SRD5A3 is an endoplasmic reticulum membrane, NADPH-dependent polyprenal reductase that acts in the terminal steps of de novo dolichol biosynthesis. In the currently accepted pathway it catalyzes the reduction of the alpha-isoprene unit of a di-trans,poly-cis-polyprenal to the corresponding dolichal, an intermediate in converting polyprenol to dolichol; the resulting dolichol is phosphorylated to dolichol-phosphate, the essential lipid carrier used to assemble the lipid-linked oligosaccharide precursor for protein N-linked glycosylation. It is a multi-pass member of the steroid 5-alpha-reductase family (polyprenal reductase subfamily; yeast ortholog DFG10). Loss-of-function mutations cause SRD5A3-congenital disorder of glycosylation (SRD5A3-CDG, CDG type Iq) and Kahrizi syndrome, characterized by ocular coloboma, cerebellar vermis hypoplasia, and intellectual disability. Despite its name, SRD5A3 is not a physiological steroid 5-alpha-reductase; a weak in-vitro testosterone-to-dihydrotestosterone activity was reported at its discovery in prostate cancer, but its established physiological role is in dolichol synthesis and glycosylation, not steroid metabolism.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0005783
endoplasmic reticulum
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetically inferred ER localization, consistent with the experimentally determined localization of SRD5A3 (an ER-membrane dolichol-pathway enzyme).
Reason: SRD5A3 acts in the ER membrane where dolichol biosynthesis and lipid-linked oligosaccharide assembly occur; this is directly supported experimentally.
Supporting Evidence:
PMID:20637498
Epitope tagged SRD5A3 localized predominantly to the ER
|
|
GO:0006488
dolichol-linked oligosaccharide biosynthetic process
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetically inferred involvement in dolichol-linked oligosaccharide (LLO) biosynthesis. SRD5A3 supplies dolichol/dolichol-phosphate, the lipid carrier on which the LLO precursor is built, so this pathway-level BP is appropriate, though not the most specific reaction SRD5A3 catalyzes.
Reason: SRD5A3 is required for LLO synthesis; loss of SRD5A3 severely reduces newly synthesized LLO and can be rescued by exogenous dolichol-phosphate, placing it upstream of LLO assembly.
Supporting Evidence:
PMID:20637498
SRD5A3 is necessary for the reduction of the alpha-isoprene unit of polyprenols to form dolichols, required for synthesis of dolichol-linked monosaccharides, and the oligosaccharide precursor used for N-glycosylation
|
|
GO:0160198
polyprenal reductase activity
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetically inferred polyprenal reductase activity, the current core molecular function of SRD5A3. This is the term carried by GOA (polyprenAL reductase activity, GO:0160198), matching the revised pathway in which SRD5A3 reduces polyprenal to dolichal rather than polyprenol directly to dolichol.
Reason: Represents the core molecular function at the correct current level of specificity; consistent with the IDA/EXP experimental annotations and UniProt EC 1.3.1.94.
Supporting Evidence:
PMID:38821050
SRD5A3 catalyzes only the second reaction
|
|
GO:0043048
dolichyl monophosphate biosynthetic process
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetically inferred involvement in dolichyl monophosphate biosynthesis, the current core biological process for SRD5A3. GO:0019408 (dolichol biosynthetic process) was obsoleted in favor of GO:0043048, so this is the correct current BP for the polyprenol-to-dolichol/dolichol-phosphate route.
Reason: SRD5A3 catalyzes a committed reductive step supplying dolichol for dolichol-phosphate synthesis; supported by strong IDA evidence in human cells.
Supporting Evidence:
PMID:20637498
SRD5A3 is necessary for the reduction of the alpha-isoprene unit of polyprenols to form dolichols
|
|
GO:0005789
endoplasmic reticulum membrane
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: Electronic mapping from the UniProt subcellular-location keyword. SRD5A3 is a multi-pass ER membrane protein, so this is correct and represents the core localization.
Reason: Consistent with experimental ER localization and the multi-pass membrane topology annotated in UniProt.
Supporting Evidence:
file:human/SRD5A3/SRD5A3-uniprot.txt
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
file:human/SRD5A3/SRD5A3-uniprot.txt
Multi-pass membrane protein
|
|
GO:0006629
lipid metabolic process
|
IEA
GO_REF:0000002 |
KEEP AS NON CORE |
Summary: Broad InterPro-to-GO mapping. Correct in that SRD5A3 acts in polyisoprenoid lipid (dolichol) metabolism, but far too general to convey its function.
Reason: Not wrong but uninformative; the specific dolichyl monophosphate biosynthetic process (GO:0043048) already captures the lipid-metabolic role more precisely.
Supporting Evidence:
file:human/SRD5A3/SRD5A3-uniprot.txt
PATHWAY: Protein modification; protein glycosylation
|
|
GO:0016627
oxidoreductase activity, acting on the CH-CH group of donors
|
IEA
GO_REF:0000002 |
KEEP AS NON CORE |
Summary: InterPro-to-GO mapping to a high-level oxidoreductase class. SRD5A3 is an NADPH-dependent reductase that reduces a C=C double bond (the alpha-isoprene unit), so this parent term is correct but general.
Reason: Accurate but non-specific; the specific polyprenal reductase activity (GO:0160198) is the informative core MF.
Supporting Evidence:
PMID:38821050
as a NADPH-dependent reductase in two non-consecutive steps
|
|
GO:0043048
dolichyl monophosphate biosynthetic process
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: InterPro-to-GO mapping (IPR039698, Dfg10/SRD5A3) to dolichyl monophosphate biosynthesis. This matches the experimentally supported core BP.
