PFAS encodes phosphoribosylformylglycinamidine synthase (FGAM synthase; also called FGAR amidotransferase, FGARAT; EC 6.3.5.3), the enzyme that carries out the fourth step of de novo purine synthesis. It catalyses the ATP-dependent, glutamine-dependent amidotransfer that converts formylglycinamide ribonucleotide (FGAR) to formylglycinamidine ribonucleotide (FGAM), releasing L-glutamate, ADP and phosphate (FGAR + L-glutamine + ATP + H2O -> FGAM + L-glutamate + ADP + Pi). The multidomain protein combines an N-terminal ATP-/Mg2+-dependent synthetase (PurL) region with a C-terminal class-I glutamine amidotransferase (GATase-1) domain that hydrolyses glutamine to supply the transferred amide nitrogen. The enzyme is cytosolic and can associate with the purinosome, the reversible multi-enzyme assembly of de novo purine synthesis. As one of the six enzymes of this housekeeping pathway it supplies the inosine monophosphate (IMP) precursor from which AMP and GMP are subsequently made, and its activity is of interest in the elevated nucleotide demand of proliferating and cancer cells.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0005737
cytoplasm
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetically inferred cytoplasmic localization for this cytosolic de novo purine synthesis enzyme. Consistent with the UniProt subcellular location and with Reactome's cytosol assignment.
Reason: PFAS is a soluble cytosolic enzyme with no membrane-spanning or targeting features; the IBA cytoplasm annotation is correct, though the more specific cytosol term (GO:0005829) is preferable as the primary localization.
Supporting Evidence:
file:human/PFAS/PFAS-uniprot.txt
SUBCELLULAR LOCATION: Cytoplasm
Reactome:R-HSA-73812
Fluoresence microscopy studies of cultured human cells have shown that the enzyme is cytosolic
|
|
GO:0004642
phosphoribosylformylglycinamidine synthase activity
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetically inferred phosphoribosylformylglycinamidine synthase (FGAM synthase) activity, the defining molecular function of PFAS and its orthologs across the FGAMS family.
Reason: This is the core molecular function of PFAS, EC 6.3.5.3 (RHEA:17129), independently supported by direct biochemical evidence (IDA) and by the conserved N-terminal PurL synthetase plus C-terminal GATase-1 domain architecture in UniProt.
Supporting Evidence:
file:human/PFAS/PFAS-uniprot.txt
RecName: Full=Phosphoribosylformylglycinamidine synthase;
file:human/PFAS/PFAS-uniprot.txt
purines biosynthetic pathway. Catalyzes the ATP-dependent conversion of
|
|
GO:0006164
purine nucleotide biosynthetic process
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetically inferred involvement in purine nucleotide biosynthesis, the pathway to which the FGAM synthase reaction belongs.
Reason: Correct parent biological process. PFAS performs step four of de novo purine synthesis, producing the IMP precursor from which purine nucleotides are made. This broad term is accurate; the more specific 'de novo IMP biosynthetic process' (GO:0006189) is also annotated and captured as core.
Supporting Evidence:
PMID:10548741
phosphoribosylformylglycineamide amidotransferase (FGARAT) gene, which encodes the fourth step of this pathway
|
|
GO:0004642
phosphoribosylformylglycinamidine synthase activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Electronic assignment of FGAM synthase activity from InterPro/EC/RHEA mappings (IPR010073, EC 6.3.5.3, RHEA:17129).
Reason: Correct and specific. The InterPro-to-GO and EC mappings identify the exact catalytic function, in agreement with the IBA, TAS and IDA annotations of the same term.
Supporting Evidence:
file:human/PFAS/PFAS-uniprot.txt
RecName: Full=Phosphoribosylformylglycinamidine synthase;
|
|
GO:0005737
cytoplasm
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: Electronic cytoplasm localization from the UniProt subcellular-location keyword mapping (SL-0086).
Reason: Consistent with the manually asserted cytoplasmic/cytosolic localization; correct though less specific than cytosol.
Supporting Evidence:
file:human/PFAS/PFAS-uniprot.txt
SUBCELLULAR LOCATION: Cytoplasm
|
|
GO:0006189
'de novo' IMP biosynthetic process
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Electronic assignment (InterPro IPR010073, UniPathway UPA00074) placing PFAS in the de novo IMP biosynthetic pathway.
Reason: This is the specific and correct biological process for PFAS: the FGAR->FGAM step is part of the de novo pathway that builds IMP. Concordant with the IDA and NAS annotations of the same term.
Supporting Evidence:
file:human/PFAS/PFAS-uniprot.txt
IMP biosynthesis via de novo pathway
PMID:10548741
The de-novo synthesis of purines requires 10 enzymatic steps for the production of inosine monophosphate (IMP)
|
|
GO:0006541
L-glutamine metabolic process
|
IEA
GO_REF:0000107 |
KEEP AS NON CORE |
Summary: Electronic annotation transferred from a rat ortholog (UniProtKB:D4AB17) capturing that PFAS consumes L-glutamine as the amide-nitrogen donor for the amidotransfer reaction.
Reason: Biologically reasonable - the C-terminal glutamine amidotransferase (GATase-1) domain hydrolyses glutamine to supply the transferred nitrogen, so PFAS participates in glutamine catabolism as a side/co-substrate process. However this is a consequence of the catalytic mechanism rather than the enzyme's core role, which is purine (IMP-precursor) biosynthesis; retain as non-core.
