Purine nucleoside phosphorylase (PNP; EC 2.4.2.1) is a cytosolic homotrimeric enzyme of purine catabolism and salvage. It catalyzes the reversible phosphorolysis of the N-glycosidic bond of 6-oxopurine (deoxy)ribonucleosides, converting inosine, guanosine and their 2'-deoxy forms (plus phosphate) to the corresponding free purine base (hypoxanthine or guanine) and (2'-deoxy)-alpha-D-ribose-1-phosphate. The liberated bases are either recycled by salvage (e.g. by HPRT1) or channeled into oxidative catabolism (hypoxanthine to xanthine to urate by xanthine oxidoreductase). PNP is highly specific for 6-oxopurine nucleosides and essentially inactive on adenine (6-amino) nucleosides. It also phosphorolyses the pyridine nucleoside nicotinamide riboside, contributing to a kinase-independent NAD+ salvage route. In humans, loss-of-function of PNP causes purine nucleoside phosphorylase deficiency, an autosomal recessive disorder in which accumulating (deoxy)guanosine and dGTP are toxic to T lymphocytes, producing a severe T-cell immunodeficiency (a cause of severe combined immunodeficiency) frequently accompanied by neurological impairment.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0004731
purine-nucleoside phosphorylase activity
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Core molecular function of PNP: phosphorolytic cleavage of purine (deoxy)ribonucleosides. Phylogenetic (IBA) annotation consistent with abundant human experimental evidence.
Reason: This is the well-established core catalytic activity of PNP (EC 2.4.2.1), directly demonstrated for the human enzyme by multiple experimental studies.
Supporting Evidence:
PMID:6771276
the phosphorolysis of inosine, deoxyinosine, guanosine, and deoxyguanosine with
PMID:23438750
catalyzes the reversible phosphorolysis of purine (deoxy)-ribonucleosides to the corresponding purine base
|
|
GO:0005829
cytosol
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: PNP is a soluble cytosolic enzyme; phylogenetic assignment of cytosolic localization is correct and matches direct evidence in human cells.
Reason: UniProt records the subcellular location as Cytoplasm, cytosol, and human immunofluorescence (HPA) and direct assays place PNP in the cytosol; this is the site of its catalytic function.
|
|
GO:0006148
inosine catabolic process
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: PNP phosphorolyses inosine to hypoxanthine, a committed step of inosine catabolism/salvage. Core biological process.
Reason: Directly demonstrated: purified human PNP catalyzes phosphorolysis of inosine, supporting its role in inosine catabolism.
Supporting Evidence:
PMID:6771276
the phosphorolysis of inosine, deoxyinosine, guanosine, and deoxyguanosine with
|
|
GO:0006149
deoxyinosine catabolic process
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: PNP phosphorolyses 2'-deoxyinosine to hypoxanthine; part of its core (deoxy)nucleoside catabolic activity.
Reason: Purified human PNP catalyzes deoxyinosine phosphorolysis, and the enzyme acts equally on ribo- and deoxyribonucleosides of 6-oxopurines.
Supporting Evidence:
PMID:6771276
the phosphorolysis of inosine, deoxyinosine, guanosine, and deoxyguanosine with
|
|
GO:0006161
deoxyguanosine catabolic process
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: PNP phosphorolyses 2'-deoxyguanosine to guanine; a core catabolic step and the one most relevant to PNP-deficiency pathology (dGTP accumulation).
Reason: Purified human PNP catalyzes deoxyguanosine phosphorolysis; failure of this step underlies the T-cell-toxic (deoxy)guanosine/dGTP buildup in PNP deficiency.
Supporting Evidence:
PMID:6771276
the phosphorolysis of inosine, deoxyinosine, guanosine, and deoxyguanosine with
|
|
GO:0034355
NAD+ biosynthetic process via the salvage pathway
|
IBA
GO_REF:0000033 |
KEEP AS NON CORE |
Summary: PNP phosphorolyses nicotinamide riboside (NR) to nicotinamide, providing a kinase-independent entry into NAD+ salvage. Real but not the core catabolic function of PNP.
Reason: Mammalian PNP is the enzyme responsible for Nrk1-independent NR utilization, cleaving NR (and nicotinic acid riboside) to feed NAD+ salvage; this is a secondary/alternative-substrate role downstream of nucleoside phosphorolysis rather than PNP's principal purine-catabolic function.
Supporting Evidence:
PMID:19001417
that mammalian purine nucleoside phosphorylase but not methylthioadenosine
|
|
GO:0046115
guanosine catabolic process
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: PNP phosphorolyses guanosine to guanine; a core catabolic/salvage step.
Reason: Purified human PNP catalyzes guanosine phosphorolysis with high affinity (KM ~6 uM), a core substrate of the enzyme.
Supporting Evidence:
PMID:6771276
the phosphorolysis of inosine, deoxyinosine, guanosine, and deoxyguanosine with
|
|
GO:0003824
catalytic activity
|
IEA
GO_REF:0000002 |
MARK AS OVER ANNOTATED |
Summary: Root-level catalytic activity term from InterPro mapping; uninformative given the specific EC 2.4.2.1 activity is annotated.
Reason: GO:0003824 is the most general molecular-function term and conveys nothing beyond the specific purine-nucleoside phosphorylase activity already annotated.
|
|
GO:0004731
purine-nucleoside phosphorylase activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Same core molecular function via automated EC/RHEA/ARBA mapping; correct.
Reason: Automated mapping (EC 2.4.2.1 / RHEA:27646) to purine-nucleoside phosphorylase activity is accurate and matches experimental evidence.
|
|
GO:0005829
cytosol
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: Cytosol from UniProt subcellular-location keyword mapping; correct.
Reason: Consistent with the curated Cytoplasm/cytosol location and direct human evidence.
|
|
GO:0009116
nucleoside metabolic process
|
IEA
GO_REF:0000002 |
KEEP AS NON CORE |
Summary: Broad but correct parent process (nucleoside metabolism) from InterPro mapping.
Reason: Accurate as a general process term but less informative than the specific purine (deoxy)nucleoside catabolic/salvage terms already present.
|
|
GO:0016763
pentosyltransferase activity
|
IEA
GO_REF:0000002 |
KEEP AS NON CORE |
Summary: Correct parent MF (PNP is a glycosyltransferase/pentosyltransferase, EC 2.4.2) but broader than the specific activity.
Reason: GO:0016763 is the accurate broad classification of the reaction chemistry; retained as a non-core parent of purine-nucleoside phosphorylase activity.
|
|
GO:0047975
guanosine phosphorylase activity
|
IEA
GO_REF:0000116 |
ACCEPT |
Summary: Substrate-specific child activity (guanosine + phosphate = guanine + ribose-1-phosphate); correct via RHEA mapping.
Reason: PNP has robust guanosine phosphorylase activity (KM ~6 uM), a specific facet of its EC 2.4.2.1 activity; automated RHEA:13233 mapping is correct.
|
|
GO:0005515
protein binding
|
IPI
PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative ... |
MARK AS OVER ANNOTATED |
Summary: Uninformative "protein binding" from a large-scale neurodegenerative-disease Y2H interactome screen; multiple heterogeneous partners with no defined functional consequence for PNP.
Reason: This and the other GO:0005515 IPI lines derive from high-throughput binary interactome mapping (yeast two-hybrid); the term is non-specific and does not inform PNP's molecular function. Retained (not removed) per curation policy on experimental IPI, but flagged as over-annotation.
