PFAS

Existing Annotations Review

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

Gene Description

Existing Annotations Review

Core Functions

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.

Participation in purine nucleotide biosynthesis: by producing the FGAM intermediate en route to IMP, PFAS provides the precursor for downstream AMP and GMP synthesis.

References

Suggested Questions for Experts

Suggested Experiments

📚 Additional Documentation

Notes

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