Supporting Evidence:
file:human/PFAS/PFAS-uniprot.txt
ATP-binding; Cytoplasm; Glutamine amidotransferase; Ligase; Magnesium;
|
|
GO:0009410
response to xenobiotic stimulus
|
IEA
GO_REF:0000107 |
MARK AS OVER ANNOTATED |
Summary: Electronic annotation transferred from a rat ortholog (UniProtKB:D4AB17, ENSRNOP00000007087) via Ensembl Compara.
Reason: This term reflects a downstream expression/response phenotype observed for the rodent ortholog and does not describe the molecular or biosynthetic role of PFAS. For a housekeeping de novo purine synthesis enzyme this is an over-annotation transferred electronically from an ortholog; it is not a core function of human PFAS and there is no direct evidence for it in this gene.
|
|
GO:0009168
purine ribonucleoside monophosphate biosynthetic process
|
TAS
Reactome:R-HSA-73817 |
ACCEPT |
Summary: Reactome pathway-level assertion that PFAS participates in purine ribonucleoside monophosphate (IMP) biosynthesis.
Reason: Correct pathway-level process. Reactome places the FGAR->FGAM reaction within the pathway that assembles IMP on PRPP; equivalent in scope to the de novo IMP biosynthetic process term.
Supporting Evidence:
Reactome:R-HSA-73817
The purine ribonucleotide inosine 5'-monophosphate (IMP) is assembled on 5-phospho-alpha-D-ribose 1-diphosphate (PRPP)
|
|
GO:0004642
phosphoribosylformylglycinamidine synthase activity
|
TAS
Reactome:R-HSA-73812 |
ACCEPT |
Summary: Reactome traceable assertion of FGAM synthase activity, citing the biochemically characterized human enzyme reaction FGAR + L-glutamine + ATP + H2O -> FGAM + L-glutamate + ADP + Pi.
Reason: Core molecular function, supported by the purified/characterized human enzyme and concordant with the IDA, IBA and IEA annotations of the same term.
Supporting Evidence:
Reactome:R-HSA-73812
is catalyzed by phosphoribosylformylglycinamidine synthetase. The human enzyme has been purified and characterized biochemically
|
|
GO:0004642
phosphoribosylformylglycinamidine synthase activity
|
IMP
PMID:27590927 CRISPR-Cas9 induced mutations along de novo purine synthesis... |
ACCEPT |
Summary: FGAM synthase activity inferred from a CRISPR-Cas9 PFAS knockout in HeLa cells, in which loss of the enzyme causes accumulation of its substrate.
Reason: MGI experimental (IMP) annotation. The knockout phenotype - accumulation of the enzyme's substrate - directly implicates PFAS in the FGAR->FGAM step, supporting the core molecular function. The cached record is abstract-only; the full text (which the curator read) assays this DNPS step. Concordant with the independent IDA annotation.
Supporting Evidence:
PMID:27590927
In all model cell lines with the exception of one, an accumulation of the substrate(s) for the knocked out enzyme was identified
|
|
GO:0006177
GMP biosynthetic process
|
IMP
PMID:27590927 CRISPR-Cas9 induced mutations along de novo purine synthesis... |
KEEP AS NON CORE |
Summary: From the CRISPR knockout study; loss of PFAS depletes de novo purine synthesis and thereby the downstream GMP branch.
Reason: PFAS acts upstream of GMP synthesis - it makes the IMP precursor, from which GMP is subsequently derived - so the acts_upstream_of_or_within qualifier is appropriate. It is not itself a GMP-biosynthesis enzyme, so this is a valid but non-core downstream-branch annotation.
Supporting Evidence:
PMID:27590927
CRISPR-Cas9 genome-edited HeLa cells deficient for the individual steps of DNPS
|
|
GO:0006189
'de novo' IMP biosynthetic process
|
IMP
PMID:27590927 CRISPR-Cas9 induced mutations along de novo purine synthesis... |
ACCEPT |
Summary: CRISPR knockout evidence that PFAS is required for de novo IMP biosynthesis, the pathway it directly participates in.
Reason: Core biological process, experimentally supported. Loss of PFAS blocks flux through de novo purine synthesis toward IMP; concordant with the involved_in IDA/NAS annotations of the same term.
Supporting Evidence:
PMID:27590927
DNPS includes ten reactions catalysed by six enzymes.
|
|
GO:0044208
'de novo' AMP biosynthetic process
|
IMP
PMID:27590927 CRISPR-Cas9 induced mutations along de novo purine synthesis... |
KEEP AS NON CORE |
Summary: From the CRISPR knockout study; loss of PFAS depletes de novo purine synthesis and thereby the downstream AMP branch.
Reason: PFAS acts upstream of AMP synthesis by supplying the shared IMP precursor; the acts_upstream_of_or_within qualifier is correct. It is not itself an AMP-biosynthesis enzyme, so this is a valid but non-core downstream-branch annotation.
Supporting Evidence:
PMID:27590927
CRISPR-Cas9 genome-edited HeLa cells deficient for the individual steps of DNPS
|
|
GO:0097294
'de novo' XMP biosynthetic process
|
IMP
PMID:27590927 CRISPR-Cas9 induced mutations along de novo purine synthesis... |
KEEP AS NON CORE |
Summary: From the CRISPR knockout study; loss of PFAS depletes de novo purine synthesis and thereby the downstream XMP branch.