Reason: Correct BP for the SRD5A3/Dfg10 family; duplicates the IDA/IBA annotations to the same term.
Supporting Evidence:
PMID:20637498
required for synthesis of dolichol-linked monosaccharides, and the oligosaccharide precursor used for N-glycosylation
|
|
GO:0047751
3-oxo-5-alpha-steroid 4-dehydrogenase (NADP+) activity
|
IEA
GO_REF:0000120 |
REMOVE |
Summary: Electronic annotation derived from the EC 1.3.1.22 (steroid) mapping via RHEA/EC (GO_REF:0000120). SRD5A3 is not a physiological steroid 5-alpha-reductase; its established function is polyprenal reduction in dolichol synthesis. The steroid EC was assigned on the basis of the gene name and weak in-vitro activity, and this purely electronic EC-mapping is a wrong inference of the enzyme's biological function.
Reason: Demonstrably wrong electronic EC/RHEA-to-GO inference. Physiological substrate is polyprenal, not a steroid; null patients have a congenital disorder of glycosylation, not a steroid/androgen phenotype, and phylogeny argues the ancestral substrate was not a steroid. Per policy, wrong IEA EC-mappings are appropriate REMOVE targets.
Supporting Evidence:
PMID:20637498
suggesting that the substrate of the enzyme encoded by the common ancestral gene was potentially not a steroid
|
|
GO:0160198
polyprenal reductase activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Electronic annotation from EC 1.3.1.94 (RHEA:80727) mapping. This is the correct core molecular function, matching the experimental annotations and UniProt RecName (Polyprenal reductase).
Reason: Correct EC-based mapping to the physiological reaction; corroborates the IDA/EXP/IBA annotations to GO:0160198.
Supporting Evidence:
file:human/SRD5A3/SRD5A3-uniprot.txt
EC=1.3.1.94
|
|
GO:0006488
dolichol-linked oligosaccharide biosynthetic process
|
IEA
GO_REF:0000107 |
ACCEPT |
Summary: Orthology-based transfer (Ensembl Compara) from mouse Srd5a3 of the LLO biosynthesis BP. Consistent with the human experimental data and the IBA annotation to the same term.
Reason: Correct pathway-level BP inferred from a well-supported ortholog; duplicates the IBA annotation.
Supporting Evidence:
PMID:20637498
the oligosaccharide precursor used for N-glycosylation
|
|
GO:0006702
androgen biosynthetic process
|
TAS
Reactome:R-HSA-193048 |
MARK AS OVER ANNOTATED |
Summary: Reactome-derived annotation placing SRD5A3 in androgen biosynthesis, based on the prostate-cancer report that SRD5A3 can convert testosterone to dihydrotestosterone in vitro (Uemura et al. 2008). SRD5A3 is named a steroid 5-alpha-reductase and shows weak in-vitro DHT-forming activity, but its physiological function is dolichol synthesis, not androgen metabolism; this is an over-annotation of a marginal side activity.
Reason: The steroid/androgen activity is weak, in-vitro, and derives from the gene name and the context of its discovery in hormone-refractory prostate cancer; loss-of-function causes a glycosylation disorder, not an androgen-deficiency phenotype. Retained (experimental basis, TAS) but flagged as over-annotation rather than removed.
Supporting Evidence:
PMID:17986282
validated its ability to produce DHT from testosterone, similar to type
|
|
GO:0043048
dolichyl monophosphate biosynthetic process
|
TAS
Reactome:R-HSA-446199 |
ACCEPT |
Summary: Reactome-authored annotation (Synthesis of dolichyl-phosphate) to the core dolichyl monophosphate biosynthetic process. Consistent with the experimental and IBA annotations.
Reason: Correct core BP; duplicates the IDA/IBA/IEA annotations to GO:0043048.
Supporting Evidence:
PMID:20637498
SRD5A3 is necessary for the reduction of the alpha-isoprene unit of polyprenols to form dolichols
|
|
GO:0003865
3-oxo-5-alpha-steroid 4-dehydrogenase activity
|
TAS
Reactome:R-HSA-9705714 |
MARK AS OVER ANNOTATED |
Summary: Reactome-derived steroid 5-alpha-reductase MF annotation (SRD5A3 dehydrogenates TEST to DHTEST), tracing to the in-vitro testosterone-to-DHT activity of Uemura et al. 2008. This is a weak, non-physiological side activity and an over-annotation relative to the enzyme's dolichol-pathway function.
Reason: Steroid 5-alpha-reductase activity is in-vitro and marginal; SRD5A3 is physiologically a polyprenal reductase. Retained (TAS/experimental origin) but flagged as over-annotation, not removed.
Supporting Evidence:
PMID:17986282
validated its ability to produce DHT from testosterone, similar to type
|
|
GO:0160198
polyprenal reductase activity
|
EXP
PMID:38821050 A pseudoautosomal glycosylation disorder prompts the revisio... |
ACCEPT |
Summary: Experimental demonstration (Wilson et al. 2024) that SRD5A3 is the NADPH-dependent polyprenal reductase catalyzing the second step of the revised dolichol-biosynthesis pathway (polyprenal to dolichal). This is the core molecular function.
Reason: Direct experimental evidence for the precise current MF term (GO:0160198).
Supporting Evidence:
PMID:38821050
SRD5A3 catalyzes only the second reaction
|
|
GO:0043048
dolichyl monophosphate biosynthetic process
|
IDA
PMID:20637498 SRD5A3 is required for converting polyprenol to dolichol and... |
ACCEPT |
Summary: Direct experimental evidence (Cantagrel et al. 2010) that SRD5A3 is required for converting polyprenol to dolichol, supplying dolichol-phosphate for glycosylation; SRD5A3-deficient cells show reduced dolichol-phosphate-dependent LLO synthesis rescuable by exogenous Dol-P. Core BP.
