CYB5R4 (NADH-cytochrome b5 reductase 4; also known as NCB5OR or b5+b5R) is a multidomain, soluble flavohemoprotein and NAD(P)H-dependent oxidoreductase. It contains an N-terminal CS/Hsp20 (p23-like) domain, a cytochrome b5-like heme-binding domain (with axial His-89 and His-112 ligating a six-coordinate low-spin heme) joined by a long hinge to a C-terminal FAD-dependent cytochrome-b5-reductase (FNR-type FAD- and NAD-binding) module. It binds stoichiometric heme and FAD and catalyzes EC 1.6.2.2 (NADH:cytochrome b5 oxidoreductase), reducing electron acceptors including cytochrome b5, cytochrome c, methemoglobin and ferricyanide; unlike the classical single-domain cytochrome b5 reductase it lacks a membrane anchor. The protein localizes to the endoplasmic reticulum and perinuclear cytoplasm. It functions in the response to oxidative and endoplasmic reticulum stress, protecting cells (notably pancreatic beta cells) from excess reactive oxygen species; loss of the orthologous gene in mice causes diabetes and lipoatrophy. Although early work proposed it as an NAD(P)H oxidase / candidate oxygen sensor, subsequent enzymology showed it preferentially reduces substrates rather than transferring electrons to molecular oxygen and is not an efficient superoxide-generating oxidase.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0004128
cytochrome-b5 reductase activity, acting on NAD(P)H
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic (IBA) assignment of the core cytochrome-b5 reductase activity. This matches the experimentally demonstrated EC 1.6.2.2 activity and is the core molecular function.
Reason: The cytochrome-b5 reductase activity acting on NAD(P)H is directly supported by experimental characterization of NCB5OR, which contains a cytochrome-b5-reductase domain and reduces cytochrome b5-type acceptors using NAD(P)H.
Supporting Evidence:
PMID:10611283
We have identified a cytosolic cytochrome b-type NAD(P)H oxidoreductase in mammals, a flavohemoprotein (b5+b5R) containing cytochrome b5 (b5) and b5 reductase (b5R) domains.
|
|
GO:0020037
heme binding
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic assignment of heme binding, supported by experimental evidence that NCB5OR binds stoichiometric heme via its cytochrome b5-like domain.
Reason: NCB5OR contains a cytochrome b5-like heme-binding domain with axial His ligands and binds stoichiometric heme experimentally.
Supporting Evidence:
PMID:15131110
Recombinant NCB5OR is soluble and has stoichiometric amounts of heme and flavin adenine dinucleotide.
|
|
GO:0005783
endoplasmic reticulum
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic assignment of ER localization, consistent with experimental colocalization of NCB5OR with the ER marker calreticulin.
Reason: NCB5OR colocalizes with the ER marker calreticulin and is annotated by UniProt to the endoplasmic reticulum.
Supporting Evidence:
PMID:15131110
we show that NCB5OR colocalizes with calreticulin, a marker for endoplasmic reticulum.
|
|
GO:0006801
superoxide metabolic process
|
IBA
GO_REF:0000033 |
KEEP AS NON CORE |
Summary: Phylogenetic assignment of superoxide metabolic process. NCB5OR can produce superoxide in vitro, but only with very slow turnover, and later enzymology concluded it preferentially reduces substrates rather than transferring electrons to oxygen, so this process is not a core in vivo function.
Reason: Superoxide production by NCB5OR occurs only at very low turnover rates in vitro; the protein is concluded to be a substrate reductase rather than an oxidase, so superoxide metabolism is at most a minor/non-core activity.
Supporting Evidence:
PMID:15131110
both full-length and truncated NCB5OR produce superoxide from oxygen with slow turnover rates
|
|
GO:0005783
endoplasmic reticulum
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Electronic (IEA) ER localization, redundant with and supported by the experimental IDA ER annotation.
Reason: ER localization is experimentally established by colocalization with calreticulin.
Supporting Evidence:
PMID:15131110
we show that NCB5OR colocalizes with calreticulin, a marker for endoplasmic reticulum.
|
|
GO:0016491
oxidoreductase activity
|
IEA
GO_REF:0000002 |
MARK AS OVER ANNOTATED |
Summary: Very general InterPro-based oxidoreductase activity. Correct but uninformative given the more specific cytochrome-b5 reductase activity annotations.
Reason: This is a high-level parent of the specific cytochrome-b5 reductase activity that is already annotated; it is correct but too general to be informative.
Supporting Evidence:
PMID:10611283
Human b5+b5R flavohemoprotein is a NAD(P)H oxidoreductase
|
|
GO:0016653
oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor
|
IEA
GO_REF:0000117 |
ACCEPT |
Summary: ARBA machine-learning annotation of oxidoreductase activity acting on NAD(P)H with a heme protein as acceptor, redundant with the experimental IDA annotation of the same term.
Reason: This activity is directly supported by experimental demonstration that NCB5OR uses NAD(P)H to reduce heme-protein acceptors such as cytochrome b5/cytochrome c and methemoglobin.
Supporting Evidence:
PMID:15131110
reduces cytochrome c, methemoglobin, ferricyanide, and molecular oxygen in vitro
|
|
GO:0020037
heme binding
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: InterPro-based heme binding annotation, redundant with and supported by the IBA heme binding annotation and experimental evidence of stoichiometric heme.
Reason: Heme binding is experimentally established and the protein has a cytochrome b5-like heme-binding domain with axial His ligands.
Supporting Evidence:
PMID:15131110
Recombinant NCB5OR is soluble and has stoichiometric amounts of heme and flavin adenine dinucleotide.
|
|
GO:0090524
cytochrome-b5 reductase activity, acting on NADH
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: EC/Rhea-based annotation of NADH-specific cytochrome-b5 reductase activity (EC 1.6.2.2). Supported by experimental catalytic activity; closely related to the NAD(P)H form.