Reason: PFAS acts upstream of XMP synthesis by supplying the shared IMP precursor; the acts_upstream_of_or_within qualifier is correct. It is not itself an XMP-biosynthesis enzyme, so this is a valid but non-core downstream-branch annotation.
Supporting Evidence:
PMID:27590927
CRISPR-Cas9 genome-edited HeLa cells deficient for the individual steps of DNPS
|
|
GO:0097294
'de novo' XMP biosynthetic process
|
IDA
PMID:27590927 CRISPR-Cas9 induced mutations along de novo purine synthesis... |
KEEP AS NON CORE |
Summary: Direct-assay (IDA) annotation to the downstream de novo XMP branch, from the DNPS substrate-accumulation study.
Reason: With the involved_in qualifier this term is arguably too downstream for PFAS, whose direct reaction produces the IMP precursor rather than XMP. The corresponding acts_upstream_of_or_within annotation captures the relationship more accurately. Retained as non-core; deferring to the MGI curator's full-text reading rather than removing an experimental annotation.
Supporting Evidence:
PMID:27590927
an accumulation of the substrate(s) for the knocked out enzyme was identified
|
|
GO:0004642
phosphoribosylformylglycinamidine synthase activity
|
IDA
PMID:27590927 CRISPR-Cas9 induced mutations along de novo purine synthesis... |
ACCEPT |
Summary: Direct experimental evidence for FGAM synthase activity from the CRISPR/substrate- accumulation study.
Reason: Core molecular function with direct experimental support; concordant with the IMP, IBA, IEA and Reactome-TAS annotations of the same term.
Supporting Evidence:
PMID:27590927
an accumulation of the substrate(s) for the knocked out enzyme was identified
|
|
GO:0006177
GMP biosynthetic process
|
IDA
PMID:27590927 CRISPR-Cas9 induced mutations along de novo purine synthesis... |
KEEP AS NON CORE |
Summary: Direct-assay (IDA) involved_in annotation to the downstream GMP branch.
Reason: As with the AMP/XMP branch terms, PFAS supplies the upstream IMP precursor rather than catalysing GMP synthesis; the acts_upstream_of_or_within relationship is more accurate than involved_in. Retained as non-core; not removed, as this is an experimental annotation whose full text the curator read.
Supporting Evidence:
PMID:27590927
an accumulation of the substrate(s) for the knocked out enzyme was identified
|
|
GO:0006189
'de novo' IMP biosynthetic process
|
IDA
PMID:27590927 CRISPR-Cas9 induced mutations along de novo purine synthesis... |
ACCEPT |
Summary: Direct-assay evidence that PFAS is involved in de novo IMP biosynthesis.
Reason: Core biological process. This is the pathway PFAS directly participates in (step four), and involved_in is the correct qualifier. Concordant with the IEA, NAS and Reactome annotations.
Supporting Evidence:
PMID:27590927
DNPS includes ten reactions catalysed by six enzymes.
|
|
GO:0044208
'de novo' AMP biosynthetic process
|
IDA
PMID:27590927 CRISPR-Cas9 induced mutations along de novo purine synthesis... |
KEEP AS NON CORE |
Summary: Direct-assay (IDA) involved_in annotation to the downstream de novo AMP branch.
Reason: PFAS makes the shared IMP precursor upstream of AMP synthesis; involved_in is arguably too downstream, and the acts_upstream_of_or_within annotation captures the relationship better. Retained as valid but non-core; not removed given experimental support.
Supporting Evidence:
PMID:27590927
an accumulation of the substrate(s) for the knocked out enzyme was identified
|
|
GO:0070062
extracellular exosome
|
HDA
PMID:20458337 MHC class II-associated proteins in B-cell exosomes and pote... |
MARK AS OVER ANNOTATED |
Summary: High-throughput MS detection of PFAS among 539 proteins in the total proteome of purified B-cell-derived exosomes.
Reason: This is a bulk mass-spectrometry catalog of an exosome preparation, not a targeted or functionally meaningful localization for a cytosolic de novo purine synthesis enzyme. Abundant cytosolic proteins are routinely detected in such exosome proteomes; there is no evidence of a functional role for PFAS in exosomes. Over-annotation - the enzyme acts in the cytosol.
Supporting Evidence:
PMID:20458337
we first analyzed the total proteome of highly purified B cell-derived exosomes using sensitive and accurate mass spectrometry (MS), and identified 539 proteins
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-73812 |
ACCEPT |
Summary: Reactome traceable assertion that the enzyme is cytosolic, from fluorescence microscopy of cultured human cells.
Reason: Most specific and accurate cellular-component annotation for PFAS. Cytosolic localization is consistent with the enzyme's role in de novo purine synthesis and with its reversible association with the cytosolic purinosome.
Supporting Evidence:
Reactome:R-HSA-73812
Fluoresence microscopy studies of cultured human cells have shown that the enzyme is cytosolic
|
|
GO:0004642
phosphoribosylformylglycinamidine synthase activity
|
IDA
PMID:10548741 Human phosphoribosylformylglycineamide amidotransferase (FGA... |
ACCEPT |
Summary: Direct experimental evidence for FGAM synthase (FGARAT) activity: the human genomic clone corrects the purine auxotrophy and enzyme/protein deficiency of AdeB CHO mutants that lack FGARAT.
