
reason: >-
Demonstrably incorrect. Beyond the UniProt CAUTION ("lacks the heme-binding
sites"), the structure paper shows by structure-based alignment that EryCII lacks
the conserved heme-ligating cysteine and is "not an active P450 enzyme", and the
2YJN structure is apo (no heme). EryCII functions as a GT activator, not a
monooxygenase. Classic domain-propagation over-annotation of a pseudoenzyme.
supported_by:
- reference_id: file:SACEN/eryCII/eryCII-uniprot.txt
supporting_text: >-
Although related to the cytochrome P450 family, lacks the heme-binding sites.
- reference_id: PMID:22056329
supporting_text: >-
the conserved cysteine is absent (Supplementary Fig. S5); thus, they are not
active P450 enzymes
- term:
id: GO:0005506
label: iron ion binding
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: >-
IEA iron ion binding inherited from the P450 signature (P450s bind a heme iron).
EryCII lacks the heme-binding sites and does not bind a catalytic iron.
action: REMOVE
reason: >-
Incorrect; depends on heme/iron cofactor binding that EryCII has lost. The UniProt
CAUTION (lacks the heme-binding sites) and the structure (no heme; absent conserved
Cys) agree.
supported_by:
- reference_id: file:SACEN/eryCII/eryCII-uniprot.txt
supporting_text: >-
Although related to the cytochrome P450 family, lacks the heme-binding sites.
- reference_id: PMID:22056329
supporting_text: >-
Having lost the heme group in the central core, the protein may be more
conformationally dynamic
- term:
id: GO:0016705
label: oxidoreductase activity, acting on paired donors, with incorporation or reduction
of molecular oxygen
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: >-
IEA oxidoreductase activity from the P450 signature. EryCII performs no
oxygen-dependent oxidoreductase chemistry; it is a non-catalytic P450 homologue.
action: REMOVE
reason: >-
Incorrect catalytic MF for a heme-less, non-catalytic P450 homologue (UniProt
CAUTION plus the apo structure / absent conserved Cys).
supported_by:
- reference_id: file:SACEN/eryCII/eryCII-uniprot.txt
supporting_text: >-
Although related to the cytochrome P450 family, lacks the heme-binding sites.
- reference_id: PMID:22056329
supporting_text: >-
the conserved cysteine is absent (Supplementary Fig. S5); thus, they are not
active P450 enzymes
- term:
id: GO:0020037
label: heme binding
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: >-
IEA heme binding from the P450 signature. EryCII explicitly lacks the
heme-binding sites, so it does not bind heme.
action: REMOVE
reason: >-
Both the UniProt CAUTION ("lacks the heme-binding sites") and primary structural
data agree: the conserved heme-ligating cysteine is absent and EryCII has "lost
the heme group in the central core" (PMID:22056329); the 2YJN structure contains
no heme ligand. The most clearly incorrect of the inherited P450 terms.
supported_by:
- reference_id: file:SACEN/eryCII/eryCII-uniprot.txt
supporting_text: >-
Although related to the cytochrome P450 family, lacks the heme-binding sites.
- reference_id: PMID:22056329
supporting_text: >-
Having lost the heme group in the central core, the protein may be more
conformationally dynamic
- term:
id: GO:0008047
label: enzyme activator activity
evidence_type: IDA
original_reference_id: PMID:22056329
qualifier: enables
review:
summary: >-
Proposed NEW annotation capturing EryCII's actual molecular function: it
allosterically activates the glycosyltransferase EryCIII (EryCIII is inactive on
its own; activity is restored by EryCII). Not present in GOA, which carries only
the inherited (incorrect) P450 catalytic terms.
action: NEW
reason: >-
Replaces the removed P450 catalytic terms with EryCII's true, experimentally
supported activator role.
supported_by:
- reference_id: PMID:22056329
supporting_text: >-
EryCII stabilizes EryCIII and also functions as an allosteric activator of the GT
core_functions:
- description: >-
EryCII is required to activate the desosaminyl transferase EryCIII: EryCIII is
inactive on its own, and EryCII allosterically activates and stabilizes it within
the alpha2-beta2 EryCII-EryCIII heterotetramer (via its N-terminal A'' helix
contacting EryCIII's acceptor domain), enabling glycosyl transfer to the macrolide
and hence the desosaminylation step of erythromycin biosynthesis (PMID:22056329,
PMID:15303858; PDB 2YJN). This activator/stabilizer role is the accurate molecular
function in place of the inherited (incorrect) P450 catalytic terms. The fold
stabilization is conformational-chaperone-like, but EryCII is a stably bound
stoichiometric subunit, not a transient folding chaperone.
molecular_function:
id: GO:0008047
label: enzyme activator activity
directly_involved_in:
- id: GO:0050821
label: protein stabilization
- id: GO:1901115
label: erythromycin biosynthetic process
in_complex:
id: GO:0032991
label: protein-containing complex
supported_by:
- reference_id: PMID:22056329
supporting_text: >-
EryCII stabilizes EryCIII and also functions as an allosteric activator of the GT
- reference_id: PMID:22056329
supporting_text: >-
one function of the auxiliary proteins is to stabilize the fold and quaternary
structure of its partner GT
suggested_questions:
- question: >-
Would a dedicated "glycosyltransferase activator activity" term (child of
GO:0008047) better capture the role of EryCII and analogous P450-homologue GT
activators (e.g. in other deoxysugar pathways)?
suggested_experiments:
- description: >-
Confirm absence of heme binding and monooxygenase activity for purified EryCII, and
quantify EryCIII GT stimulation as a function of EryCII, to formally retire the P450
catalytic annotations.