Supporting Evidence:
PMID:32814053
generated by systematic yeast two-hybrid
|
|
GO:0042802
identical protein binding
|
IPI
PMID:20212140 Four generations of transition-state analogues for human pur... |
ACCEPT |
Summary: Self-association reflecting PNP's obligate homotrimeric quaternary structure; biologically meaningful.
Reason: Human PNP is a homotrimer with catalytic sites at subunit interfaces, so identical-protein (self) binding is a genuine structural property of the enzyme.
Supporting Evidence:
PMID:20212140
Four generations of transition-state analogues for human purine nucleoside
|
|
GO:0042802
identical protein binding
|
IPI
PMID:25502805 A massively parallel pipeline to clone DNA variants and exam... |
ACCEPT |
Summary: Self-association consistent with the homotrimeric architecture of PNP.
Reason: Homotrimer formation is a well-established structural feature; identical protein binding is appropriate.
Supporting Evidence:
PMID:23438750
Human PNP is a homotrimer
|
|
GO:0042802
identical protein binding
|
IPI
PMID:31515488 Extensive disruption of protein interactions by genetic vari... |
ACCEPT |
Summary: Self-association consistent with the homotrimeric architecture of PNP.
Reason: Homotrimer formation is a well-established structural feature; identical protein binding is appropriate.
Supporting Evidence:
PMID:23438750
Human PNP is a homotrimer
|
|
GO:0042802
identical protein binding
|
IPI
PMID:32296183 A reference map of the human binary protein interactome. |
ACCEPT |
Summary: Self-association consistent with the homotrimeric architecture of PNP.
Reason: Homotrimer formation is a well-established structural feature; identical protein binding is appropriate.
Supporting Evidence:
PMID:23438750
Human PNP is a homotrimer
|
|
GO:0005829
cytosol
|
IDA
GO_REF:0000052 |
ACCEPT |
Summary: Direct immunofluorescence (HPA) localization to cytosol; correct core location.
Reason: Direct human-cell evidence for cytosolic localization, the functional site of the enzyme.
|
|
GO:0047975
guanosine phosphorylase activity
|
EXP
PMID:9305964 Purine nucleoside phosphorylase. 3. Reversal of purine base ... |
ACCEPT |
Summary: Experimentally measured guanosine phosphorylase activity (a specific facet of EC 2.4.2.1) for human PNP.
Reason: Kinetic characterization of human PNP includes guanosine as a high-affinity substrate, supporting guanosine phosphorylase activity.
Supporting Evidence:
PMID:9305964
highly specific for 6-oxopurine
|
|
GO:0004731
purine-nucleoside phosphorylase activity
|
IDA
PMID:6771276 Characterization of purine nucleoside phosphorylase from hum... |
ACCEPT |
Summary: Direct assay of purified human (granulocyte) PNP demonstrating phosphorolysis of 6-oxopurine (deoxy)nucleosides. Core function.
Reason: Purified human enzyme catalyzes phosphorolysis of inosine, deoxyinosine, guanosine and deoxyguanosine, directly establishing the activity.
Supporting Evidence:
PMID:6771276
the phosphorolysis of inosine, deoxyinosine, guanosine, and deoxyguanosine with
|
|
GO:0006149
deoxyinosine catabolic process
|
IDA
PMID:6771276 Characterization of purine nucleoside phosphorylase from hum... |
ACCEPT |
Summary: PNP phosphorolyses 2'-deoxyinosine (to hypoxanthine); part of deoxyinosine catabolism.
Reason: Directly demonstrated deoxyinosine phosphorolysis by the purified human enzyme.
Supporting Evidence:
PMID:6771276
the phosphorolysis of inosine, deoxyinosine, guanosine, and deoxyguanosine with
|
|
GO:0006157
deoxyadenosine catabolic process
|
IDA
PMID:6771276 Characterization of purine nucleoside phosphorylase from hum... |
KEEP AS NON CORE |
Summary: Pathway-level (acts_upstream_of_or_within) annotation for deoxyadenosine catabolism. PNP does not act directly on deoxyadenosine (an adenine nucleoside), but participates downstream in the pathway after deamination.
Reason: The cited paper explicitly states that adenine (deoxy)ribonucleosides are NOT substrates of PNP, so this is not a direct enzymatic activity; however the curator's acts_upstream_of_or_within annotation reflects PNP's downstream role in the broader deoxyadenosine catabolic pathway (relevant to the dATP/dGTP accumulation of PNP deficiency). Retained as non-core rather than removed.
Supporting Evidence:
PMID:6771276
ribonucleosides and deoxyribonucleosides of adenine and the pyrimidines are not
|
|
GO:0006204
IMP catabolic process
|
IDA
PMID:6771276 Characterization of purine nucleoside phosphorylase from hum... |
KEEP AS NON CORE |
Summary: Pathway-level annotation for IMP catabolism. PNP acts on inosine (the dephosphorylated nucleoside), not on IMP directly, but functions downstream in the IMP-degradation pathway.
Reason: PNP's substrate is inosine (from IMP after 5'-nucleotidase), not IMP itself; the acts_upstream_of_or_within qualifier captures its downstream role in the IMP catabolic pathway. Retained as non-core.
|
|
GO:0046059
dAMP catabolic process
|
IDA
PMID:6771276 Characterization of purine nucleoside phosphorylase from hum... |
KEEP AS NON CORE |
Summary: Pathway-level annotation for dAMP catabolism. PNP does not act on dAMP or on adenine deoxynucleosides directly; downstream/pathway-context annotation.
Reason: PNP does not phosphorolyse adenine nucleosides (the paper states adenine deoxyribonucleosides are not substrates) and acts on nucleosides not nucleotides; the annotation reflects downstream pathway participation. Retained as non-core rather than removed for an experimental IDA.
Supporting Evidence:
PMID:6771276
ribonucleosides and deoxyribonucleosides of adenine and the pyrimidines are not
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-9735775 |
ACCEPT |
Summary: Cytosol localization from Reactome (defective-PNP inosine reaction); correct core location.
Reason: Consistent with the established cytosolic site of PNP function.
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-9735789 |
ACCEPT |
Summary: Cytosol localization from Reactome (defective-PNP guanosine reaction); correct.
Reason: Consistent with the established cytosolic site of PNP function.
|
|
GO:0006149
deoxyinosine catabolic process
|
IDA
PMID:6771276 Characterization of purine nucleoside phosphorylase from hum... |
ACCEPT |
Summary: Duplicate (involved_in) annotation of deoxyinosine catabolism; directly supported.
Reason: Direct assay of deoxyinosine phosphorolysis by purified human PNP.
Supporting Evidence:
PMID:6771276
the phosphorolysis of inosine, deoxyinosine, guanosine, and deoxyguanosine with
|
|
GO:0006157
deoxyadenosine catabolic process
|
IDA
PMID:6771276 Characterization of purine nucleoside phosphorylase from hum... |
KEEP AS NON CORE |
Summary: involved_in duplicate of the deoxyadenosine-catabolism pathway annotation. PNP does not act on deoxyadenosine directly.
Reason: As above: adenine deoxyribonucleosides are not PNP substrates, so this reflects a downstream/pathway role rather than a direct activity; retained as non-core.