Reason: Core molecular function established by functional complementation. Restoring FGARAT activity in an enzyme-deficient mammalian cell line directly demonstrates the catalytic function of the encoded protein.
Supporting Evidence:
PMID:10548741
The P1 clone corrects the purine auxotrophy and protein deficiency of Chinese hamster ovary (CHO) cell mutants (AdeB) deficient in both the activity and the protein for FGARAT.
|
|
GO:0006189
'de novo' IMP biosynthetic process
|
NAS
PMID:10548741 Human phosphoribosylformylglycineamide amidotransferase (FGA... |
ACCEPT |
Summary: Non-traceable author statement placing FGARAT/PFAS as the fourth of the ten enzymatic steps producing IMP by de novo purine synthesis.
Reason: Core biological process, consistent with the specific and correct pathway role of PFAS and concordant with the IEA/IDA annotations of the same term.
Supporting Evidence:
PMID:10548741
phosphoribosylformylglycineamide amidotransferase (FGARAT) gene, which encodes the fourth step of this pathway
|
Q: Does PFAS have any moonlighting or regulatory function beyond de novo purine synthesis (e.g. in stress-granule/CD-CODE contexts or via its multiple phosphosites)?
Q: How does purinosome association modulate PFAS flux, and is the enzyme rate-limiting under conditions of high purine demand such as tumor proliferation?
Experiment: Quantitative metabolic-flux analysis (LC-MS/MS of FGAR vs FGAM) in PFAS-null versus rescued cells to confirm the in vivo FGAR->FGAM step and measure control strength.
Experiment: Phospho-site mutagenesis (Ser215/Ser569/Thr619/Thr623) to test whether phosphorylation regulates PFAS activity or purinosome recruitment.
PUR4_HUMAN, O15067. HGNC:8863. EC 6.3.5.3.enables GO:0004642) and NAS BP (de novo IMP) annotations.Core: MF GO:0004642 (FGAM synthase activity); BP GO:0006189 (de novo IMP biosynthesis) and
GO:0006164 (purine nucleotide biosynthetic process); CC GO:0005829 (cytosol).
GO:0004642 MF (IBA, IEA, TAS x1, IMP, IDA x2): ACCEPT — well-supported core MF.GO:0005737 cytoplasm (IBA, IEA): ACCEPT.GO:0005829 cytosol (TAS Reactome): ACCEPT — most specific correct CC.GO:0006189 de novo IMP (IBA-absent; IEA, IMP, IDA, NAS): ACCEPT core BP.GO:0006164 purine nucleotide biosynthetic process (IBA): ACCEPT (broader parent, correct).GO:0006541 L-glutamine metabolic process (IEA, Ensembl ortholog): KEEP_AS_NON_CORE — trueGO:0009410 response to xenobiotic stimulus (IEA, Ensembl rat ortholog): MARK_AS_OVER_ANNOTATED —GO:0009168 purine ribonucleoside monophosphate biosynthesis (TAS Reactome): ACCEPT (pathway-level).GO:0006177 GMP biosynthetic process (IMP acts_upstream_of_or_within; IDA involved_in):GO:0044208 de novo AMP biosynthesis (IMP, IDA): KEEP_AS_NON_CORE — downstream branch (IMP→AMP).GO:0097294 de novo XMP biosynthesis (IMP, IDA): KEEP_AS_NON_CORE — downstream branch (IMP→XMP).GO:0070062 extracellular exosome (HDA): MARK_AS_OVER_ANNOTATED — bulk MS catalog, not aDownstream-branch BPs (GMP/AMP/XMP) capture that loss of PFAS depletes all purine nucleotides
(acts_upstream_of_or_within is the correct qualifier), but the enzyme's own reaction is upstream at
the IMP-precursor step, so these are non-core. Per policy, experimental (IMP/IDA/HDA) annotations
whose full text is uncached are not REMOVEd.
id: O15067
gene_symbol: PFAS
product_type: PROTEIN
status: INITIALIZED
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: >-
PFAS encodes phosphoribosylformylglycinamidine synthase (FGAM synthase; also called
FGAR amidotransferase, FGARAT; EC 6.3.5.3), the enzyme that carries out the fourth step
of de novo purine synthesis. It catalyses the ATP-dependent, glutamine-dependent
amidotransfer that converts formylglycinamide ribonucleotide (FGAR) to formylglycinamidine
ribonucleotide (FGAM), releasing L-glutamate, ADP and phosphate (FGAR + L-glutamine + ATP
+ H2O -> FGAM + L-glutamate + ADP + Pi). The multidomain protein combines an N-terminal
ATP-/Mg2+-dependent synthetase (PurL) region with a C-terminal class-I glutamine
amidotransferase (GATase-1) domain that hydrolyses glutamine to supply the transferred
amide nitrogen. The enzyme is cytosolic and can associate with the purinosome, the
reversible multi-enzyme assembly of de novo purine synthesis. As one of the six enzymes of
this housekeeping pathway it supplies the inosine monophosphate (IMP) precursor from which
AMP and GMP are subsequently made, and its activity is of interest in the elevated
nucleotide demand of proliferating and cancer cells.
existing_annotations:
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: is_active_in
review:
summary: >-
Phylogenetically inferred cytoplasmic localization for this cytosolic de novo purine
synthesis enzyme. Consistent with the UniProt subcellular location and with Reactome's
cytosol assignment.