Reason: UniProt records the catalytic reaction 2 Fe(III)-[cytochrome b5] + NADH = 2 Fe(II)-[cytochrome b5] + NAD+ + H+ (EC 1.6.2.2), demonstrated experimentally.
Supporting Evidence:
file:human/CYB5R4/CYB5R4-uniprot.txt
EC=1.6.2.2 {ECO:0000305|PubMed:10611283}; Reaction=2 Fe(III)-[cytochrome b5] + NADH = 2 Fe(II)-[cytochrome b5] + NAD(+) + H(+)
|
|
GO:0004128
cytochrome-b5 reductase activity, acting on NAD(P)H
|
IEA
GO_REF:0000107 |
ACCEPT |
Summary: Ensembl Compara ortholog transfer of the core cytochrome-b5 reductase activity, redundant with the experimental IDA annotation of the same term.
Reason: The core cytochrome-b5 reductase activity acting on NAD(P)H is directly demonstrated experimentally.
Supporting Evidence:
PMID:10611283
The recombinant b5+b5R protein can be reduced by NAD(P)H ... and by cytochrome c reduction in vitro.
|
|
GO:0015701
bicarbonate transport
|
TAS
Reactome:R-HSA-1237044 |
MARK AS OVER ANNOTATED |
Summary: Reactome pathway-context annotation ("Erythrocytes take up carbon dioxide and release oxygen"). CYB5R4 is a redox enzyme, not a bicarbonate transporter; this is a pathway-membership artifact rather than a true molecular role.
Reason: CYB5R4 has no bicarbonate transport activity; the term derives from inclusion in a broad erythrocyte gas-exchange Reactome pathway and does not reflect the protein's function.
Supporting Evidence:
file:human/CYB5R4/CYB5R4-uniprot.txt
NADH-cytochrome b5 reductase involved in endoplasmic reticulum stress response pathway.
|
|
GO:0004128
cytochrome-b5 reductase activity, acting on NAD(P)H
|
TAS
Reactome:R-HSA-6806831 |
ACCEPT |
Summary: Reactome TAS annotation of the core cytochrome-b5 reductase activity (in the context of methemoglobin reduction), consistent with experimental data.
Reason: The cytochrome-b5 reductase activity is experimentally demonstrated and NCB5OR reduces methemoglobin in vitro.
Supporting Evidence:
PMID:15131110
reduces cytochrome c, methemoglobin, ferricyanide, and molecular oxygen in vitro
|
|
GO:0072593
reactive oxygen species metabolic process
|
IDA
PMID:15131110 NCB5OR is a novel soluble NAD(P)H reductase localized in the... |
KEEP AS NON CORE |
Summary: ROS metabolic process supported by NCB5OR's redox chemistry and role in protecting cells against oxidant stress; consistent with the slow superoxide-producing activity and substrate-reducing behavior.
Reason: NCB5OR participates in cellular ROS handling/oxidant-stress protection, but this is a downstream physiological consequence of its redox activity rather than the core catalytic function.
Supporting Evidence:
PMID:15131110
both full-length and truncated NCB5OR produce superoxide from oxygen with slow turnover rates
|
|
GO:0005789
endoplasmic reticulum membrane
|
TAS
Reactome:R-HSA-6806831 |
MARK AS OVER ANNOTATED |
Summary: Reactome annotation to ER membrane. NCB5OR is explicitly a soluble protein lacking a membrane anchor, so an ER membrane localization is not accurate; it is associated with the ER but as a soluble protein.
Reason: Unlike classical single-domain cytochrome b5 reductase, NCB5OR has no membrane anchor and is soluble; the appropriate localization is the ER compartment, not the ER membrane.
Supporting Evidence:
PMID:10611283
b5+b5R also has binding motifs for heme, FAD, and NAD(P)H prosthetic groups but no membrane anchor.
|
|
GO:0030073
insulin secretion
|
ISS
GO_REF:0000024 |
KEEP AS NON CORE |
Summary: ISS transfer from the mouse ortholog (Q3TDX8). The Ncb5or-null mouse has a diabetes/beta-cell phenotype, so a role in insulin secretion is plausible but indirect and phenotype-driven, not a core molecular function.
Reason: A role in insulin secretion reflects the physiological consequence of beta-cell dysfunction in Ncb5or-deficient mice rather than a direct biochemical function of the enzyme.
Supporting Evidence:
file:human/CYB5R4/CYB5R4-uniprot.txt
Plays a critical role in protecting pancreatic beta-cells against oxidant stress
|
|
GO:0042593
glucose homeostasis
|
ISS
GO_REF:0000024 |
KEEP AS NON CORE |
Summary: ISS transfer from the mouse ortholog. Consistent with the diabetic phenotype of Ncb5or-null mice, but a downstream physiological role rather than a core molecular function.
Reason: Glucose homeostasis is a systemic phenotype linked to beta-cell protection in mouse models, not a direct enzymatic function of CYB5R4.
Supporting Evidence:
file:human/CYB5R4/CYB5R4-uniprot.txt
Plays a critical role in protecting pancreatic beta-cells against oxidant stress
|
|
GO:0046677
response to antibiotic
|
ISS
GO_REF:0000024 |
REMOVE |
Summary: ISS transfer from the mouse ortholog. There is no biological evidence linking CYB5R4 to an antibiotic response; this appears to be a spurious/non-specific transferred annotation.
Reason: No experimental or mechanistic support connects CYB5R4 to a response to antibiotic; the term is implausible for a soluble ER redox enzyme and is not supported by the literature.