Supporting Evidence:
PMID:6771276
ribonucleosides and deoxyribonucleosides of adenine and the pyrimidines are not
|
|
GO:0006204
IMP catabolic process
|
IDA
PMID:6771276 Characterization of purine nucleoside phosphorylase from hum... |
KEEP AS NON CORE |
Summary: involved_in duplicate of the IMP-catabolism pathway annotation; PNP acts on inosine downstream of IMP.
Reason: PNP's direct substrate is inosine, not IMP; retained as a downstream pathway-level annotation.
|
|
GO:0000255
allantoin metabolic process
|
IDA
PMID:6771276 Characterization of purine nucleoside phosphorylase from hum... |
MARK AS OVER ANNOTATED |
Summary: Allantoin metabolism is several steps downstream of PNP (via urate) and does not occur in humans, who lack urate oxidase; this appears to be an over-propagated/incorrect pathway annotation for the human gene.
Reason: The cited human granulocyte study characterizes PNP nucleoside phosphorolysis and does not address allantoin; humans do not synthesize allantoin (uricase is a pseudogene), so an allantoin metabolic process annotation is not appropriate for human PNP. Flagged as over-annotation rather than removed, since it is an experimental IDA whose full text was not reviewed here.
|
|
GO:0046059
dAMP catabolic process
|
IDA
PMID:6771276 Characterization of purine nucleoside phosphorylase from hum... |
KEEP AS NON CORE |
Summary: involved_in duplicate of the dAMP-catabolism pathway annotation; PNP acts on nucleosides, not dAMP, and not on adenine nucleosides.
Reason: Retained as a downstream pathway-level annotation; PNP does not directly act on dAMP or adenine (deoxy)nucleosides.
Supporting Evidence:
PMID:6771276
ribonucleosides and deoxyribonucleosides of adenine and the pyrimidines are not
|
|
GO:0004731
purine-nucleoside phosphorylase activity
|
IDA
PMID:5056638 Purine nucleoside phosphorylase activity of human erythrocyt... |
ACCEPT |
Summary: PNP enzymatic activity measured in human erythrocytes; supports the core molecular function.
Reason: Human erythrocyte PNP activity assay supports the enzyme's phosphorylase activity (abstract-only cache; defer to the experimental curator).
|
|
GO:0004731
purine-nucleoside phosphorylase activity
|
IDA
PMID:23438750 Catalytic site conformations in human PNP by 19F-NMR and cry... |
ACCEPT |
Summary: Kinetic/structural characterization of human PNP demonstrating phosphorolysis of purine (deoxy)ribonucleosides. Core function.
Reason: Directly establishes reversible phosphorolysis of purine (deoxy)ribonucleosides by the human enzyme, including steady-state kinetics for inosine.
Supporting Evidence:
PMID:23438750
catalyzes the reversible phosphorolysis of purine (deoxy)-ribonucleosides to the corresponding purine base
|
|
GO:0006148
inosine catabolic process
|
IDA
PMID:23438750 Catalytic site conformations in human PNP by 19F-NMR and cry... |
ACCEPT |
Summary: PNP phosphorolyses inosine (to hypoxanthine); core catabolic step, kinetically characterized.
Reason: Inosine phosphorolysis is directly characterized (steady-state kinetics) for the human enzyme.
Supporting Evidence:
PMID:23438750
catalyzes the reversible phosphorolysis of purine (deoxy)-ribonucleosides to the corresponding purine base
|
|
GO:0043101
purine-containing compound salvage
|
IDA
PMID:18938130 Effect of the phosphate substrate on drug-inhibitor binding ... |
ACCEPT |
Summary: PNP participates in purine salvage by generating free bases (hypoxanthine, guanine) for re-use; core biological role.
Reason: PNP's phosphorolysis of purine nucleosides yields free bases that are salvaged (e.g. by HPRT1); the reaction equilibrium in vivo also supports nucleoside (re)synthesis, consistent with a salvage role. UniProt assigns the pathway "purine nucleoside salvage".
|
|
GO:0009165
nucleotide biosynthetic process
|
IGI
PMID:19001417 Nicotinamide riboside and nicotinic acid riboside salvage in... |
MARK AS OVER ANNOTATED |
Summary: Broad "nucleotide biosynthetic process" from a genetic-interaction study of NR salvage; PNP itself catabolizes nucleosides, so nucleotide biosynthesis is an over-broad downstream framing.
Reason: PNP produces free bases/ribose-1-phosphate that can be recycled into nucleotides via salvage, but PNP is a phosphorylase (nucleoside catabolism), and GO:0009165 is a broad biosynthetic term better assigned to the downstream salvage kinases. The specific NR-catabolism and salvage terms already capture the relevant biology.
|
|
GO:0005576
extracellular region
|
TAS
Reactome:R-HSA-6798748 |
KEEP AS NON CORE |
Summary: Extracellular localization via Reactome neutrophil-degranulation (secretory-granule exocytosis) pathway; PNP is detected extracellularly but this is not its functional compartment.
Reason: PNP is a cytosolic enzyme released during neutrophil degranulation/secretion and detected in the extracellular space; not the site of its catalytic function.
|
|
GO:0005576
extracellular region
|
TAS
Reactome:R-HSA-6800434 |
KEEP AS NON CORE |
Summary: Extracellular localization via Reactome ficolin-rich-granule exocytosis; detected extracellularly, non-functional compartment.
Reason: Same as the secretory-granule route: released cytosolic protein, not the functional location.
|
|
GO:0034774
secretory granule lumen
|
TAS
Reactome:R-HSA-6798748 |
KEEP AS NON CORE |
Summary: Secretory-granule-lumen localization from neutrophil-degranulation Reactome pathway; reflects presence in granules, not functional site.
Reason: PNP is packaged in neutrophil granules and released on degranulation; a non-core localization for a cytosolic enzyme.
|
|
GO:1904813
ficolin-1-rich granule lumen
|
TAS
Reactome:R-HSA-6800434 |
KEEP AS NON CORE |
Summary: Ficolin-1-rich granule lumen from neutrophil-degranulation Reactome; non-core localization.
Reason: Reflects granule content in neutrophils, not the cytosolic functional site.
|
|
GO:0070062
extracellular exosome
|
HDA
PMID:23533145 In-depth proteomic analyses of exosomes isolated from expres... |
KEEP AS NON CORE |
Summary: Detected in extracellular exosomes by high-throughput proteomics; PNP is an abundant cytosolic protein commonly captured in exosome preparations.
Reason: Exosome proteomics frequently recovers abundant cytosolic enzymes; this does not indicate a functional exosomal role for PNP.
|
|
GO:0070062
extracellular exosome
|
HDA
PMID:19056867 Large-scale proteomics and phosphoproteomics of urinary exos... |
KEEP AS NON CORE |
Summary: Detected in urinary exosomes by proteomics; non-functional localization.
Reason: High-throughput exosome/proteomics detection of an abundant cytosolic enzyme; not its functional compartment.
|
|
GO:0070062
extracellular exosome
|
HDA
PMID:20458337 MHC class II-associated proteins in B-cell exosomes and pote... |
KEEP AS NON CORE |
Summary: Detected in B-cell exosomes by proteomics; non-functional localization.
Reason: As above; proteomic detection in exosomes does not establish a functional role.
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-112033 |
ACCEPT |
Summary: Cytosol localization from Reactome (PNP inosine synthesis reaction); correct core location.