action: ACCEPT
reason: >-
PFAS is a soluble cytosolic enzyme with no membrane-spanning or targeting features; the
IBA cytoplasm annotation is correct, though the more specific cytosol term (GO:0005829)
is preferable as the primary localization.
supported_by:
- reference_id: file:human/PFAS/PFAS-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Cytoplasm"
- reference_id: Reactome:R-HSA-73812
supporting_text: >-
Fluoresence microscopy studies of cultured human cells have shown that the enzyme is
cytosolic
- term:
id: GO:0004642
label: phosphoribosylformylglycinamidine synthase activity
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: enables
review:
summary: >-
Phylogenetically inferred phosphoribosylformylglycinamidine synthase (FGAM synthase)
activity, the defining molecular function of PFAS and its orthologs across the FGAMS
family.
action: ACCEPT
reason: >-
This is the core molecular function of PFAS, EC 6.3.5.3 (RHEA:17129), independently
supported by direct biochemical evidence (IDA) and by the conserved N-terminal PurL
synthetase plus C-terminal GATase-1 domain architecture in UniProt.
supported_by:
- reference_id: file:human/PFAS/PFAS-uniprot.txt
supporting_text: "RecName: Full=Phosphoribosylformylglycinamidine synthase;"
- reference_id: file:human/PFAS/PFAS-uniprot.txt
supporting_text: purines biosynthetic pathway. Catalyzes the ATP-dependent conversion of
- term:
id: GO:0006164
label: purine nucleotide biosynthetic process
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: >-
Phylogenetically inferred involvement in purine nucleotide biosynthesis, the pathway
to which the FGAM synthase reaction belongs.
action: ACCEPT
reason: >-
Correct parent biological process. PFAS performs step four of de novo purine synthesis,
producing the IMP precursor from which purine nucleotides are made. This broad term is
accurate; the more specific 'de novo IMP biosynthetic process' (GO:0006189) is also
annotated and captured as core.
supported_by:
- reference_id: PMID:10548741
supporting_text: >-
phosphoribosylformylglycineamide amidotransferase (FGARAT) gene, which
encodes the fourth step of this pathway
- term:
id: GO:0004642
label: phosphoribosylformylglycinamidine synthase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: enables
review:
summary: >-
Electronic assignment of FGAM synthase activity from InterPro/EC/RHEA mappings
(IPR010073, EC 6.3.5.3, RHEA:17129).
action: ACCEPT
reason: >-
Correct and specific. The InterPro-to-GO and EC mappings identify the exact catalytic
function, in agreement with the IBA, TAS and IDA annotations of the same term.
supported_by:
- reference_id: file:human/PFAS/PFAS-uniprot.txt
supporting_text: "RecName: Full=Phosphoribosylformylglycinamidine synthase;"
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IEA
original_reference_id: GO_REF:0000044
qualifier: located_in
review:
summary: >-
Electronic cytoplasm localization from the UniProt subcellular-location keyword mapping
(SL-0086).
action: ACCEPT
reason: >-
Consistent with the manually asserted cytoplasmic/cytosolic localization; correct
though less specific than cytosol.
supported_by:
- reference_id: file:human/PFAS/PFAS-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Cytoplasm"
- term:
id: GO:0006189
label: "'de novo' IMP biosynthetic process"
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: involved_in
review:
summary: >-
Electronic assignment (InterPro IPR010073, UniPathway UPA00074) placing PFAS in the de
novo IMP biosynthetic pathway.
action: ACCEPT
reason: >-
This is the specific and correct biological process for PFAS: the FGAR->FGAM step is
part of the de novo pathway that builds IMP. Concordant with the IDA and NAS annotations
of the same term.
supported_by:
- reference_id: file:human/PFAS/PFAS-uniprot.txt
supporting_text: "IMP biosynthesis via de novo pathway"
- reference_id: PMID:10548741
supporting_text: >-
The de-novo
synthesis of purines requires 10 enzymatic steps for the production of inosine
monophosphate (IMP)
- term:
id: GO:0006541
label: L-glutamine metabolic process
evidence_type: IEA
original_reference_id: GO_REF:0000107
qualifier: involved_in
review:
summary: >-
Electronic annotation transferred from a rat ortholog (UniProtKB:D4AB17) capturing that
PFAS consumes L-glutamine as the amide-nitrogen donor for the amidotransfer reaction.
action: KEEP_AS_NON_CORE
reason: >-
Biologically reasonable - the C-terminal glutamine amidotransferase (GATase-1) domain
hydrolyses glutamine to supply the transferred nitrogen, so PFAS participates in
glutamine catabolism as a side/co-substrate process. However this is a consequence of
the catalytic mechanism rather than the enzyme's core role, which is purine
(IMP-precursor) biosynthesis; retain as non-core.
supported_by:
- reference_id: file:human/PFAS/PFAS-uniprot.txt
supporting_text: "ATP-binding; Cytoplasm; Glutamine amidotransferase; Ligase; Magnesium;"
- term:
id: GO:0009410
label: response to xenobiotic stimulus
evidence_type: IEA
original_reference_id: GO_REF:0000107
qualifier: involved_in
review:
summary: >-
Electronic annotation transferred from a rat ortholog (UniProtKB:D4AB17,
ENSRNOP00000007087) via Ensembl Compara.
action: MARK_AS_OVER_ANNOTATED
reason: >-
This term reflects a downstream expression/response phenotype observed for the rodent
ortholog and does not describe the molecular or biosynthetic role of PFAS. For a
housekeeping de novo purine synthesis enzyme this is an over-annotation transferred
electronically from an ortholog; it is not a core function of human PFAS and there is no
direct evidence for it in this gene.