Supporting Evidence:
file:human/CYB5R4/CYB5R4-uniprot.txt
NADH-cytochrome b5 reductase involved in endoplasmic reticulum stress response pathway.
|
|
GO:0048468
cell development
|
ISS
GO_REF:0000024 |
MARK AS OVER ANNOTATED |
Summary: Very general ISS transfer ("cell development"). Too broad to be informative and not directly supported by mechanistic data on CYB5R4.
Reason: Cell development is a high-level, non-specific process term that does not capture the redox/stress-protection function of CYB5R4 and is only indirectly inferred from mouse phenotypes.
Supporting Evidence:
file:human/CYB5R4/CYB5R4-uniprot.txt
Plays a critical role in protecting pancreatic beta-cells against oxidant stress
|
|
GO:0003032
detection of oxygen
|
NAS
PMID:10611283 Identification of a cytochrome b-type NAD(P)H oxidoreductase... |
REMOVE |
Summary: NAS annotation based on the early hypothesis that b5+b5R is a candidate oxygen sensor. Later enzymology showed it is a substrate reductase, not an efficient oxygen-utilizing oxidase, undermining the oxygen-sensing proposal.
Reason: The oxygen-sensor/oxygen-detection role was a speculative proposal in the 1999 paper that was superseded by 2004 enzymology showing NCB5OR preferentially reduces substrates rather than reacting with molecular oxygen; there is no direct evidence for oxygen detection.
Supporting Evidence:
PMID:15131110
endogenous NCB5OR is a soluble NAD(P)H reductase preferentially reducing substrate(s) rather than transferring electrons to molecular oxygen
|
|
GO:0004128
cytochrome-b5 reductase activity, acting on NAD(P)H
|
IDA
PMID:10611283 Identification of a cytochrome b-type NAD(P)H oxidoreductase... |
ACCEPT |
Summary: Direct experimental demonstration of the core NAD(P)H-dependent cytochrome-b5 reductase activity. This is the central molecular function of CYB5R4.
Reason: The recombinant protein is reduced by NAD(P)H and reduces cytochrome b5-type/cytochrome c acceptors, directly demonstrating cytochrome-b5 reductase activity (EC 1.6.2.2).
Supporting Evidence:
PMID:10611283
The recombinant b5+b5R protein can be reduced by NAD(P)H ... and by cytochrome c reduction in vitro.
|
|
GO:0005783
endoplasmic reticulum
|
IDA
PMID:15131110 NCB5OR is a novel soluble NAD(P)H reductase localized in the... |
ACCEPT |
Summary: Direct experimental ER localization via colocalization with the ER marker calreticulin. This is the well-supported subcellular localization.
Reason: Subcellular fractionation and confocal microscopy show colocalization with calreticulin, establishing ER localization.
Supporting Evidence:
PMID:15131110
we show that NCB5OR colocalizes with calreticulin, a marker for endoplasmic reticulum.
|
|
GO:0006801
superoxide metabolic process
|
IDA
PMID:10611283 Identification of a cytochrome b-type NAD(P)H oxidoreductase... |
KEEP AS NON CORE |
Summary: Based on in vitro superoxide production observed with air and excess NAD(P)H. Later work showed this occurs only at very slow turnover and that NCB5OR is not a bona fide oxidase, making superoxide metabolism a non-core activity.
Reason: Superoxide production is a slow, minor in vitro activity; NCB5OR is concluded to preferentially reduce substrates rather than generate superoxide, so this is not a core function.
Supporting Evidence:
PMID:10611283
superoxide production in the presence of air and excess NAD(P)H
|
|
GO:0016174
NAD(P)H oxidase H2O2-forming activity
|
IDA
NOT
PMID:15131110 NCB5OR is a novel soluble NAD(P)H reductase localized in the... |
ACCEPT |
Summary: Correctly negated annotation. The 2004 enzymology concluded that NCB5OR is not an NAD(P)H oxidase for superoxide/H2O2 production, refuting the earlier oxidase interpretation.
Reason: The NOT annotation accurately reflects the experimental conclusion that NCB5OR is a substrate reductase, not an NAD(P)H oxidase.
Supporting Evidence:
PMID:15131110
therefore not an NAD(P)H oxidase for superoxide production
|
|
GO:0016174
NAD(P)H oxidase H2O2-forming activity
|
IDA
PMID:10611283 Identification of a cytochrome b-type NAD(P)H oxidoreductase... |
REMOVE |
Summary: Positive (non-negated) NAD(P)H oxidase annotation from the original 1999 report. This interpretation was explicitly refuted by the 2004 study, which established the NOT annotation for the same activity.
Reason: The proposed NAD(P)H oxidase activity was superseded and refuted; NCB5OR produces superoxide only at negligible rates and is concluded not to be an oxidase, so this positive annotation is incorrect.
Supporting Evidence:
PMID:15131110
endogenous NCB5OR is a soluble NAD(P)H reductase preferentially reducing substrate(s) rather than transferring electrons to molecular oxygen and therefore not an NAD(P)H oxidase for superoxide production
|
|
GO:0016653
oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor
|
IDA
PMID:15131110 NCB5OR is a novel soluble NAD(P)H reductase localized in the... |
ACCEPT |
Summary: Direct experimental demonstration that NCB5OR uses NAD(P)H to reduce heme-protein acceptors (cytochrome c, methemoglobin). This is a core, well-supported molecular function.
Reason: NCB5OR actively reduces cytochrome c and methemoglobin using NAD(P)H, directly demonstrating oxidoreductase activity acting on NAD(P)H with a heme protein as acceptor.