Reason: Strong IDA evidence for the core dolichyl monophosphate biosynthetic process (note GO:0019408 dolichol biosynthetic process was obsoleted into GO:0043048).
Supporting Evidence:
PMID:20637498
SRD5A3 is necessary for the reduction of the alpha-isoprene unit of polyprenols to form dolichols
|
|
GO:0043048
dolichyl monophosphate biosynthetic process
|
IDA
PMID:38821050 A pseudoautosomal glycosylation disorder prompts the revisio... |
ACCEPT |
Summary: Direct experimental evidence (Wilson et al. 2024) that SRD5A3 acts in dolichol biosynthesis, catalyzing the NADPH-dependent polyprenal-to-dolichal step feeding dolichol/dolichol-phosphate production. Core BP.
Reason: Strong IDA evidence for the core dolichyl monophosphate biosynthetic process in the revised pathway.
Supporting Evidence:
PMID:38821050
SRD5A3 catalyzes only the second reaction
|
|
GO:0005789
endoplasmic reticulum membrane
|
IDA
PMID:20637498 SRD5A3 is required for converting polyprenol to dolichol and... |
ACCEPT |
Summary: Direct experimental evidence that epitope-tagged SRD5A3 localizes predominantly to the ER, where dolichol synthesis and LLO assembly occur. Core localization.
Reason: Experimentally supported active-in ER membrane localization for a multi-pass membrane enzyme.
Supporting Evidence:
PMID:20637498
Epitope tagged SRD5A3 localized predominantly to the ER
|
|
GO:0160198
polyprenal reductase activity
|
IDA
PMID:38821050 A pseudoautosomal glycosylation disorder prompts the revisio... |
ACCEPT |
Summary: Direct experimental evidence (Wilson et al. 2024) for SRD5A3 polyprenal reductase activity, the core molecular function. Duplicates the EXP annotation to the same term.
Reason: Direct experimental support for the precise current MF.
Supporting Evidence:
PMID:38821050
as a NADPH-dependent reductase in two non-consecutive steps
|
|
GO:0047751
3-oxo-5-alpha-steroid 4-dehydrogenase (NADP+) activity
|
IDA
PMID:17986282 Novel 5 alpha-steroid reductase (SRD5A3, type-3) is overexpr... |
MARK AS OVER ANNOTATED |
Summary: Experimental annotation from the discovery paper (Uemura et al. 2008), which showed in-vitro conversion of testosterone to dihydrotestosterone by SRD5A3 overexpressed in prostate-cancer cells. This established the "steroid 5-alpha-reductase 3" naming but reflects a weak, non-physiological side activity; SRD5A3's physiological role is polyprenal reduction in dolichol synthesis.
Reason: Experimental (IDA), so retained rather than removed, but flagged as an over-annotation. The 5-alpha-steroid reductase activity is in-vitro and marginal, and does not represent the enzyme's physiological function (null mutations cause a glycosylation disorder, not androgen deficiency).
Supporting Evidence:
PMID:17986282
validated its ability to produce DHT from testosterone, similar to type
PMID:17986282
resulted in a significant decrease in DHT production and a drastic reduction in cell
|
|
GO:0016628
oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
|
TAS
Reactome:R-HSA-4755572 |
KEEP AS NON CORE |
Summary: Reactome-derived high-level oxidoreductase MF annotation. Correct as a parent class of the polyprenal reductase reaction (NADPH-dependent reduction of a C=C bond) but general.
Reason: Accurate parent term; the specific polyprenal reductase activity (GO:0160198) is the informative core MF.
Supporting Evidence:
PMID:38821050
as a NADPH-dependent reductase in two non-consecutive steps
|
|
GO:0005789
endoplasmic reticulum membrane
|
TAS
Reactome:R-HSA-4755572 |
ACCEPT |
Summary: Reactome-authored ER membrane localization, consistent with the experimental IDA localization. Core localization.
Reason: Correct localization for this multi-pass ER membrane enzyme; duplicates the IDA/IEA ER-membrane annotations.
Supporting Evidence:
PMID:20637498
Epitope tagged SRD5A3 localized predominantly to the ER
|
|
GO:0005789
endoplasmic reticulum membrane
|
TAS
Reactome:R-HSA-9705714 |
ACCEPT |
Summary: Reactome-authored ER membrane localization (from the steroid-reaction module), consistent with experimental data. Core localization.
Reason: Correct ER membrane localization; duplicates other ER-membrane annotations.
Supporting Evidence:
PMID:20637498
Epitope tagged SRD5A3 localized predominantly to the ER
|
|
GO:0005789
endoplasmic reticulum membrane
|
TAS
Reactome:R-HSA-9937295 |
ACCEPT |
Summary: Reactome-authored ER membrane localization (from the revised polyprenal-to-dolichal reaction module), consistent with experimental data. Core localization.
Reason: Correct ER membrane localization; duplicates other ER-membrane annotations.
Supporting Evidence:
PMID:20637498
Epitope tagged SRD5A3 localized predominantly to the ER
|
|
GO:0005783
endoplasmic reticulum
|
IDA
PMID:20637498 SRD5A3 is required for converting polyprenol to dolichol and... |
ACCEPT |
Summary: Direct experimental evidence that epitope-tagged SRD5A3 localizes predominantly to the ER. Correct, though the more specific ER membrane term (GO:0005789) better captures its location as a multi-pass membrane protein.
Reason: Experimentally supported ER localization; the coexisting ER-membrane annotations provide the more specific compartment.