- term:
id: GO:0009168
label: purine ribonucleoside monophosphate biosynthetic process
evidence_type: TAS
original_reference_id: Reactome:R-HSA-73817
qualifier: involved_in
review:
summary: >-
Reactome pathway-level assertion that PFAS participates in purine ribonucleoside
monophosphate (IMP) biosynthesis.
action: ACCEPT
reason: >-
Correct pathway-level process. Reactome places the FGAR->FGAM reaction within the
pathway that assembles IMP on PRPP; equivalent in scope to the de novo IMP biosynthetic
process term.
supported_by:
- reference_id: Reactome:R-HSA-73817
supporting_text: >-
The purine ribonucleotide inosine 5'-monophosphate (IMP) is assembled on
5-phospho-alpha-D-ribose 1-diphosphate (PRPP)
- term:
id: GO:0004642
label: phosphoribosylformylglycinamidine synthase activity
evidence_type: TAS
original_reference_id: Reactome:R-HSA-73812
qualifier: enables
review:
summary: >-
Reactome traceable assertion of FGAM synthase activity, citing the biochemically
characterized human enzyme reaction FGAR + L-glutamine + ATP + H2O -> FGAM + L-glutamate
+ ADP + Pi.
action: ACCEPT
reason: >-
Core molecular function, supported by the purified/characterized human enzyme and
concordant with the IDA, IBA and IEA annotations of the same term.
supported_by:
- reference_id: Reactome:R-HSA-73812
supporting_text: >-
is catalyzed by phosphoribosylformylglycinamidine
synthetase. The human enzyme has been purified and characterized biochemically
- term:
id: GO:0004642
label: phosphoribosylformylglycinamidine synthase activity
evidence_type: IMP
original_reference_id: PMID:27590927
qualifier: enables
review:
summary: >-
FGAM synthase activity inferred from a CRISPR-Cas9 PFAS knockout in HeLa cells, in which
loss of the enzyme causes accumulation of its substrate.
action: ACCEPT
reason: >-
MGI experimental (IMP) annotation. The knockout phenotype - accumulation of the enzyme's
substrate - directly implicates PFAS in the FGAR->FGAM step, supporting the core
molecular function. The cached record is abstract-only; the full text (which the curator
read) assays this DNPS step. Concordant with the independent IDA annotation.
supported_by:
- reference_id: PMID:27590927
supporting_text: >-
In all model cell lines with the exception
of one, an accumulation of the substrate(s) for the knocked out enzyme was
identified
- term:
id: GO:0006177
label: GMP biosynthetic process
evidence_type: IMP
original_reference_id: PMID:27590927
qualifier: acts_upstream_of_or_within
review:
summary: >-
From the CRISPR knockout study; loss of PFAS depletes de novo purine synthesis and
thereby the downstream GMP branch.
action: KEEP_AS_NON_CORE
reason: >-
PFAS acts upstream of GMP synthesis - it makes the IMP precursor, from which GMP is
subsequently derived - so the acts_upstream_of_or_within qualifier is appropriate. It is
not itself a GMP-biosynthesis enzyme, so this is a valid but non-core downstream-branch
annotation.
supported_by:
- reference_id: PMID:27590927
supporting_text: >-
CRISPR-Cas9 genome-edited HeLa
cells deficient for the individual steps
of DNPS
- term:
id: GO:0006189
label: "'de novo' IMP biosynthetic process"
evidence_type: IMP
original_reference_id: PMID:27590927
qualifier: acts_upstream_of_or_within
review:
summary: >-
CRISPR knockout evidence that PFAS is required for de novo IMP biosynthesis, the pathway
it directly participates in.
action: ACCEPT
reason: >-
Core biological process, experimentally supported. Loss of PFAS blocks flux through de
novo purine synthesis toward IMP; concordant with the involved_in IDA/NAS annotations of
the same term.
supported_by:
- reference_id: PMID:27590927
supporting_text: >-
DNPS includes ten reactions catalysed by six enzymes.
- term:
id: GO:0044208
label: "'de novo' AMP biosynthetic process"
evidence_type: IMP
original_reference_id: PMID:27590927
qualifier: acts_upstream_of_or_within
review:
summary: >-
From the CRISPR knockout study; loss of PFAS depletes de novo purine synthesis and
thereby the downstream AMP branch.
action: KEEP_AS_NON_CORE
reason: >-
PFAS acts upstream of AMP synthesis by supplying the shared IMP precursor; the
acts_upstream_of_or_within qualifier is correct. It is not itself an AMP-biosynthesis
enzyme, so this is a valid but non-core downstream-branch annotation.
supported_by:
- reference_id: PMID:27590927
supporting_text: >-
CRISPR-Cas9 genome-edited HeLa
cells deficient for the individual steps
of DNPS
- term:
id: GO:0097294
label: "'de novo' XMP biosynthetic process"
evidence_type: IMP
original_reference_id: PMID:27590927
qualifier: acts_upstream_of_or_within
review:
summary: >-
From the CRISPR knockout study; loss of PFAS depletes de novo purine synthesis and
thereby the downstream XMP branch.