Supporting Evidence:
PMID:15131110
reduces cytochrome c, methemoglobin, ferricyanide, and molecular oxygen in vitro
|
|
GO:0048471
perinuclear region of cytoplasm
|
IDA
PMID:10611283 Identification of a cytochrome b-type NAD(P)H oxidoreductase... |
ACCEPT |
Summary: Direct observation of cytosolic perinuclear localization in COS-7 cells. Consistent with the soluble nature of the protein and its ER/perinuclear association.
Reason: Confocal microscopy of myc-tagged b5+b5R showed cytosolic localization in the perinuclear space, supporting this localization term.
Supporting Evidence:
PMID:10611283
confocal microscopy revealed a cytosolic localization at the perinuclear space.
|
|
GO:0050660
flavin adenine dinucleotide binding
|
IC
PMID:15131110 NCB5OR is a novel soluble NAD(P)H reductase localized in the... |
NEW |
Summary: Proposed annotation not present in the current GOA for CYB5R4.
Reason: NCB5OR contains a defined FAD-binding domain and was shown to contain stoichiometric FAD, yet GO:0050660 is absent from existing annotations.
Supporting Evidence:
PMID:15131110
Recombinant NCB5OR is soluble and has stoichiometric amounts of heme and flavin adenine dinucleotide.
|
|
GO:0034976
response to endoplasmic reticulum stress
|
IC
file:human/CYB5R4/CYB5R4-uniprot.txt |
NEW |
Summary: Proposed annotation not present in the current GOA for CYB5R4.
Reason: The protein is annotated by UniProt as functioning in the ER stress response pathway and is ER-localized, supporting a response to ER stress process term.
Supporting Evidence:
file:human/CYB5R4/CYB5R4-uniprot.txt
NADH-cytochrome b5 reductase involved in endoplasmic reticulum stress response pathway.
|
Q: What are the physiological electron acceptor(s) of CYB5R4 in vivo, given that it lacks a membrane anchor and is soluble within the ER/perinuclear compartment?
Q: How does the N-terminal CS/Hsp20 (p23-like) domain contribute to function, folding, or partner interactions of CYB5R4?
Q: By what mechanism does CYB5R4 protect pancreatic beta cells from oxidative and ER stress, and is this a direct antioxidant role or an indirect consequence of its reductase activity?
Experiment: Identify the endogenous electron acceptor(s) and interacting partners of CYB5R4 in beta cells using proximity labeling (BioID/APEX) and reconstituted electron-transfer assays with candidate cytochrome b5 / desaturase systems.
Experiment: Generate beta-cell-specific CYB5R4 knockout or catalytic-dead (heme/FAD-binding mutant) cell lines and measure ER stress markers, ROS levels, and insulin secretion under oxidative challenge to define the mechanism of cytoprotection.
Experiment: Perform steady-state and stopped-flow enzymology comparing reduction of physiological heme-protein acceptors versus molecular oxygen to quantitatively confirm that substrate reduction, not oxidase activity, dominates in vivo.
UniProt: Q7L1T6 (NB5R4_HUMAN), 521 aa, EC 1.6.2.2. Gene synonym NCB5OR.
*-deep-research*.md file found in this gene directory.Cytonuclear proteostasis | Chaperone | HSP90 system | HSP90 cochaperone | CS domain containing ; PN-node mapping: type (HSP90 cochaperone)=mapped, scope=ok_for_propagation_to_go, GO:0051879 Hsp90 protein binding (subtype/group/class/branch = no_mapping)This file is generated from the current PROTEOSTASIS phase-1 dossier and local gene-review artifacts. Edit the source review, PN mapping, or dossier rather than this generated note when correcting the underlying curation.
id: Q7L1T6
gene_symbol: CYB5R4
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: >-
CYB5R4 (NADH-cytochrome b5 reductase 4; also known as NCB5OR or b5+b5R) is a
multidomain, soluble flavohemoprotein and NAD(P)H-dependent oxidoreductase. It
contains an N-terminal CS/Hsp20 (p23-like) domain, a cytochrome b5-like
heme-binding domain (with axial His-89 and His-112 ligating a six-coordinate
low-spin heme) joined by a long hinge to a C-terminal FAD-dependent
cytochrome-b5-reductase (FNR-type FAD- and NAD-binding) module. It binds
stoichiometric heme and FAD and catalyzes EC 1.6.2.2 (NADH:cytochrome b5
oxidoreductase), reducing electron acceptors including cytochrome b5,
cytochrome c, methemoglobin and ferricyanide; unlike the classical
single-domain cytochrome b5 reductase it lacks a membrane anchor. The protein
localizes to the endoplasmic reticulum and perinuclear cytoplasm. It functions
in the response to oxidative and endoplasmic reticulum stress, protecting cells
(notably pancreatic beta cells) from excess reactive oxygen species; loss of
the orthologous gene in mice causes diabetes and lipoatrophy. Although early
work proposed it as an NAD(P)H oxidase / candidate oxygen sensor, subsequent
enzymology showed it preferentially reduces substrates rather than transferring
electrons to molecular oxygen and is not an efficient superoxide-generating
oxidase.