Reason: Consistent with the established cytosolic site of PNP function.
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-112034 |
ACCEPT |
Summary: Cytosol localization from Reactome (PNP guanosine synthesis reaction); correct.
Reason: Consistent with the established cytosolic site of PNP function.
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-74242 |
ACCEPT |
Summary: Cytosol localization from Reactome (PNP inosine phosphorolysis); correct.
Reason: Consistent with the established cytosolic site of PNP function.
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-74249 |
ACCEPT |
Summary: Cytosol localization from Reactome (PNP guanosine phosphorolysis); correct.
Reason: Consistent with the established cytosolic site of PNP function.
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-9755044 |
ACCEPT |
Summary: Cytosol localization from Reactome (PNP-mediated ribavirin transformation); correct core location.
Reason: Consistent with the established cytosolic site of PNP function.
|
|
GO:0032743
positive regulation of interleukin-2 production
|
IMP
PMID:16930574 Intracellular delivery of purine nucleoside phosphorylase (P... |
KEEP AS NON CORE |
Summary: Restoring PNP in PNP-deficient T lymphocytes corrects IL-2 secretion; an indirect, downstream immunological consequence of the metabolic enzyme.
Reason: PNP does not directly regulate IL-2 transcription; loss of PNP causes dGTP-mediated T-cell dysfunction, and enzyme replacement rescues IL-2 secretion. This is a physiological consequence, not a core molecular role.
Supporting Evidence:
PMID:16930574
functions of PNP-deficient T lymphocytes including their response to stimulation
|
|
GO:0001882
nucleoside binding
|
IDA
PMID:9305962 Purine nucleoside phosphorylase. 1. Structure-function studi... |
ACCEPT |
Summary: PNP binds its purine-nucleoside substrate in the active site; supporting molecular function underlying catalysis.
Reason: Structure-function studies define the purine-binding/active site of human PNP that engages the nucleoside substrate.
Supporting Evidence:
PMID:9305962
Purine nucleoside phosphorylase. 1. Structure-function studies.
|
|
GO:0002060
purine nucleobase binding
|
IDA
PMID:9305962 Purine nucleoside phosphorylase. 1. Structure-function studi... |
ACCEPT |
Summary: PNP binds the purine base (product/substrate) in its active site; supporting MF consistent with structural studies.
Reason: The purine base binding site (Asn243/Glu201) is defined by structure-function mutagenesis; base binding is integral to the phosphorolysis reaction.
Supporting Evidence:
PMID:9305962
Purine nucleoside phosphorylase. 1. Structure-function studies.
|
|
GO:0004731
purine-nucleoside phosphorylase activity
|
IDA
PMID:16930574 Intracellular delivery of purine nucleoside phosphorylase (P... |
ACCEPT |
Summary: PNP enzymatic activity assayed in the enzyme-replacement study; supports the core molecular function.
Reason: Intracellular PNP activity is measured/restored in PNP-deficient lymphocytes, confirming the enzyme's phosphorylase activity.
Supporting Evidence:
PMID:16930574
Purine nucleoside phosphorylase (PNP) is an intracellular enzyme crucial for
|
|
GO:0004731
purine-nucleoside phosphorylase activity
|
IDA
PMID:18938130 Effect of the phosphate substrate on drug-inhibitor binding ... |
ACCEPT |
Summary: PNP enzymatic activity measured by ITC-based assay; supports the core MF.
Reason: The study assays human PNP enzymatic activity (7-methylguanosine + phosphate), confirming phosphorylase activity.
|
|
GO:0004731
purine-nucleoside phosphorylase activity
|
IDA
PMID:3029074 A human purine nucleoside phosphorylase deficiency caused by... |
ACCEPT |
Summary: PNP catalytic activity (and its loss in the E89K deficiency variant) directly demonstrated; supports the core MF.
Reason: Reversion of the single-base E89K mutation restores PNP catalytic activity, directly linking the gene product to phosphorylase activity.
Supporting Evidence:
PMID:3029074
This single base mutation alters the codon at position 89 from Glu to Lys, a
|
|
GO:0004731
purine-nucleoside phosphorylase activity
|
IDA
PMID:9305962 Purine nucleoside phosphorylase. 1. Structure-function studi... |
ACCEPT |
Summary: Steady-state kinetics of human PNP and active-site mutants; core MF.
Reason: Structure-function/mutagenesis study directly characterizes the phosphorylase activity of human PNP.
Supporting Evidence:
PMID:9305962
Purine nucleoside phosphorylase. 1. Structure-function studies.
|
|
GO:0005737
cytoplasm
|
IDA
PMID:16930574 Intracellular delivery of purine nucleoside phosphorylase (P... |
ACCEPT |
Summary: Direct evidence that PNP is predominantly cytoplasmic; consistent with the cytosol annotations.
Reason: Endogenous and delivered PNP are predominantly distributed in the cytoplasm, supporting the cytoplasm/cytosol localization.
Supporting Evidence:
PMID:16930574
distributed in the cytoplasm
|
|
GO:0005737
cytoplasm
|
IDA
PMID:3029074 A human purine nucleoside phosphorylase deficiency caused by... |
ACCEPT |
Summary: Cytoplasmic localization of PNP; consistent with cytosolic function.
Reason: Consistent with the curated cytoplasm/cytosol location of the enzyme.
|
|
GO:0006139
nucleobase-containing compound metabolic process
|
IDA
PMID:3029074 A human purine nucleoside phosphorylase deficiency caused by... |
MARK AS OVER ANNOTATED |
Summary: Very broad "nucleobase-containing compound metabolic process"; correct but far less informative than the specific purine catabolic/salvage terms.
Reason: This high-level parent term is subsumed by the specific inosine/guanosine (deoxy)nucleoside catabolic and purine salvage terms already annotated.
|
|
GO:0006738
nicotinamide riboside catabolic process
|
IDA
PMID:19001417 Nicotinamide riboside and nicotinic acid riboside salvage in... |
ACCEPT |
Summary: PNP phosphorolyses nicotinamide riboside to nicotinamide, a genuine alternative-substrate activity feeding NAD+ salvage.
Reason: Mammalian PNP (not MTAP) is responsible for kinase-independent NR utilization, cleaving NR to nicotinamide; directly demonstrated in mammalian extracts and by Immucillin-H (PNP-specific inhibitor) sensitivity.
Supporting Evidence:
PMID:19001417
that mammalian purine nucleoside phosphorylase but not methylthioadenosine
|
|
GO:0006955
immune response
|
IMP
PMID:16930574 Intracellular delivery of purine nucleoside phosphorylase (P... |
KEEP AS NON CORE |
Summary: PNP is required for normal T-cell immune function; its deficiency causes T-cell immunodeficiency. Indirect, downstream physiological role.
Reason: "Immune response" is a broad downstream consequence of PNP's metabolic role (dGTP toxicity to T lymphocytes on loss of function); enzyme replacement in PNP-deficient T cells corrects their function. Not a core molecular function.
Supporting Evidence:
PMID:16930574
functions of PNP-deficient T lymphocytes including their response to stimulation
|
|
GO:0009410
response to xenobiotic stimulus
|
IMP
PMID:15047506 Role of purine nucleoside phosphorylase in interactions betw... |
KEEP AS NON CORE |
Summary: PNP phosphorolyses the antiviral prodrug 2',3'-dideoxyinosine (ddI), a drug/xenobiotic-metabolism role.