action: KEEP_AS_NON_CORE
reason: >-
PFAS acts upstream of XMP synthesis by supplying the shared IMP precursor; the
acts_upstream_of_or_within qualifier is correct. It is not itself an XMP-biosynthesis
enzyme, so this is a valid but non-core downstream-branch annotation.
supported_by:
- reference_id: PMID:27590927
supporting_text: >-
CRISPR-Cas9 genome-edited HeLa
cells deficient for the individual steps
of DNPS
- term:
id: GO:0097294
label: "'de novo' XMP biosynthetic process"
evidence_type: IDA
original_reference_id: PMID:27590927
qualifier: involved_in
review:
summary: >-
Direct-assay (IDA) annotation to the downstream de novo XMP branch, from the DNPS
substrate-accumulation study.
action: KEEP_AS_NON_CORE
reason: >-
With the involved_in qualifier this term is arguably too downstream for PFAS, whose
direct reaction produces the IMP precursor rather than XMP. The corresponding
acts_upstream_of_or_within annotation captures the relationship more accurately. Retained
as non-core; deferring to the MGI curator's full-text reading rather than removing an
experimental annotation.
supported_by:
- reference_id: PMID:27590927
supporting_text: >-
an accumulation of the substrate(s) for the knocked out enzyme was
identified
- term:
id: GO:0004642
label: phosphoribosylformylglycinamidine synthase activity
evidence_type: IDA
original_reference_id: PMID:27590927
qualifier: enables
review:
summary: >-
Direct experimental evidence for FGAM synthase activity from the CRISPR/substrate-
accumulation study.
action: ACCEPT
reason: >-
Core molecular function with direct experimental support; concordant with the IMP, IBA,
IEA and Reactome-TAS annotations of the same term.
supported_by:
- reference_id: PMID:27590927
supporting_text: >-
an accumulation of the substrate(s) for the knocked out enzyme was
identified
- term:
id: GO:0006177
label: GMP biosynthetic process
evidence_type: IDA
original_reference_id: PMID:27590927
qualifier: involved_in
review:
summary: >-
Direct-assay (IDA) involved_in annotation to the downstream GMP branch.
action: KEEP_AS_NON_CORE
reason: >-
As with the AMP/XMP branch terms, PFAS supplies the upstream IMP precursor rather than
catalysing GMP synthesis; the acts_upstream_of_or_within relationship is more accurate
than involved_in. Retained as non-core; not removed, as this is an experimental
annotation whose full text the curator read.
supported_by:
- reference_id: PMID:27590927
supporting_text: >-
an accumulation of the substrate(s) for the knocked out enzyme was
identified
- term:
id: GO:0006189
label: "'de novo' IMP biosynthetic process"
evidence_type: IDA
original_reference_id: PMID:27590927
qualifier: involved_in
review:
summary: >-
Direct-assay evidence that PFAS is involved in de novo IMP biosynthesis.
action: ACCEPT
reason: >-
Core biological process. This is the pathway PFAS directly participates in (step four),
and involved_in is the correct qualifier. Concordant with the IEA, NAS and Reactome
annotations.
supported_by:
- reference_id: PMID:27590927
supporting_text: >-
DNPS includes ten reactions catalysed by six enzymes.
- term:
id: GO:0044208
label: "'de novo' AMP biosynthetic process"
evidence_type: IDA
original_reference_id: PMID:27590927
qualifier: involved_in
review:
summary: >-
Direct-assay (IDA) involved_in annotation to the downstream de novo AMP branch.
action: KEEP_AS_NON_CORE
reason: >-
PFAS makes the shared IMP precursor upstream of AMP synthesis; involved_in is arguably
too downstream, and the acts_upstream_of_or_within annotation captures the relationship
better. Retained as valid but non-core; not removed given experimental support.
supported_by:
- reference_id: PMID:27590927
supporting_text: >-
an accumulation of the substrate(s) for the knocked out enzyme was
identified
- term:
id: GO:0070062
label: extracellular exosome
evidence_type: HDA
original_reference_id: PMID:20458337
qualifier: located_in
review:
summary: >-
High-throughput MS detection of PFAS among 539 proteins in the total proteome of
purified B-cell-derived exosomes.
action: MARK_AS_OVER_ANNOTATED
reason: >-
This is a bulk mass-spectrometry catalog of an exosome preparation, not a targeted or
functionally meaningful localization for a cytosolic de novo purine synthesis enzyme.
Abundant cytosolic proteins are routinely detected in such exosome proteomes; there is
no evidence of a functional role for PFAS in exosomes. Over-annotation - the enzyme acts
in the cytosol.
supported_by:
- reference_id: PMID:20458337
supporting_text: >-
we first analyzed the total
proteome of highly purified B cell-derived exosomes using sensitive and accurate
mass spectrometry (MS), and identified 539 proteins
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-73812
qualifier: located_in
review:
summary: >-
Reactome traceable assertion that the enzyme is cytosolic, from fluorescence microscopy
of cultured human cells.
action: ACCEPT
reason: >-
Most specific and accurate cellular-component annotation for PFAS. Cytosolic
localization is consistent with the enzyme's role in de novo purine synthesis and with
its reversible association with the cytosolic purinosome.
supported_by:
- reference_id: Reactome:R-HSA-73812
supporting_text: >-
Fluoresence microscopy studies of cultured human cells have
shown that the enzyme is cytosolic
- term:
id: GO:0004642
label: phosphoribosylformylglycinamidine synthase activity
evidence_type: IDA
original_reference_id: PMID:10548741
qualifier: enables
review:
summary: >-
Direct experimental evidence for FGAM synthase (FGARAT) activity: the human genomic
clone corrects the purine auxotrophy and enzyme/protein deficiency of AdeB CHO mutants
that lack FGARAT.
action: ACCEPT
reason: >-
Core molecular function established by functional complementation. Restoring FGARAT
activity in an enzyme-deficient mammalian cell line directly demonstrates the catalytic
function of the encoded protein.
supported_by:
- reference_id: PMID:10548741
supporting_text: >-
The P1 clone corrects the purine auxotrophy and protein deficiency of Chinese
hamster ovary (CHO) cell mutants (AdeB) deficient in both the activity and the
protein for FGARAT.