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO
terms
findings: []
- id: GO_REF:0000024
title: Manual transfer of experimentally-verified manual GO annotation data to orthologs
by curator judgment of sequence similarity
findings: []
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings: []
- id: GO_REF:0000107
title: Automatic transfer of experimentally verified manual GO annotation data to
orthologs using Ensembl Compara
findings: []
- id: GO_REF:0000117
title: Electronic Gene Ontology annotations created by ARBA machine learning models
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: PMID:10611283
title: Identification of a cytochrome b-type NAD(P)H oxidoreductase ubiquitously
expressed in human cells.
findings:
- statement: Human b5+b5R (NCB5OR) is a flavohemoprotein with cytochrome b5 and b5
reductase domains that binds heme, FAD and NAD(P)H, is reduced by NAD(P)H, reduces
cytochrome c in vitro, and localizes to the cytosolic perinuclear space; proposed
as a candidate oxygen sensor.
reference_section_type: ABSTRACT
- id: PMID:15131110
title: NCB5OR is a novel soluble NAD(P)H reductase localized in the endoplasmic
reticulum.
findings:
- statement: Recombinant NCB5OR is soluble with stoichiometric heme and FAD, colocalizes
with calreticulin (ER marker), actively reduces cytochrome c, and produces superoxide
only with very slow turnover, indicating it preferentially reduces substrates
rather than acting as an NAD(P)H oxidase.
reference_section_type: ABSTRACT
- id: Reactome:R-HSA-1237044
title: Erythrocytes take up carbon dioxide and release oxygen
findings: []
- id: Reactome:R-HSA-6806831
title: CYB5Rs reduce MetHb to HbA
findings: []
- id: file:human/CYB5R4/CYB5R4-uniprot.txt
title: UniProt entry Q7L1T6 (NB5R4_HUMAN), Cytochrome b5 reductase 4
findings: []
existing_annotations:
- term:
id: GO:0004128
label: cytochrome-b5 reductase activity, acting on NAD(P)H
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: enables
review:
summary: Phylogenetic (IBA) assignment of the core cytochrome-b5 reductase activity.
This matches the experimentally demonstrated EC 1.6.2.2 activity and is the
core molecular function.
action: ACCEPT
reason: The cytochrome-b5 reductase activity acting on NAD(P)H is directly supported
by experimental characterization of NCB5OR, which contains a cytochrome-b5-reductase
domain and reduces cytochrome b5-type acceptors using NAD(P)H.
supported_by:
- reference_id: PMID:10611283
supporting_text: We have identified a cytosolic cytochrome b-type NAD(P)H oxidoreductase
in mammals, a flavohemoprotein (b5+b5R) containing cytochrome b5 (b5) and b5
reductase (b5R) domains.
- term:
id: GO:0020037
label: heme binding
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: enables
review:
summary: Phylogenetic assignment of heme binding, supported by experimental evidence
that NCB5OR binds stoichiometric heme via its cytochrome b5-like domain.
action: ACCEPT
reason: NCB5OR contains a cytochrome b5-like heme-binding domain with axial His
ligands and binds stoichiometric heme experimentally.
supported_by:
- reference_id: PMID:15131110
supporting_text: Recombinant NCB5OR is soluble and has stoichiometric amounts
of heme and flavin adenine dinucleotide.
- term:
id: GO:0005783
label: endoplasmic reticulum
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: is_active_in
review:
summary: Phylogenetic assignment of ER localization, consistent with experimental
colocalization of NCB5OR with the ER marker calreticulin.
action: ACCEPT
reason: NCB5OR colocalizes with the ER marker calreticulin and is annotated by
UniProt to the endoplasmic reticulum.
supported_by:
- reference_id: PMID:15131110
supporting_text: we show that NCB5OR colocalizes with calreticulin, a marker
for endoplasmic reticulum.
- term:
id: GO:0006801
label: superoxide metabolic process
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: Phylogenetic assignment of superoxide metabolic process. NCB5OR can produce
superoxide in vitro, but only with very slow turnover, and later enzymology
concluded it preferentially reduces substrates rather than transferring electrons
to oxygen, so this process is not a core in vivo function.
action: KEEP_AS_NON_CORE
reason: Superoxide production by NCB5OR occurs only at very low turnover rates
in vitro; the protein is concluded to be a substrate reductase rather than an
oxidase, so superoxide metabolism is at most a minor/non-core activity.
supported_by:
- reference_id: PMID:15131110
supporting_text: both full-length and truncated NCB5OR produce superoxide from
oxygen with slow turnover rates
- term:
id: GO:0005783
label: endoplasmic reticulum
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: located_in
review:
summary: Electronic (IEA) ER localization, redundant with and supported by the
experimental IDA ER annotation.
action: ACCEPT
reason: ER localization is experimentally established by colocalization with calreticulin.
supported_by:
- reference_id: PMID:15131110
supporting_text: we show that NCB5OR colocalizes with calreticulin, a marker
for endoplasmic reticulum.
- term:
id: GO:0016491
label: oxidoreductase activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: Very general InterPro-based oxidoreductase activity. Correct but uninformative
given the more specific cytochrome-b5 reductase activity annotations.
action: MARK_AS_OVER_ANNOTATED
reason: This is a high-level parent of the specific cytochrome-b5 reductase activity
that is already annotated; it is correct but too general to be informative.
supported_by:
- reference_id: PMID:10611283
supporting_text: Human b5+b5R flavohemoprotein is a NAD(P)H oxidoreductase
- term:
id: GO:0016653
label: oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor
evidence_type: IEA
original_reference_id: GO_REF:0000117
qualifier: enables
review:
summary: ARBA machine-learning annotation of oxidoreductase activity acting on
NAD(P)H with a heme protein as acceptor, redundant with the experimental IDA
annotation of the same term.
action: ACCEPT
reason: This activity is directly supported by experimental demonstration that
NCB5OR uses NAD(P)H to reduce heme-protein acceptors such as cytochrome b5/cytochrome
c and methemoglobin.
supported_by:
- reference_id: PMID:15131110
supporting_text: reduces cytochrome c, methemoglobin, ferricyanide, and molecular
oxygen in vitro
- term:
id: GO:0020037
label: heme binding
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: InterPro-based heme binding annotation, redundant with and supported
by the IBA heme binding annotation and experimental evidence of stoichiometric
heme.
action: ACCEPT
reason: Heme binding is experimentally established and the protein has a cytochrome
b5-like heme-binding domain with axial His ligands.
supported_by:
- reference_id: PMID:15131110
supporting_text: Recombinant NCB5OR is soluble and has stoichiometric amounts
of heme and flavin adenine dinucleotide.