Supporting Evidence:
PMID:20637498
Epitope tagged SRD5A3 localized predominantly to the ER
|
|
GO:0016628
oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
|
IDA
PMID:20637498 SRD5A3 is required for converting polyprenol to dolichol and... |
KEEP AS NON CORE |
Summary: Experimental annotation to a high-level NADP-dependent CH-CH oxidoreductase class, based on the demonstration that SRD5A3 reduces the alpha-isoprene C=C bond of polyprenol to form dolichol. Correct but general.
Reason: Accurate parent term for the reductase activity; the specific polyprenal reductase activity (GO:0160198) is the informative core MF.
Supporting Evidence:
PMID:20637498
SRD5A3 is necessary for the reduction of the alpha-isoprene unit of polyprenols to form dolichols
|
Q: Given the revised pathway (Wilson et al. 2024), is the physiological substrate of SRD5A3 strictly polyprenal, and does it have any residual direct polyprenol-reducing activity in vivo?
Q: Is the in-vitro testosterone-to-dihydrotestosterone activity of SRD5A3 physiologically relevant in any tissue (e.g. prostate cancer), or purely an artifact of overexpression?
Experiment: Structural/biochemical characterization of SRD5A3 with polyprenal versus steroid substrates to quantify catalytic efficiency and confirm the physiological substrate.
Experiment: Tissue-specific conditional knockouts to test whether any androgen/steroid phenotype arises independently of the glycosylation defect.
UniProtKB:Q9H8P0 (SR5A3_HUMAN). HGNC:25812. 318 aa, multi-pass ER membrane protein.
Steroid 5-alpha reductase family, polyprenal/polyprenol reductase subfamily. Yeast
ortholog = DFG10.
SRD5A3 is the ER-membrane, NADPH-dependent reductase that acts in the terminal steps of
de novo dolichol biosynthesis, supplying dolichol → dolichol-phosphate, the lipid
carrier for N-glycosylation. Loss of function causes SRD5A3-CDG (CDG type Iq;
MIM:612379) and Kahrizi syndrome (KHRZ; MIM:612713), with ocular coloboma, cerebellar
vermis hypoplasia, psychomotor/intellectual disability.
Two successive views of the reaction:
- Cantagrel et al. 2010 (PMID:20637498, Cell): SRD5A3 "is necessary for the reduction
of the alpha-isoprene unit of polyprenols to form dolichols, required for synthesis of
dolichol-linked monosaccharides, and the oligosaccharide precursor used for
N-glycosylation" — i.e. the long-sought polyprenol reductase. Epitope-tagged SRD5A3
"localized predominantly to the ER." SRD5A3 was the only member of the human 5α-reductase
family able to rescue the yeast dfg10 CPY-underglycosylation phenotype; H296G mutant is
catalytically dead. Phylogeny suggested the ancestral substrate "was potentially not a
steroid."
- Wilson et al. 2024 (PMID:38821050, Cell): revised the pathway — dolichol synthesis
"requires a three-step detour involving additional metabolites, where SRD5A3 catalyzes
only the second reaction" (the NADPH-dependent reduction of polyprenal → dolichal;
the first/third steps are done by DHRSX). Hence the current MF term is
GO:0160198 polyprenal reductase activity (EC 1.3.1.94; RHEA:80727), and UniProt's
RecName is now "Polyprenal reductase" with a CAUTION note that it was initially
characterised as a polyprenol reductase but "catalyzes an intermediate step in this
pathway and reduce[s] polyprenal."
The gene name ("steroid 5-alpha-reductase 3") and the EC 1.3.1.22 annotation come from
its discovery in prostate cancer:
- Uemura et al. 2008 (PMID:17986282, Cancer Sci): identified SRD5A2L/SRD5A3 as a
"putative 5 alpha-steroid reductase" overexpressed in hormone-refractory prostate cancer;
in-vitro LC-MS/MS validated DHT production from testosterone; H296 mutagenesis abolished
activity. This is the origin of the 3-oxo-5-alpha-steroid 4-dehydrogenase (NADP+)
annotation (GO:0047751 IDA) and the Reactome "SRD5A3 dehydrogenates TEST to DHTEST" /
androgen-biosynthesis TAS annotations.
- Fouad Mansour et al. 2016 (PMID:26855069; NOT cached) is the ECO:0000305 basis for the
UniProt EC 1.3.1.22 steroid catalytic-activity block.
Physiological role is dolichol/glycosylation, NOT steroid metabolism: null patients have
CDG, not an androgen/steroid phenotype; phylogeny argues against a steroid ancestral
substrate; steroid activity is weak/in-vitro. Steroid-5α-reductase / androgen-biosynthesis
GO annotations are therefore treated as MARK_AS_OVER_ANNOTATED (experimental IDA/TAS,
so not REMOVE per policy) except the plainly wrong IEA EC-mapping GO:0047751 via
GO_REF:0000120, which is a demonstrably wrong electronic inference and is REMOVEd.
id: Q9H8P0
gene_symbol: SRD5A3
product_type: PROTEIN
status: INITIALIZED
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: SRD5A3 is an endoplasmic reticulum membrane, NADPH-dependent polyprenal
reductase that acts in the terminal steps of de novo dolichol biosynthesis. In the
currently accepted pathway it catalyzes the reduction of the alpha-isoprene unit
of a di-trans,poly-cis-polyprenal to the corresponding dolichal, an intermediate
in converting polyprenol to dolichol; the resulting dolichol is phosphorylated to
dolichol-phosphate, the essential lipid carrier used to assemble the lipid-linked
oligosaccharide precursor for protein N-linked glycosylation. It is a multi-pass
member of the steroid 5-alpha-reductase family (polyprenal reductase subfamily;
yeast ortholog DFG10). Loss-of-function mutations cause SRD5A3-congenital disorder
of glycosylation (SRD5A3-CDG, CDG type Iq) and Kahrizi syndrome, characterized by
ocular coloboma, cerebellar vermis hypoplasia, and intellectual disability. Despite
its name, SRD5A3 is not a physiological steroid 5-alpha-reductase; a weak in-vitro
testosterone-to-dihydrotestosterone activity was reported at its discovery in prostate
cancer, but its established physiological role is in dolichol synthesis and glycosylation,
not steroid metabolism.