Reason: PNP-dependent breakdown of the xenobiotic ddI is a pharmacologically relevant but peripheral activity reflecting its broad nucleoside-phosphorolysis chemistry, not a core physiological process.
Supporting Evidence:
PMID:15047506
A metabolic route for ddI clearance is its breakdown by purine nucleoside
|
|
GO:0042301
phosphate ion binding
|
IDA
PMID:18938130 Effect of the phosphate substrate on drug-inhibitor binding ... |
ACCEPT |
Summary: PNP binds inorganic phosphate, the co-substrate/nucleophile of phosphorolysis, in a dedicated phosphate-binding site; supporting MF.
Reason: Phosphate is the second substrate of the phosphorolysis reaction and binds a defined active-site pocket; phosphate binding is integral to catalysis and modulates inhibitor binding.
Supporting Evidence:
PMID:18938130
Effect of the phosphate substrate on drug-inhibitor binding to human purine
|
|
GO:0034418
urate biosynthetic process
|
IDA
PMID:16964310 TAT-mediated intracellular delivery of purine nucleoside pho... |
KEEP AS NON CORE |
Summary: PNP acts upstream in urate production (PNP -> hypoxanthine -> xanthine oxidase -> urate); an indirect downstream pathway role.
Reason: PNP generates hypoxanthine, the substrate for downstream oxidation to urate by xanthine oxidoreductase; PNP does not itself synthesize urate, so this is a pathway-level (acts_upstream_of_or_within) annotation.
|
|
GO:0042102
positive regulation of T cell proliferation
|
IDA
PMID:16964310 TAT-mediated intracellular delivery of purine nucleoside pho... |
KEEP AS NON CORE |
Summary: Restoring PNP in PNP-deficient mice corrects T-cell immunity; an indirect downstream immunological consequence.
Reason: PNP is not a direct regulator of T-cell proliferation; its loss causes dGTP-mediated T-cell toxicity, and enzyme replacement (TAT-PNP) rescues immune function in PNP-deficient mice. Physiological consequence, not core function.
Supporting Evidence:
PMID:16964310
severe T cell immunodeficiency, neurological
|
|
GO:0004731
purine-nucleoside phosphorylase activity
|
IDA
PMID:16964310 TAT-mediated intracellular delivery of purine nucleoside pho... |
ACCEPT |
Summary: PNP catalytic activity assayed/restored in the mouse enzyme-replacement study; supports the core MF.
Reason: TAT-PNP delivery restores PNP enzymatic activity in PNP-deficient tissues, confirming the phosphorylase activity of the enzyme.
Supporting Evidence:
PMID:16964310
severe T cell immunodeficiency, neurological
|
|
GO:0006148
inosine catabolic process
|
IDA
PMID:16964310 TAT-mediated intracellular delivery of purine nucleoside pho... |
ACCEPT |
Summary: PNP catabolizes inosine; restoring the activity corrects nucleoside homeostasis in PNP-deficient mice. Core catabolic role.
Reason: Correction of abnormal nucleoside homeostasis on PNP replacement is consistent with PNP's core inosine-catabolic function.
Supporting Evidence:
PMID:16964310
abnormal nucleoside homeostasis, severe T cell immunodeficiency, neurological
|
|
GO:0046638
positive regulation of alpha-beta T cell differentiation
|
IDA
PMID:16964310 TAT-mediated intracellular delivery of purine nucleoside pho... |
KEEP AS NON CORE |
Summary: Indirect downstream immunological consequence of PNP activity (T-cell development/function rescued by enzyme replacement).
Reason: PNP does not directly regulate alpha-beta T-cell differentiation; the phenotype reflects relief of dGTP toxicity to developing/activated T cells upon restoring enzyme activity. Non-core physiological consequence.
Supporting Evidence:
PMID:16964310
severe T cell immunodeficiency, neurological
|
402 Payment Required (no credits). No -deep-research-*.md file was created; none fabricated.PNP-uniprot.txt, PNP-goa.tsv, and cached publications/PMID_*.md (all 19 cited PMIDs present).id: P00491
gene_symbol: PNP
product_type: PROTEIN
status: INITIALIZED
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: >-
Purine nucleoside phosphorylase (PNP; EC 2.4.2.1) is a cytosolic homotrimeric
enzyme of purine catabolism and salvage. It catalyzes the reversible
phosphorolysis of the N-glycosidic bond of 6-oxopurine (deoxy)ribonucleosides,
converting inosine, guanosine and their 2'-deoxy forms (plus phosphate) to the
corresponding free purine base (hypoxanthine or guanine) and
(2'-deoxy)-alpha-D-ribose-1-phosphate. The liberated bases are either recycled
by salvage (e.g. by HPRT1) or channeled into oxidative catabolism (hypoxanthine
to xanthine to urate by xanthine oxidoreductase). PNP is highly specific for
6-oxopurine nucleosides and essentially inactive on adenine (6-amino) nucleosides.
It also phosphorolyses the pyridine nucleoside nicotinamide riboside, contributing
to a kinase-independent NAD+ salvage route. In humans, loss-of-function of PNP
causes purine nucleoside phosphorylase deficiency, an autosomal recessive disorder
in which accumulating (deoxy)guanosine and dGTP are toxic to T lymphocytes,
producing a severe T-cell immunodeficiency (a cause of severe combined
immunodeficiency) frequently accompanied by neurological impairment.
existing_annotations:
- term:
id: GO:0004731
label: purine-nucleoside phosphorylase activity
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: enables
review:
summary: >-
Core molecular function of PNP: phosphorolytic cleavage of purine
(deoxy)ribonucleosides. Phylogenetic (IBA) annotation consistent with
abundant human experimental evidence.
action: ACCEPT
reason: >-
This is the well-established core catalytic activity of PNP (EC 2.4.2.1),
directly demonstrated for the human enzyme by multiple experimental studies.
supported_by:
- reference_id: PMID:6771276
supporting_text: "the phosphorolysis of inosine, deoxyinosine, guanosine, and deoxyguanosine with"
- reference_id: PMID:23438750
supporting_text: "catalyzes the reversible phosphorolysis of purine (deoxy)-ribonucleosides to the corresponding purine base"
- term:
id: GO:0005829
label: cytosol
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: is_active_in
review:
summary: >-
PNP is a soluble cytosolic enzyme; phylogenetic assignment of cytosolic
localization is correct and matches direct evidence in human cells.
action: ACCEPT
reason: >-
UniProt records the subcellular location as Cytoplasm, cytosol, and human
immunofluorescence (HPA) and direct assays place PNP in the cytosol; this is
the site of its catalytic function.