- term:
id: GO:0090524
label: cytochrome-b5 reductase activity, acting on NADH
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: enables
review:
summary: EC/Rhea-based annotation of NADH-specific cytochrome-b5 reductase activity
(EC 1.6.2.2). Supported by experimental catalytic activity; closely related
to the NAD(P)H form.
action: ACCEPT
reason: UniProt records the catalytic reaction 2 Fe(III)-[cytochrome b5] + NADH
= 2 Fe(II)-[cytochrome b5] + NAD+ + H+ (EC 1.6.2.2), demonstrated experimentally.
supported_by:
- reference_id: file:human/CYB5R4/CYB5R4-uniprot.txt
supporting_text: 'EC=1.6.2.2 {ECO:0000305|PubMed:10611283}; Reaction=2 Fe(III)-[cytochrome
b5] + NADH = 2 Fe(II)-[cytochrome b5] + NAD(+) + H(+)'
- term:
id: GO:0004128
label: cytochrome-b5 reductase activity, acting on NAD(P)H
evidence_type: IEA
original_reference_id: GO_REF:0000107
qualifier: enables
review:
summary: Ensembl Compara ortholog transfer of the core cytochrome-b5 reductase
activity, redundant with the experimental IDA annotation of the same term.
action: ACCEPT
reason: The core cytochrome-b5 reductase activity acting on NAD(P)H is directly
demonstrated experimentally.
supported_by:
- reference_id: PMID:10611283
supporting_text: The recombinant b5+b5R protein can be reduced by NAD(P)H ...
and by cytochrome c reduction in vitro.
- term:
id: GO:0015701
label: bicarbonate transport
evidence_type: TAS
original_reference_id: Reactome:R-HSA-1237044
qualifier: involved_in
review:
summary: Reactome pathway-context annotation ("Erythrocytes take up carbon dioxide
and release oxygen"). CYB5R4 is a redox enzyme, not a bicarbonate transporter;
this is a pathway-membership artifact rather than a true molecular role.
action: MARK_AS_OVER_ANNOTATED
reason: CYB5R4 has no bicarbonate transport activity; the term derives from inclusion
in a broad erythrocyte gas-exchange Reactome pathway and does not reflect the
protein's function.
supported_by:
- reference_id: file:human/CYB5R4/CYB5R4-uniprot.txt
supporting_text: NADH-cytochrome b5 reductase involved in endoplasmic reticulum
stress response pathway.
- term:
id: GO:0004128
label: cytochrome-b5 reductase activity, acting on NAD(P)H
evidence_type: TAS
original_reference_id: Reactome:R-HSA-6806831
qualifier: enables
review:
summary: Reactome TAS annotation of the core cytochrome-b5 reductase activity (in
the context of methemoglobin reduction), consistent with experimental data.
action: ACCEPT
reason: The cytochrome-b5 reductase activity is experimentally demonstrated and
NCB5OR reduces methemoglobin in vitro.
supported_by:
- reference_id: PMID:15131110
supporting_text: reduces cytochrome c, methemoglobin, ferricyanide, and molecular
oxygen in vitro
- term:
id: GO:0072593
label: reactive oxygen species metabolic process
evidence_type: IDA
original_reference_id: PMID:15131110
qualifier: involved_in
review:
summary: ROS metabolic process supported by NCB5OR's redox chemistry and role
in protecting cells against oxidant stress; consistent with the slow superoxide-producing
activity and substrate-reducing behavior.
action: KEEP_AS_NON_CORE
reason: NCB5OR participates in cellular ROS handling/oxidant-stress protection,
but this is a downstream physiological consequence of its redox activity rather
than the core catalytic function.
supported_by:
- reference_id: PMID:15131110
supporting_text: both full-length and truncated NCB5OR produce superoxide from
oxygen with slow turnover rates
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: TAS
original_reference_id: Reactome:R-HSA-6806831
qualifier: located_in
review:
summary: Reactome annotation to ER membrane. NCB5OR is explicitly a soluble protein
lacking a membrane anchor, so an ER membrane localization is not accurate; it
is associated with the ER but as a soluble protein.
action: MARK_AS_OVER_ANNOTATED
reason: Unlike classical single-domain cytochrome b5 reductase, NCB5OR has no membrane
anchor and is soluble; the appropriate localization is the ER compartment, not
the ER membrane.
supported_by:
- reference_id: PMID:10611283
supporting_text: b5+b5R also has binding motifs for heme, FAD, and NAD(P)H prosthetic
groups but no membrane anchor.
- term:
id: GO:0030073
label: insulin secretion
evidence_type: ISS
original_reference_id: GO_REF:0000024
qualifier: involved_in
review:
summary: ISS transfer from the mouse ortholog (Q3TDX8). The Ncb5or-null mouse has
a diabetes/beta-cell phenotype, so a role in insulin secretion is plausible
but indirect and phenotype-driven, not a core molecular function.
action: KEEP_AS_NON_CORE
reason: A role in insulin secretion reflects the physiological consequence of beta-cell
dysfunction in Ncb5or-deficient mice rather than a direct biochemical function
of the enzyme.
supported_by:
- reference_id: file:human/CYB5R4/CYB5R4-uniprot.txt
supporting_text: Plays a critical role in protecting pancreatic beta-cells against
oxidant stress
- term:
id: GO:0042593
label: glucose homeostasis
evidence_type: ISS
original_reference_id: GO_REF:0000024
qualifier: involved_in
review:
summary: ISS transfer from the mouse ortholog. Consistent with the diabetic phenotype
of Ncb5or-null mice, but a downstream physiological role rather than a core molecular
function.