existing_annotations:
- term:
id: GO:0005783
label: endoplasmic reticulum
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: is_active_in
review:
summary: Phylogenetically inferred ER localization, consistent with the experimentally
determined localization of SRD5A3 (an ER-membrane dolichol-pathway enzyme).
action: ACCEPT
reason: SRD5A3 acts in the ER membrane where dolichol biosynthesis and lipid-linked
oligosaccharide assembly occur; this is directly supported experimentally.
supported_by:
- reference_id: PMID:20637498
supporting_text: Epitope tagged SRD5A3 localized predominantly to the ER
- term:
id: GO:0006488
label: dolichol-linked oligosaccharide biosynthetic process
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: Phylogenetically inferred involvement in dolichol-linked oligosaccharide
(LLO) biosynthesis. SRD5A3 supplies dolichol/dolichol-phosphate, the lipid carrier
on which the LLO precursor is built, so this pathway-level BP is appropriate,
though not the most specific reaction SRD5A3 catalyzes.
action: ACCEPT
reason: SRD5A3 is required for LLO synthesis; loss of SRD5A3 severely reduces newly
synthesized LLO and can be rescued by exogenous dolichol-phosphate, placing it
upstream of LLO assembly.
supported_by:
- reference_id: PMID:20637498
supporting_text: SRD5A3 is necessary for the reduction of the alpha-isoprene
unit of polyprenols to form dolichols, required for synthesis of dolichol-linked
monosaccharides, and the oligosaccharide precursor used for N-glycosylation
- term:
id: GO:0160198
label: polyprenal reductase activity
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: enables
review:
summary: Phylogenetically inferred polyprenal reductase activity, the current core
molecular function of SRD5A3. This is the term carried by GOA (polyprenAL reductase
activity, GO:0160198), matching the revised pathway in which SRD5A3 reduces polyprenal
to dolichal rather than polyprenol directly to dolichol.
action: ACCEPT
reason: Represents the core molecular function at the correct current level of
specificity; consistent with the IDA/EXP experimental annotations and UniProt
EC 1.3.1.94.
supported_by:
- reference_id: PMID:38821050
supporting_text: SRD5A3 catalyzes only the second reaction
- term:
id: GO:0043048
label: dolichyl monophosphate biosynthetic process
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: Phylogenetically inferred involvement in dolichyl monophosphate biosynthesis,
the current core biological process for SRD5A3. GO:0019408 (dolichol biosynthetic
process) was obsoleted in favor of GO:0043048, so this is the correct current
BP for the polyprenol-to-dolichol/dolichol-phosphate route.
action: ACCEPT
reason: SRD5A3 catalyzes a committed reductive step supplying dolichol for dolichol-phosphate
synthesis; supported by strong IDA evidence in human cells.
supported_by:
- reference_id: PMID:20637498
supporting_text: SRD5A3 is necessary for the reduction of the alpha-isoprene
unit of polyprenols to form dolichols
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: IEA
original_reference_id: GO_REF:0000044
qualifier: located_in
review:
summary: Electronic mapping from the UniProt subcellular-location keyword. SRD5A3
is a multi-pass ER membrane protein, so this is correct and represents the core
localization.
action: ACCEPT
reason: Consistent with experimental ER localization and the multi-pass membrane
topology annotated in UniProt.
supported_by:
- reference_id: file:human/SRD5A3/SRD5A3-uniprot.txt
supporting_text: 'SUBCELLULAR LOCATION: Endoplasmic reticulum membrane'
- reference_id: file:human/SRD5A3/SRD5A3-uniprot.txt
supporting_text: Multi-pass membrane protein
- term:
id: GO:0006629
label: lipid metabolic process
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: involved_in
review:
summary: Broad InterPro-to-GO mapping. Correct in that SRD5A3 acts in polyisoprenoid
lipid (dolichol) metabolism, but far too general to convey its function.
action: KEEP_AS_NON_CORE
reason: Not wrong but uninformative; the specific dolichyl monophosphate biosynthetic
process (GO:0043048) already captures the lipid-metabolic role more precisely.
supported_by:
- reference_id: file:human/SRD5A3/SRD5A3-uniprot.txt
supporting_text: 'PATHWAY: Protein modification; protein glycosylation'
- term:
id: GO:0016627
label: oxidoreductase activity, acting on the CH-CH group of donors
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: InterPro-to-GO mapping to a high-level oxidoreductase class. SRD5A3 is
an NADPH-dependent reductase that reduces a C=C double bond (the alpha-isoprene
unit), so this parent term is correct but general.
action: KEEP_AS_NON_CORE
reason: Accurate but non-specific; the specific polyprenal reductase activity (GO:0160198)
is the informative core MF.
supported_by:
- reference_id: PMID:38821050
supporting_text: as a NADPH-dependent reductase in two non-consecutive steps
- term:
id: GO:0043048
label: dolichyl monophosphate biosynthetic process
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: involved_in
review:
summary: InterPro-to-GO mapping (IPR039698, Dfg10/SRD5A3) to dolichyl monophosphate
biosynthesis. This matches the experimentally supported core BP.