- term:
id: GO:0006148
label: inosine catabolic process
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: >-
PNP phosphorolyses inosine to hypoxanthine, a committed step of inosine
catabolism/salvage. Core biological process.
action: ACCEPT
reason: >-
Directly demonstrated: purified human PNP catalyzes phosphorolysis of inosine,
supporting its role in inosine catabolism.
supported_by:
- reference_id: PMID:6771276
supporting_text: "the phosphorolysis of inosine, deoxyinosine, guanosine, and deoxyguanosine with"
- term:
id: GO:0006149
label: deoxyinosine catabolic process
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: >-
PNP phosphorolyses 2'-deoxyinosine to hypoxanthine; part of its core
(deoxy)nucleoside catabolic activity.
action: ACCEPT
reason: >-
Purified human PNP catalyzes deoxyinosine phosphorolysis, and the enzyme acts
equally on ribo- and deoxyribonucleosides of 6-oxopurines.
supported_by:
- reference_id: PMID:6771276
supporting_text: "the phosphorolysis of inosine, deoxyinosine, guanosine, and deoxyguanosine with"
- term:
id: GO:0006161
label: deoxyguanosine catabolic process
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: >-
PNP phosphorolyses 2'-deoxyguanosine to guanine; a core catabolic step and
the one most relevant to PNP-deficiency pathology (dGTP accumulation).
action: ACCEPT
reason: >-
Purified human PNP catalyzes deoxyguanosine phosphorolysis; failure of this
step underlies the T-cell-toxic (deoxy)guanosine/dGTP buildup in PNP deficiency.
supported_by:
- reference_id: PMID:6771276
supporting_text: "the phosphorolysis of inosine, deoxyinosine, guanosine, and deoxyguanosine with"
- term:
id: GO:0034355
label: NAD+ biosynthetic process via the salvage pathway
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: >-
PNP phosphorolyses nicotinamide riboside (NR) to nicotinamide, providing a
kinase-independent entry into NAD+ salvage. Real but not the core catabolic
function of PNP.
action: KEEP_AS_NON_CORE
reason: >-
Mammalian PNP is the enzyme responsible for Nrk1-independent NR utilization,
cleaving NR (and nicotinic acid riboside) to feed NAD+ salvage; this is a
secondary/alternative-substrate role downstream of nucleoside phosphorolysis
rather than PNP's principal purine-catabolic function.
supported_by:
- reference_id: PMID:19001417
supporting_text: "that mammalian purine nucleoside phosphorylase but not methylthioadenosine"
- term:
id: GO:0046115
label: guanosine catabolic process
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: >-
PNP phosphorolyses guanosine to guanine; a core catabolic/salvage step.
action: ACCEPT
reason: >-
Purified human PNP catalyzes guanosine phosphorolysis with high affinity
(KM ~6 uM), a core substrate of the enzyme.
supported_by:
- reference_id: PMID:6771276
supporting_text: "the phosphorolysis of inosine, deoxyinosine, guanosine, and deoxyguanosine with"
- term:
id: GO:0003824
label: catalytic activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: >-
Root-level catalytic activity term from InterPro mapping; uninformative given
the specific EC 2.4.2.1 activity is annotated.
action: MARK_AS_OVER_ANNOTATED
reason: >-
GO:0003824 is the most general molecular-function term and conveys nothing
beyond the specific purine-nucleoside phosphorylase activity already annotated.
- term:
id: GO:0004731
label: purine-nucleoside phosphorylase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: enables
review:
summary: >-
Same core molecular function via automated EC/RHEA/ARBA mapping; correct.
action: ACCEPT
reason: >-
Automated mapping (EC 2.4.2.1 / RHEA:27646) to purine-nucleoside phosphorylase
activity is accurate and matches experimental evidence.
- term:
id: GO:0005829
label: cytosol
evidence_type: IEA
original_reference_id: GO_REF:0000044
qualifier: located_in
review:
summary: >-
Cytosol from UniProt subcellular-location keyword mapping; correct.
action: ACCEPT
reason: >-
Consistent with the curated Cytoplasm/cytosol location and direct human
evidence.
- term:
id: GO:0009116
label: nucleoside metabolic process
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: involved_in
review:
summary: >-
Broad but correct parent process (nucleoside metabolism) from InterPro mapping.
action: KEEP_AS_NON_CORE
reason: >-
Accurate as a general process term but less informative than the specific
purine (deoxy)nucleoside catabolic/salvage terms already present.
- term:
id: GO:0016763
label: pentosyltransferase activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: >-
Correct parent MF (PNP is a glycosyltransferase/pentosyltransferase, EC 2.4.2)
but broader than the specific activity.
action: KEEP_AS_NON_CORE
reason: >-
GO:0016763 is the accurate broad classification of the reaction chemistry;
retained as a non-core parent of purine-nucleoside phosphorylase activity.
- term:
id: GO:0047975
label: guanosine phosphorylase activity
evidence_type: IEA
original_reference_id: GO_REF:0000116
qualifier: enables
review:
summary: >-
Substrate-specific child activity (guanosine + phosphate = guanine +
ribose-1-phosphate); correct via RHEA mapping.
action: ACCEPT
reason: >-
PNP has robust guanosine phosphorylase activity (KM ~6 uM), a specific facet of
its EC 2.4.2.1 activity; automated RHEA:13233 mapping is correct.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:32814053
qualifier: enables
review:
summary: >-
Uninformative "protein binding" from a large-scale neurodegenerative-disease
Y2H interactome screen; multiple heterogeneous partners with no defined
functional consequence for PNP.
action: MARK_AS_OVER_ANNOTATED
reason: >-
This and the other GO:0005515 IPI lines derive from high-throughput binary
interactome mapping (yeast two-hybrid); the term is non-specific and does not
inform PNP's molecular function. Retained (not removed) per curation policy on
experimental IPI, but flagged as over-annotation.
supported_by:
- reference_id: PMID:32814053
supporting_text: "generated by systematic yeast two-hybrid"
- term:
id: GO:0042802
label: identical protein binding
evidence_type: IPI
original_reference_id: PMID:20212140
qualifier: enables
review:
summary: >-
Self-association reflecting PNP's obligate homotrimeric quaternary structure;
biologically meaningful.
action: ACCEPT
reason: >-
Human PNP is a homotrimer with catalytic sites at subunit interfaces, so
identical-protein (self) binding is a genuine structural property of the enzyme.
supported_by:
- reference_id: PMID:20212140
supporting_text: "Four generations of transition-state analogues for human purine nucleoside"
additional_reference_ids:
- PMID:23438750
- term:
id: GO:0042802
label: identical protein binding
evidence_type: IPI
original_reference_id: PMID:25502805
qualifier: enables
review:
summary: >-
Self-association consistent with the homotrimeric architecture of PNP.
action: ACCEPT
reason: >-
Homotrimer formation is a well-established structural feature; identical
protein binding is appropriate.
supported_by:
- reference_id: PMID:23438750
supporting_text: "Human PNP is a homotrimer"
- term:
id: GO:0042802
label: identical protein binding
evidence_type: IPI
original_reference_id: PMID:31515488
qualifier: enables
review:
summary: >-
Self-association consistent with the homotrimeric architecture of PNP.
action: ACCEPT
reason: >-
Homotrimer formation is a well-established structural feature; identical
protein binding is appropriate.
supported_by:
- reference_id: PMID:23438750
supporting_text: "Human PNP is a homotrimer"
- term:
id: GO:0042802
label: identical protein binding
evidence_type: IPI
original_reference_id: PMID:32296183
qualifier: enables
review:
summary: >-
Self-association consistent with the homotrimeric architecture of PNP.
action: ACCEPT
reason: >-
Homotrimer formation is a well-established structural feature; identical
protein binding is appropriate.
supported_by:
- reference_id: PMID:23438750
supporting_text: "Human PNP is a homotrimer"
- term:
id: GO:0005829
label: cytosol
evidence_type: IDA
original_reference_id: GO_REF:0000052
qualifier: located_in
review:
summary: >-
Direct immunofluorescence (HPA) localization to cytosol; correct core location.
action: ACCEPT
reason: >-
Direct human-cell evidence for cytosolic localization, the functional site of
the enzyme.