action: KEEP_AS_NON_CORE
reason: Glucose homeostasis is a systemic phenotype linked to beta-cell protection
in mouse models, not a direct enzymatic function of CYB5R4.
supported_by:
- reference_id: file:human/CYB5R4/CYB5R4-uniprot.txt
supporting_text: Plays a critical role in protecting pancreatic beta-cells against
oxidant stress
- term:
id: GO:0046677
label: response to antibiotic
evidence_type: ISS
original_reference_id: GO_REF:0000024
qualifier: involved_in
review:
summary: ISS transfer from the mouse ortholog. There is no biological evidence
linking CYB5R4 to an antibiotic response; this appears to be a spurious/non-specific
transferred annotation.
action: REMOVE
reason: No experimental or mechanistic support connects CYB5R4 to a response to
antibiotic; the term is implausible for a soluble ER redox enzyme and is not
supported by the literature.
supported_by:
- reference_id: file:human/CYB5R4/CYB5R4-uniprot.txt
supporting_text: NADH-cytochrome b5 reductase involved in endoplasmic reticulum
stress response pathway.
- term:
id: GO:0048468
label: cell development
evidence_type: ISS
original_reference_id: GO_REF:0000024
qualifier: involved_in
review:
summary: Very general ISS transfer ("cell development"). Too broad to be informative
and not directly supported by mechanistic data on CYB5R4.
action: MARK_AS_OVER_ANNOTATED
reason: Cell development is a high-level, non-specific process term that does not
capture the redox/stress-protection function of CYB5R4 and is only indirectly
inferred from mouse phenotypes.
supported_by:
- reference_id: file:human/CYB5R4/CYB5R4-uniprot.txt
supporting_text: Plays a critical role in protecting pancreatic beta-cells against
oxidant stress
- term:
id: GO:0003032
label: detection of oxygen
evidence_type: NAS
original_reference_id: PMID:10611283
qualifier: involved_in
review:
summary: NAS annotation based on the early hypothesis that b5+b5R is a candidate
oxygen sensor. Later enzymology showed it is a substrate reductase, not an efficient
oxygen-utilizing oxidase, undermining the oxygen-sensing proposal.
action: REMOVE
reason: The oxygen-sensor/oxygen-detection role was a speculative proposal in the
1999 paper that was superseded by 2004 enzymology showing NCB5OR preferentially
reduces substrates rather than reacting with molecular oxygen; there is no direct
evidence for oxygen detection.
supported_by:
- reference_id: PMID:15131110
supporting_text: endogenous NCB5OR is a soluble NAD(P)H reductase preferentially
reducing substrate(s) rather than transferring electrons to molecular oxygen
- term:
id: GO:0004128
label: cytochrome-b5 reductase activity, acting on NAD(P)H
evidence_type: IDA
original_reference_id: PMID:10611283
qualifier: enables
review:
summary: Direct experimental demonstration of the core NAD(P)H-dependent cytochrome-b5
reductase activity. This is the central molecular function of CYB5R4.
action: ACCEPT
reason: The recombinant protein is reduced by NAD(P)H and reduces cytochrome b5-type/cytochrome
c acceptors, directly demonstrating cytochrome-b5 reductase activity (EC 1.6.2.2).
supported_by:
- reference_id: PMID:10611283
supporting_text: The recombinant b5+b5R protein can be reduced by NAD(P)H ...
and by cytochrome c reduction in vitro.
- term:
id: GO:0005783
label: endoplasmic reticulum
evidence_type: IDA
original_reference_id: PMID:15131110
qualifier: located_in
review:
summary: Direct experimental ER localization via colocalization with the ER marker
calreticulin. This is the well-supported subcellular localization.
action: ACCEPT
reason: Subcellular fractionation and confocal microscopy show colocalization with
calreticulin, establishing ER localization.
supported_by:
- reference_id: PMID:15131110
supporting_text: we show that NCB5OR colocalizes with calreticulin, a marker
for endoplasmic reticulum.
- term:
id: GO:0006801
label: superoxide metabolic process
evidence_type: IDA
original_reference_id: PMID:10611283
qualifier: involved_in
review:
summary: Based on in vitro superoxide production observed with air and excess NAD(P)H.
Later work showed this occurs only at very slow turnover and that NCB5OR is not
a bona fide oxidase, making superoxide metabolism a non-core activity.
action: KEEP_AS_NON_CORE
reason: Superoxide production is a slow, minor in vitro activity; NCB5OR is concluded
to preferentially reduce substrates rather than generate superoxide, so this
is not a core function.
supported_by:
- reference_id: PMID:10611283
supporting_text: superoxide production in the presence of air and excess NAD(P)H
- term:
id: GO:0016174
label: NAD(P)H oxidase H2O2-forming activity
evidence_type: IDA
original_reference_id: PMID:15131110
qualifier: enables
negated: true
review:
summary: Correctly negated annotation. The 2004 enzymology concluded that NCB5OR
is not an NAD(P)H oxidase for superoxide/H2O2 production, refuting the earlier
oxidase interpretation.
action: ACCEPT
reason: The NOT annotation accurately reflects the experimental conclusion that
NCB5OR is a substrate reductase, not an NAD(P)H oxidase.
supported_by:
- reference_id: PMID:15131110
supporting_text: therefore not an NAD(P)H oxidase for superoxide production
- term:
id: GO:0016174
label: NAD(P)H oxidase H2O2-forming activity
evidence_type: IDA
original_reference_id: PMID:10611283
qualifier: enables
review:
summary: Positive (non-negated) NAD(P)H oxidase annotation from the original 1999
report. This interpretation was explicitly refuted by the 2004 study, which
established the NOT annotation for the same activity.