action: ACCEPT
reason: Correct BP for the SRD5A3/Dfg10 family; duplicates the IDA/IBA annotations
to the same term.
supported_by:
- reference_id: PMID:20637498
supporting_text: required for synthesis of dolichol-linked monosaccharides, and
the oligosaccharide precursor used for N-glycosylation
- term:
id: GO:0047751
label: 3-oxo-5-alpha-steroid 4-dehydrogenase (NADP+) activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: enables
review:
summary: Electronic annotation derived from the EC 1.3.1.22 (steroid) mapping via
RHEA/EC (GO_REF:0000120). SRD5A3 is not a physiological steroid 5-alpha-reductase;
its established function is polyprenal reduction in dolichol synthesis. The steroid
EC was assigned on the basis of the gene name and weak in-vitro activity, and
this purely electronic EC-mapping is a wrong inference of the enzyme's biological
function.
action: REMOVE
reason: Demonstrably wrong electronic EC/RHEA-to-GO inference. Physiological substrate
is polyprenal, not a steroid; null patients have a congenital disorder of glycosylation,
not a steroid/androgen phenotype, and phylogeny argues the ancestral substrate
was not a steroid. Per policy, wrong IEA EC-mappings are appropriate REMOVE targets.
supported_by:
- reference_id: PMID:20637498
supporting_text: suggesting that the substrate of the enzyme encoded by the common
ancestral gene was potentially not a steroid
- term:
id: GO:0160198
label: polyprenal reductase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: enables
review:
summary: Electronic annotation from EC 1.3.1.94 (RHEA:80727) mapping. This is the
correct core molecular function, matching the experimental annotations and UniProt
RecName (Polyprenal reductase).
action: ACCEPT
reason: Correct EC-based mapping to the physiological reaction; corroborates the
IDA/EXP/IBA annotations to GO:0160198.
supported_by:
- reference_id: file:human/SRD5A3/SRD5A3-uniprot.txt
supporting_text: EC=1.3.1.94
- term:
id: GO:0006488
label: dolichol-linked oligosaccharide biosynthetic process
evidence_type: IEA
original_reference_id: GO_REF:0000107
qualifier: involved_in
review:
summary: Orthology-based transfer (Ensembl Compara) from mouse Srd5a3 of the LLO
biosynthesis BP. Consistent with the human experimental data and the IBA annotation
to the same term.
action: ACCEPT
reason: Correct pathway-level BP inferred from a well-supported ortholog; duplicates
the IBA annotation.
supported_by:
- reference_id: PMID:20637498
supporting_text: the oligosaccharide precursor used for N-glycosylation
- term:
id: GO:0006702
label: androgen biosynthetic process
evidence_type: TAS
original_reference_id: Reactome:R-HSA-193048
qualifier: involved_in
review:
summary: Reactome-derived annotation placing SRD5A3 in androgen biosynthesis, based
on the prostate-cancer report that SRD5A3 can convert testosterone to dihydrotestosterone
in vitro (Uemura et al. 2008). SRD5A3 is named a steroid 5-alpha-reductase and
shows weak in-vitro DHT-forming activity, but its physiological function is dolichol
synthesis, not androgen metabolism; this is an over-annotation of a marginal
side activity.
action: MARK_AS_OVER_ANNOTATED
reason: The steroid/androgen activity is weak, in-vitro, and derives from the gene
name and the context of its discovery in hormone-refractory prostate cancer;
loss-of-function causes a glycosylation disorder, not an androgen-deficiency phenotype.
Retained (experimental basis, TAS) but flagged as over-annotation rather than
removed.
supported_by:
- reference_id: PMID:17986282
supporting_text: validated its ability to produce DHT from testosterone, similar
to type
- term:
id: GO:0043048
label: dolichyl monophosphate biosynthetic process
evidence_type: TAS
original_reference_id: Reactome:R-HSA-446199
qualifier: involved_in
review:
summary: Reactome-authored annotation (Synthesis of dolichyl-phosphate) to the
core dolichyl monophosphate biosynthetic process. Consistent with the experimental
and IBA annotations.
action: ACCEPT
reason: Correct core BP; duplicates the IDA/IBA/IEA annotations to GO:0043048.
supported_by:
- reference_id: PMID:20637498
supporting_text: SRD5A3 is necessary for the reduction of the alpha-isoprene
unit of polyprenols to form dolichols
- term:
id: GO:0003865
label: 3-oxo-5-alpha-steroid 4-dehydrogenase activity
evidence_type: TAS
original_reference_id: Reactome:R-HSA-9705714
qualifier: enables
review:
summary: Reactome-derived steroid 5-alpha-reductase MF annotation (SRD5A3 dehydrogenates
TEST to DHTEST), tracing to the in-vitro testosterone-to-DHT activity of Uemura
et al. 2008. This is a weak, non-physiological side activity and an over-annotation
relative to the enzyme's dolichol-pathway function.
action: MARK_AS_OVER_ANNOTATED
reason: Steroid 5-alpha-reductase activity is in-vitro and marginal; SRD5A3 is
physiologically a polyprenal reductase. Retained (TAS/experimental origin) but
flagged as over-annotation, not removed.
supported_by:
- reference_id: PMID:17986282
supporting_text: validated its ability to produce DHT from testosterone, similar
to type
- term:
id: GO:0160198
label: polyprenal reductase activity
evidence_type: EXP
original_reference_id: PMID:38821050
qualifier: enables
review:
summary: Experimental demonstration (Wilson et al. 2024) that SRD5A3 is the NADPH-dependent
polyprenal reductase catalyzing the second step of the revised dolichol-biosynthesis
pathway (polyprenal to dolichal). This is the core molecular function.
action: ACCEPT
reason: Direct experimental evidence for the precise current MF term (GO:0160198).