- term:
id: GO:0047975
label: guanosine phosphorylase activity
evidence_type: EXP
original_reference_id: PMID:9305964
qualifier: enables
review:
summary: >-
Experimentally measured guanosine phosphorylase activity (a specific facet of
EC 2.4.2.1) for human PNP.
action: ACCEPT
reason: >-
Kinetic characterization of human PNP includes guanosine as a high-affinity
substrate, supporting guanosine phosphorylase activity.
supported_by:
- reference_id: PMID:9305964
supporting_text: "highly specific for 6-oxopurine"
- term:
id: GO:0004731
label: purine-nucleoside phosphorylase activity
evidence_type: IDA
original_reference_id: PMID:6771276
qualifier: enables
review:
summary: >-
Direct assay of purified human (granulocyte) PNP demonstrating phosphorolysis
of 6-oxopurine (deoxy)nucleosides. Core function.
action: ACCEPT
reason: >-
Purified human enzyme catalyzes phosphorolysis of inosine, deoxyinosine,
guanosine and deoxyguanosine, directly establishing the activity.
supported_by:
- reference_id: PMID:6771276
supporting_text: "the phosphorolysis of inosine, deoxyinosine, guanosine, and deoxyguanosine with"
- term:
id: GO:0006149
label: deoxyinosine catabolic process
evidence_type: IDA
original_reference_id: PMID:6771276
qualifier: acts_upstream_of_or_within
review:
summary: >-
PNP phosphorolyses 2'-deoxyinosine (to hypoxanthine); part of deoxyinosine
catabolism.
action: ACCEPT
reason: >-
Directly demonstrated deoxyinosine phosphorolysis by the purified human enzyme.
supported_by:
- reference_id: PMID:6771276
supporting_text: "the phosphorolysis of inosine, deoxyinosine, guanosine, and deoxyguanosine with"
- term:
id: GO:0006157
label: deoxyadenosine catabolic process
evidence_type: IDA
original_reference_id: PMID:6771276
qualifier: acts_upstream_of_or_within
review:
summary: >-
Pathway-level (acts_upstream_of_or_within) annotation for deoxyadenosine
catabolism. PNP does not act directly on deoxyadenosine (an adenine
nucleoside), but participates downstream in the pathway after deamination.
action: KEEP_AS_NON_CORE
reason: >-
The cited paper explicitly states that adenine (deoxy)ribonucleosides are NOT
substrates of PNP, so this is not a direct enzymatic activity; however the
curator's acts_upstream_of_or_within annotation reflects PNP's downstream role
in the broader deoxyadenosine catabolic pathway (relevant to the dATP/dGTP
accumulation of PNP deficiency). Retained as non-core rather than removed.
supported_by:
- reference_id: PMID:6771276
supporting_text: "ribonucleosides and deoxyribonucleosides of adenine and the pyrimidines are not"
- term:
id: GO:0006204
label: IMP catabolic process
evidence_type: IDA
original_reference_id: PMID:6771276
qualifier: acts_upstream_of_or_within
review:
summary: >-
Pathway-level annotation for IMP catabolism. PNP acts on inosine (the
dephosphorylated nucleoside), not on IMP directly, but functions downstream in
the IMP-degradation pathway.
action: KEEP_AS_NON_CORE
reason: >-
PNP's substrate is inosine (from IMP after 5'-nucleotidase), not IMP itself;
the acts_upstream_of_or_within qualifier captures its downstream role in the
IMP catabolic pathway. Retained as non-core.
- term:
id: GO:0046059
label: dAMP catabolic process
evidence_type: IDA
original_reference_id: PMID:6771276
qualifier: acts_upstream_of_or_within
review:
summary: >-
Pathway-level annotation for dAMP catabolism. PNP does not act on dAMP or on
adenine deoxynucleosides directly; downstream/pathway-context annotation.
action: KEEP_AS_NON_CORE
reason: >-
PNP does not phosphorolyse adenine nucleosides (the paper states adenine
deoxyribonucleosides are not substrates) and acts on nucleosides not
nucleotides; the annotation reflects downstream pathway participation.
Retained as non-core rather than removed for an experimental IDA.
supported_by:
- reference_id: PMID:6771276
supporting_text: "ribonucleosides and deoxyribonucleosides of adenine and the pyrimidines are not"
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-9735775
qualifier: located_in
review:
summary: >-
Cytosol localization from Reactome (defective-PNP inosine reaction); correct
core location.
action: ACCEPT
reason: >-
Consistent with the established cytosolic site of PNP function.
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-9735789
qualifier: located_in
review:
summary: >-
Cytosol localization from Reactome (defective-PNP guanosine reaction); correct.
action: ACCEPT
reason: >-
Consistent with the established cytosolic site of PNP function.
- term:
id: GO:0006149
label: deoxyinosine catabolic process
evidence_type: IDA
original_reference_id: PMID:6771276
qualifier: involved_in
review:
summary: >-
Duplicate (involved_in) annotation of deoxyinosine catabolism; directly
supported.
action: ACCEPT
reason: >-
Direct assay of deoxyinosine phosphorolysis by purified human PNP.
supported_by:
- reference_id: PMID:6771276
supporting_text: "the phosphorolysis of inosine, deoxyinosine, guanosine, and deoxyguanosine with"
- term:
id: GO:0006157
label: deoxyadenosine catabolic process
evidence_type: IDA
original_reference_id: PMID:6771276
qualifier: involved_in
review:
summary: >-
involved_in duplicate of the deoxyadenosine-catabolism pathway annotation.
PNP does not act on deoxyadenosine directly.
action: KEEP_AS_NON_CORE
reason: >-
As above: adenine deoxyribonucleosides are not PNP substrates, so this
reflects a downstream/pathway role rather than a direct activity; retained as
non-core.
supported_by:
- reference_id: PMID:6771276
supporting_text: "ribonucleosides and deoxyribonucleosides of adenine and the pyrimidines are not"
- term:
id: GO:0006204
label: IMP catabolic process
evidence_type: IDA
original_reference_id: PMID:6771276
qualifier: involved_in
review:
summary: >-
involved_in duplicate of the IMP-catabolism pathway annotation; PNP acts on
inosine downstream of IMP.
action: KEEP_AS_NON_CORE
reason: >-
PNP's direct substrate is inosine, not IMP; retained as a downstream
pathway-level annotation.
- term:
id: GO:0000255
label: allantoin metabolic process
evidence_type: IDA
original_reference_id: PMID:6771276
qualifier: involved_in
review:
summary: >-
Allantoin metabolism is several steps downstream of PNP (via urate) and does
not occur in humans, who lack urate oxidase; this appears to be an
over-propagated/incorrect pathway annotation for the human gene.
action: MARK_AS_OVER_ANNOTATED
reason: >-
The cited human granulocyte study characterizes PNP nucleoside phosphorolysis
and does not address allantoin; humans do not synthesize allantoin (uricase is
a pseudogene), so an allantoin metabolic process annotation is not appropriate
for human PNP. Flagged as over-annotation rather than removed, since it is an
experimental IDA whose full text was not reviewed here.