action: REMOVE
reason: The proposed NAD(P)H oxidase activity was superseded and refuted; NCB5OR
produces superoxide only at negligible rates and is concluded not to be an oxidase,
so this positive annotation is incorrect.
supported_by:
- reference_id: PMID:15131110
supporting_text: endogenous NCB5OR is a soluble NAD(P)H reductase preferentially
reducing substrate(s) rather than transferring electrons to molecular oxygen
and therefore not an NAD(P)H oxidase for superoxide production
- term:
id: GO:0016653
label: oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor
evidence_type: IDA
original_reference_id: PMID:15131110
qualifier: enables
review:
summary: Direct experimental demonstration that NCB5OR uses NAD(P)H to reduce heme-protein
acceptors (cytochrome c, methemoglobin). This is a core, well-supported molecular
function.
action: ACCEPT
reason: NCB5OR actively reduces cytochrome c and methemoglobin using NAD(P)H, directly
demonstrating oxidoreductase activity acting on NAD(P)H with a heme protein as
acceptor.
supported_by:
- reference_id: PMID:15131110
supporting_text: reduces cytochrome c, methemoglobin, ferricyanide, and molecular
oxygen in vitro
- term:
id: GO:0048471
label: perinuclear region of cytoplasm
evidence_type: IDA
original_reference_id: PMID:10611283
qualifier: located_in
review:
summary: Direct observation of cytosolic perinuclear localization in COS-7 cells.
Consistent with the soluble nature of the protein and its ER/perinuclear association.
action: ACCEPT
reason: Confocal microscopy of myc-tagged b5+b5R showed cytosolic localization
in the perinuclear space, supporting this localization term.
supported_by:
- reference_id: PMID:10611283
supporting_text: confocal microscopy revealed a cytosolic localization at the
perinuclear space.
- term:
id: GO:0050660
label: flavin adenine dinucleotide binding
evidence_type: IC
original_reference_id: PMID:15131110
qualifier: enables
review:
summary: Proposed annotation not present in the current GOA for CYB5R4.
action: NEW
reason: NCB5OR contains a defined FAD-binding domain and was shown to contain
stoichiometric FAD, yet GO:0050660 is absent from existing annotations.
supported_by:
- reference_id: PMID:15131110
supporting_text: Recombinant NCB5OR is soluble and has stoichiometric amounts of
heme and flavin adenine dinucleotide.
- term:
id: GO:0034976
label: response to endoplasmic reticulum stress
evidence_type: IC
original_reference_id: file:human/CYB5R4/CYB5R4-uniprot.txt
qualifier: involved_in
review:
summary: Proposed annotation not present in the current GOA for CYB5R4.
action: NEW
reason: The protein is annotated by UniProt as functioning in the ER stress response
pathway and is ER-localized, supporting a response to ER stress process term.
supported_by:
- reference_id: file:human/CYB5R4/CYB5R4-uniprot.txt
supporting_text: NADH-cytochrome b5 reductase involved in endoplasmic reticulum
stress response pathway.
core_functions:
- description: NAD(P)H-dependent cytochrome-b5 reductase that transfers electrons from
NAD(P)H, via bound FAD and a cytochrome b5-like heme center, to heme-protein acceptors
(cytochrome b5, cytochrome c, methemoglobin), catalyzing EC 1.6.2.2.
supported_by:
- reference_id: PMID:10611283
supporting_text: The recombinant b5+b5R protein can be reduced by NAD(P)H ... and
by cytochrome c reduction in vitro.
- reference_id: PMID:15131110
supporting_text: reduces cytochrome c, methemoglobin, ferricyanide, and molecular
oxygen in vitro
molecular_function:
id: GO:0004128
label: cytochrome-b5 reductase activity, acting on NAD(P)H
- description: Soluble ER/perinuclear flavohemoprotein binding stoichiometric heme
(via a cytochrome b5-like domain) and FAD, supporting electron transfer.
supported_by:
- reference_id: PMID:15131110
supporting_text: Recombinant NCB5OR is soluble and has stoichiometric amounts of
heme and flavin adenine dinucleotide.
molecular_function:
id: GO:0016653
label: oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor
- description: Contributes to protection of cells (notably pancreatic beta cells) from
oxidative and endoplasmic reticulum stress, helping limit excess reactive oxygen
species.
supported_by:
- reference_id: file:human/CYB5R4/CYB5R4-uniprot.txt
supporting_text: Plays a critical role in protecting pancreatic beta-cells against
oxidant stress, possibly by protecting the cell from excess buildup of reactive
oxygen species (ROS).
proposed_new_terms: []
suggested_questions:
- question: What are the physiological electron acceptor(s) of CYB5R4 in vivo, given
that it lacks a membrane anchor and is soluble within the ER/perinuclear compartment?
- question: How does the N-terminal CS/Hsp20 (p23-like) domain contribute to function,
folding, or partner interactions of CYB5R4?
- question: By what mechanism does CYB5R4 protect pancreatic beta cells from oxidative
and ER stress, and is this a direct antioxidant role or an indirect consequence
of its reductase activity?
suggested_experiments:
- description: Identify the endogenous electron acceptor(s) and interacting partners
of CYB5R4 in beta cells using proximity labeling (BioID/APEX) and reconstituted
electron-transfer assays with candidate cytochrome b5 / desaturase systems.
- description: Generate beta-cell-specific CYB5R4 knockout or catalytic-dead (heme/FAD-binding
mutant) cell lines and measure ER stress markers, ROS levels, and insulin secretion
under oxidative challenge to define the mechanism of cytoprotection.
- description: Perform steady-state and stopped-flow enzymology comparing reduction
of physiological heme-protein acceptors versus molecular oxygen to quantitatively
confirm that substrate reduction, not oxidase activity, dominates in vivo.