supported_by:
- reference_id: PMID:38821050
supporting_text: SRD5A3 catalyzes only the second reaction
- term:
id: GO:0043048
label: dolichyl monophosphate biosynthetic process
evidence_type: IDA
original_reference_id: PMID:20637498
qualifier: involved_in
review:
summary: Direct experimental evidence (Cantagrel et al. 2010) that SRD5A3 is required
for converting polyprenol to dolichol, supplying dolichol-phosphate for glycosylation;
SRD5A3-deficient cells show reduced dolichol-phosphate-dependent LLO synthesis
rescuable by exogenous Dol-P. Core BP.
action: ACCEPT
reason: Strong IDA evidence for the core dolichyl monophosphate biosynthetic process
(note GO:0019408 dolichol biosynthetic process was obsoleted into GO:0043048).
supported_by:
- reference_id: PMID:20637498
supporting_text: SRD5A3 is necessary for the reduction of the alpha-isoprene
unit of polyprenols to form dolichols
- term:
id: GO:0043048
label: dolichyl monophosphate biosynthetic process
evidence_type: IDA
original_reference_id: PMID:38821050
qualifier: involved_in
review:
summary: Direct experimental evidence (Wilson et al. 2024) that SRD5A3 acts in
dolichol biosynthesis, catalyzing the NADPH-dependent polyprenal-to-dolichal
step feeding dolichol/dolichol-phosphate production. Core BP.
action: ACCEPT
reason: Strong IDA evidence for the core dolichyl monophosphate biosynthetic process
in the revised pathway.
supported_by:
- reference_id: PMID:38821050
supporting_text: SRD5A3 catalyzes only the second reaction
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: IDA
original_reference_id: PMID:20637498
qualifier: is_active_in
review:
summary: Direct experimental evidence that epitope-tagged SRD5A3 localizes predominantly
to the ER, where dolichol synthesis and LLO assembly occur. Core localization.
action: ACCEPT
reason: Experimentally supported active-in ER membrane localization for a multi-pass
membrane enzyme.
supported_by:
- reference_id: PMID:20637498
supporting_text: Epitope tagged SRD5A3 localized predominantly to the ER
- term:
id: GO:0160198
label: polyprenal reductase activity
evidence_type: IDA
original_reference_id: PMID:38821050
qualifier: enables
review:
summary: Direct experimental evidence (Wilson et al. 2024) for SRD5A3 polyprenal
reductase activity, the core molecular function. Duplicates the EXP annotation
to the same term.
action: ACCEPT
reason: Direct experimental support for the precise current MF.
supported_by:
- reference_id: PMID:38821050
supporting_text: as a NADPH-dependent reductase in two non-consecutive steps
- term:
id: GO:0047751
label: 3-oxo-5-alpha-steroid 4-dehydrogenase (NADP+) activity
evidence_type: IDA
original_reference_id: PMID:17986282
qualifier: enables
review:
summary: Experimental annotation from the discovery paper (Uemura et al. 2008),
which showed in-vitro conversion of testosterone to dihydrotestosterone by SRD5A3
overexpressed in prostate-cancer cells. This established the "steroid 5-alpha-reductase
3" naming but reflects a weak, non-physiological side activity; SRD5A3's physiological
role is polyprenal reduction in dolichol synthesis.
action: MARK_AS_OVER_ANNOTATED
reason: Experimental (IDA), so retained rather than removed, but flagged as an
over-annotation. The 5-alpha-steroid reductase activity is in-vitro and marginal,
and does not represent the enzyme's physiological function (null mutations cause
a glycosylation disorder, not androgen deficiency).
supported_by:
- reference_id: PMID:17986282
supporting_text: validated its ability to produce DHT from testosterone, similar
to type
- reference_id: PMID:17986282
supporting_text: resulted in a significant decrease in DHT production and a drastic
reduction in cell
- term:
id: GO:0016628
label: oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP
as acceptor
evidence_type: TAS
original_reference_id: Reactome:R-HSA-4755572
qualifier: enables
review:
summary: Reactome-derived high-level oxidoreductase MF annotation. Correct as a
parent class of the polyprenal reductase reaction (NADPH-dependent reduction
of a C=C bond) but general.
action: KEEP_AS_NON_CORE
reason: Accurate parent term; the specific polyprenal reductase activity (GO:0160198)
is the informative core MF.
supported_by:
- reference_id: PMID:38821050
supporting_text: as a NADPH-dependent reductase in two non-consecutive steps
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: TAS
original_reference_id: Reactome:R-HSA-4755572
qualifier: located_in
review:
summary: Reactome-authored ER membrane localization, consistent with the experimental
IDA localization. Core localization.
action: ACCEPT
reason: Correct localization for this multi-pass ER membrane enzyme; duplicates
the IDA/IEA ER-membrane annotations.
supported_by:
- reference_id: PMID:20637498
supporting_text: Epitope tagged SRD5A3 localized predominantly to the ER
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: TAS
original_reference_id: Reactome:R-HSA-9705714
qualifier: located_in
review:
summary: Reactome-authored ER membrane localization (from the steroid-reaction
module), consistent with experimental data. Core localization.
action: ACCEPT
reason: Correct ER membrane localization; duplicates other ER-membrane annotations.
supported_by:
- reference_id: PMID:20637498
supporting_text: Epitope tagged SRD5A3 localized predominantly to the ER
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: TAS
original_reference_id: Reactome:R-HSA-9937295
qualifier: located_in
review:
summary: Reactome-authored ER membrane localization (from the revised polyprenal-to-dolichal
reaction module), consistent with experimental data. Core localization.