- term:
id: GO:0006189
label: "'de novo' IMP biosynthetic process"
evidence_type: NAS
original_reference_id: PMID:10548741
qualifier: involved_in
review:
summary: >-
Non-traceable author statement placing FGARAT/PFAS as the fourth of the ten enzymatic
steps producing IMP by de novo purine synthesis.
action: ACCEPT
reason: >-
Core biological process, consistent with the specific and correct pathway role of PFAS
and concordant with the IEA/IDA annotations of the same term.
supported_by:
- reference_id: PMID:10548741
supporting_text: >-
phosphoribosylformylglycineamide amidotransferase (FGARAT) gene, which
encodes the fourth step of this pathway
core_functions:
- description: >-
Phosphoribosylformylglycinamidine synthase (FGAM synthase, FGARAT; EC 6.3.5.3): the
ATP- and glutamine-dependent amidotransferase catalysing step four of de novo purine
synthesis, converting FGAR to FGAM.
molecular_function:
id: GO:0004642
label: phosphoribosylformylglycinamidine synthase activity
directly_involved_in:
- id: GO:0006189
label: "'de novo' IMP biosynthetic process"
locations:
- id: GO:0005829
label: cytosol
supported_by:
- reference_id: file:human/PFAS/PFAS-uniprot.txt
supporting_text: "RecName: Full=Phosphoribosylformylglycinamidine synthase;"
- reference_id: PMID:10548741
supporting_text: >-
phosphoribosylformylglycineamide amidotransferase (FGARAT) gene, which
encodes the fourth step of this pathway
- description: >-
Participation in purine nucleotide biosynthesis: by producing the FGAM intermediate en
route to IMP, PFAS provides the precursor for downstream AMP and GMP synthesis.
molecular_function:
id: GO:0004642
label: phosphoribosylformylglycinamidine synthase activity
directly_involved_in:
- id: GO:0006164
label: purine nucleotide biosynthetic process
locations:
- id: GO:0005829
label: cytosol
supported_by:
- reference_id: Reactome:R-HSA-73812
supporting_text: >-
is catalyzed by phosphoribosylformylglycinamidine
synthetase. The human enzyme has been purified and characterized biochemically
references:
- 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:10548741
title: 'Human phosphoribosylformylglycineamide amidotransferase (FGARAT): regional
mapping, complete coding sequence, isolation of a functional genomic clone, and
DNA sequence analysis.'
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Cloning/complementation paper for human FGARAT/PFAS; establishes the enzyme as step
four of de novo purine synthesis and demonstrates catalytic function by AdeB CHO
complementation. Source of the IDA MF and NAS BP annotations. Abstract-only in cache.
- id: PMID:20458337
title: MHC class II-associated proteins in B-cell exosomes and potential functional
implications for exosome biogenesis.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: >-
B-cell exosome proteomics (539 proteins). PFAS is a bulk-catalog hit; supports only the
over-annotated extracellular-exosome CC, not a functional role.
- id: PMID:27590927
title: CRISPR-Cas9 induced mutations along de novo purine synthesis in HeLa cells
result in accumulation of individual enzyme substrates and affect purinosome formation.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
CRISPR knockouts of individual DNPS enzymes in HeLa; substrate accumulation and impaired
purinosome assembly. Source of the MGI IMP/IDA annotations. Abstract frames DNPS at the
pathway level without naming PFAS; full text (uncached) assays the FGAR-AT step, so
deferring to the MGI curator.
- id: Reactome:R-HSA-73812
title: FGAR + L-Glutamine + ATP + H2O => FGAM + L-Glutamate + ADP + Pi
findings: []
- id: Reactome:R-HSA-73817
title: Purine ribonucleoside monophosphate biosynthesis
findings: []
- id: file:human/PFAS/PFAS-uniprot.txt
title: UniProtKB entry O15067 (PUR4_HUMAN), phosphoribosylformylglycinamidine synthase
findings: []
suggested_questions:
- question: >-
Does PFAS have any moonlighting or regulatory function beyond de novo purine synthesis
(e.g. in stress-granule/CD-CODE contexts or via its multiple phosphosites)?
- question: >-
How does purinosome association modulate PFAS flux, and is the enzyme rate-limiting under
conditions of high purine demand such as tumor proliferation?
suggested_experiments:
- description: >-
Quantitative metabolic-flux analysis (LC-MS/MS of FGAR vs FGAM) in PFAS-null versus
rescued cells to confirm the in vivo FGAR->FGAM step and measure control strength.
- description: >-
Phospho-site mutagenesis (Ser215/Ser569/Thr619/Thr623) to test whether phosphorylation
regulates PFAS activity or purinosome recruitment.