action: ACCEPT
reason: Correct ER membrane localization; duplicates other ER-membrane annotations.
supported_by:
- reference_id: PMID:20637498
supporting_text: Epitope tagged SRD5A3 localized predominantly to the ER
- term:
id: GO:0005783
label: endoplasmic reticulum
evidence_type: IDA
original_reference_id: PMID:20637498
qualifier: located_in
review:
summary: Direct experimental evidence that epitope-tagged SRD5A3 localizes predominantly
to the ER. Correct, though the more specific ER membrane term (GO:0005789) better
captures its location as a multi-pass membrane protein.
action: ACCEPT
reason: Experimentally supported ER localization; the coexisting ER-membrane annotations
provide the more specific compartment.
supported_by:
- reference_id: PMID:20637498
supporting_text: Epitope tagged SRD5A3 localized predominantly to the ER
- term:
id: GO:0016628
label: oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP
as acceptor
evidence_type: IDA
original_reference_id: PMID:20637498
qualifier: enables
review:
summary: Experimental annotation to a high-level NADP-dependent CH-CH oxidoreductase
class, based on the demonstration that SRD5A3 reduces the alpha-isoprene C=C
bond of polyprenol to form dolichol. Correct but general.
action: KEEP_AS_NON_CORE
reason: Accurate parent term for the reductase activity; the specific polyprenal
reductase activity (GO:0160198) is the informative core MF.
supported_by:
- reference_id: PMID:20637498
supporting_text: SRD5A3 is necessary for the reduction of the alpha-isoprene
unit of polyprenols to form dolichols
core_functions:
- description: NADPH-dependent polyprenal reductase acting in the terminal steps of
de novo dolichol biosynthesis, reducing the alpha-isoprene unit of di-trans,poly-cis-polyprenal
to the corresponding dolichal en route to dolichol
molecular_function:
id: GO:0160198
label: polyprenal reductase activity
directly_involved_in:
- id: GO:0043048
label: dolichyl monophosphate biosynthetic process
locations:
- id: GO:0005789
label: endoplasmic reticulum membrane
supported_by:
- reference_id: PMID:38821050
supporting_text: SRD5A3 catalyzes only the second reaction
- reference_id: PMID:20637498
supporting_text: SRD5A3 is necessary for the reduction of the alpha-isoprene unit
of polyprenols to form dolichols
- description: Supplies dolichol/dolichol-phosphate, the lipid carrier used to build
the lipid-linked oligosaccharide precursor, thereby enabling protein N-linked glycosylation
molecular_function:
id: GO:0160198
label: polyprenal reductase activity
directly_involved_in:
- id: GO:0006488
label: dolichol-linked oligosaccharide biosynthetic process
locations:
- id: GO:0005789
label: endoplasmic reticulum membrane
supported_by:
- reference_id: PMID:20637498
supporting_text: required for synthesis of dolichol-linked monosaccharides, and
the oligosaccharide precursor used for N-glycosylation
proposed_new_terms: []
suggested_questions:
- question: Given the revised pathway (Wilson et al. 2024), is the physiological substrate
of SRD5A3 strictly polyprenal, and does it have any residual direct polyprenol-reducing
activity in vivo?
- question: Is the in-vitro testosterone-to-dihydrotestosterone activity of SRD5A3
physiologically relevant in any tissue (e.g. prostate cancer), or purely an artifact
of overexpression?
suggested_experiments:
- description: Structural/biochemical characterization of SRD5A3 with polyprenal versus
steroid substrates to quantify catalytic efficiency and confirm the physiological
substrate.
- description: Tissue-specific conditional knockouts to test whether any androgen/steroid
phenotype arises independently of the glycosylation defect.
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO
terms
findings: []
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings: []
- id: GO_REF:0000044
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
vocabulary mapping, accompanied by conservative changes to GO terms applied by
UniProt
findings: []
- id: GO_REF:0000107
title: Automatic transfer of experimentally verified manual GO annotation data to
orthologs using Ensembl Compara
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: PMID:17986282
title: Novel 5 alpha-steroid reductase (SRD5A3, type-3) is overexpressed in hormone-refractory
prostate cancer.
findings: []
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: PubMed-verified discovery paper; establishes the steroid 5-alpha-reductase
naming and in-vitro testosterone-to-DHT activity, which is a weak side activity
rather than the physiological function. Supports the steroid annotations flagged
as over-annotated.
- id: PMID:20637498
title: SRD5A3 is required for converting polyprenol to dolichol and is mutated in
a congenital glycosylation disorder.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: Landmark paper identifying SRD5A3 as the polyprenol reductase required
for dolichol synthesis and N-glycosylation; establishes ER localization and SRD5A3-CDG.
- id: PMID:38821050
title: A pseudoautosomal glycosylation disorder prompts the revision of dolichol
biosynthesis.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: Revises the pathway; shows SRD5A3 catalyzes the second (polyprenal-to-dolichal)
NADPH-dependent reduction step, supporting the GO:0160198 polyprenal reductase
MF term.
- id: Reactome:R-HSA-193048
title: Androgen biosynthesis
findings: []
- id: Reactome:R-HSA-446199
title: Synthesis of dolichyl-phosphate
findings: []
- id: Reactome:R-HSA-4755572
title: Defective SRD5A3 does not reduce pPNOL to DCHOL
findings: []
- id: Reactome:R-HSA-9705714
title: SRD5A3 dehydrogenates TEST to DHTEST
findings: []
- id: Reactome:R-HSA-9937295
title: SRD5A3 reduces polyprenal to dolichal
findings: []
- id: file:human/SRD5A3/SRD5A3-uniprot.txt
title: UniProtKB Q9H8P0 (SR5A3_HUMAN) record
findings: []