- term:
id: GO:0046059
label: dAMP catabolic process
evidence_type: IDA
original_reference_id: PMID:6771276
qualifier: involved_in
review:
summary: >-
involved_in duplicate of the dAMP-catabolism pathway annotation; PNP acts on
nucleosides, not dAMP, and not on adenine nucleosides.
action: KEEP_AS_NON_CORE
reason: >-
Retained as a downstream pathway-level annotation; PNP does not directly act on
dAMP or adenine (deoxy)nucleosides.
supported_by:
- reference_id: PMID:6771276
supporting_text: "ribonucleosides and deoxyribonucleosides of adenine and the pyrimidines are not"
- term:
id: GO:0004731
label: purine-nucleoside phosphorylase activity
evidence_type: IDA
original_reference_id: PMID:5056638
qualifier: enables
review:
summary: >-
PNP enzymatic activity measured in human erythrocytes; supports the core
molecular function.
action: ACCEPT
reason: >-
Human erythrocyte PNP activity assay supports the enzyme's phosphorylase
activity (abstract-only cache; defer to the experimental curator).
- term:
id: GO:0004731
label: purine-nucleoside phosphorylase activity
evidence_type: IDA
original_reference_id: PMID:23438750
qualifier: enables
review:
summary: >-
Kinetic/structural characterization of human PNP demonstrating phosphorolysis
of purine (deoxy)ribonucleosides. Core function.
action: ACCEPT
reason: >-
Directly establishes reversible phosphorolysis of purine (deoxy)ribonucleosides
by the human enzyme, including steady-state kinetics for inosine.
supported_by:
- reference_id: PMID:23438750
supporting_text: "catalyzes the reversible phosphorolysis of purine (deoxy)-ribonucleosides to the corresponding purine base"
- term:
id: GO:0006148
label: inosine catabolic process
evidence_type: IDA
original_reference_id: PMID:23438750
qualifier: involved_in
review:
summary: >-
PNP phosphorolyses inosine (to hypoxanthine); core catabolic step, kinetically
characterized.
action: ACCEPT
reason: >-
Inosine phosphorolysis is directly characterized (steady-state kinetics) for
the human enzyme.
supported_by:
- reference_id: PMID:23438750
supporting_text: "catalyzes the reversible phosphorolysis of purine (deoxy)-ribonucleosides to the corresponding purine base"
- term:
id: GO:0043101
label: purine-containing compound salvage
evidence_type: IDA
original_reference_id: PMID:18938130
qualifier: involved_in
review:
summary: >-
PNP participates in purine salvage by generating free bases (hypoxanthine,
guanine) for re-use; core biological role.
action: ACCEPT
reason: >-
PNP's phosphorolysis of purine nucleosides yields free bases that are salvaged
(e.g. by HPRT1); the reaction equilibrium in vivo also supports nucleoside
(re)synthesis, consistent with a salvage role. UniProt assigns the pathway
"purine nucleoside salvage".
- term:
id: GO:0009165
label: nucleotide biosynthetic process
evidence_type: IGI
original_reference_id: PMID:19001417
qualifier: involved_in
review:
summary: >-
Broad "nucleotide biosynthetic process" from a genetic-interaction study of NR
salvage; PNP itself catabolizes nucleosides, so nucleotide biosynthesis is an
over-broad downstream framing.
action: MARK_AS_OVER_ANNOTATED
reason: >-
PNP produces free bases/ribose-1-phosphate that can be recycled into
nucleotides via salvage, but PNP is a phosphorylase (nucleoside catabolism),
and GO:0009165 is a broad biosynthetic term better assigned to the downstream
salvage kinases. The specific NR-catabolism and salvage terms already capture
the relevant biology.
- term:
id: GO:0005576
label: extracellular region
evidence_type: TAS
original_reference_id: Reactome:R-HSA-6798748
qualifier: located_in
review:
summary: >-
Extracellular localization via Reactome neutrophil-degranulation
(secretory-granule exocytosis) pathway; PNP is detected extracellularly but
this is not its functional compartment.
action: KEEP_AS_NON_CORE
reason: >-
PNP is a cytosolic enzyme released during neutrophil degranulation/secretion
and detected in the extracellular space; not the site of its catalytic function.
- term:
id: GO:0005576
label: extracellular region
evidence_type: TAS
original_reference_id: Reactome:R-HSA-6800434
qualifier: located_in
review:
summary: >-
Extracellular localization via Reactome ficolin-rich-granule exocytosis;
detected extracellularly, non-functional compartment.
action: KEEP_AS_NON_CORE
reason: >-
Same as the secretory-granule route: released cytosolic protein, not the
functional location.
- term:
id: GO:0034774
label: secretory granule lumen
evidence_type: TAS
original_reference_id: Reactome:R-HSA-6798748
qualifier: located_in
review:
summary: >-
Secretory-granule-lumen localization from neutrophil-degranulation Reactome
pathway; reflects presence in granules, not functional site.
action: KEEP_AS_NON_CORE
reason: >-
PNP is packaged in neutrophil granules and released on degranulation; a
non-core localization for a cytosolic enzyme.
- term:
id: GO:1904813
label: ficolin-1-rich granule lumen
evidence_type: TAS
original_reference_id: Reactome:R-HSA-6800434
qualifier: located_in
review:
summary: >-
Ficolin-1-rich granule lumen from neutrophil-degranulation Reactome; non-core
localization.
action: KEEP_AS_NON_CORE
reason: >-
Reflects granule content in neutrophils, not the cytosolic functional site.
- term:
id: GO:0070062
label: extracellular exosome
evidence_type: HDA
original_reference_id: PMID:23533145
qualifier: located_in
review:
summary: >-
Detected in extracellular exosomes by high-throughput proteomics; PNP is an
abundant cytosolic protein commonly captured in exosome preparations.
action: KEEP_AS_NON_CORE
reason: >-
Exosome proteomics frequently recovers abundant cytosolic enzymes; this does
not indicate a functional exosomal role for PNP.
- term:
id: GO:0070062
label: extracellular exosome
evidence_type: HDA
original_reference_id: PMID:19056867
qualifier: located_in
review:
summary: >-
Detected in urinary exosomes by proteomics; non-functional localization.
action: KEEP_AS_NON_CORE
reason: >-
High-throughput exosome/proteomics detection of an abundant cytosolic enzyme;
not its functional compartment.
- term:
id: GO:0070062
label: extracellular exosome
evidence_type: HDA
original_reference_id: PMID:20458337
qualifier: located_in
review:
summary: >-
Detected in B-cell exosomes by proteomics; non-functional localization.
action: KEEP_AS_NON_CORE
reason: >-
As above; proteomic detection in exosomes does not establish a functional role.
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-112033
qualifier: located_in
review:
summary: >-
Cytosol localization from Reactome (PNP inosine synthesis reaction); correct
core location.
action: ACCEPT
reason: >-
Consistent with the established cytosolic site of PNP function.
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-112034
qualifier: located_in
review:
summary: >-
Cytosol localization from Reactome (PNP guanosine synthesis reaction); correct.
action: ACCEPT
reason: >-
Consistent with the established cytosolic site of PNP function.
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-74242
qualifier: located_in
review:
summary: >-
Cytosol localization from Reactome (PNP inosine phosphorolysis); correct.
action: ACCEPT
reason: >-
Consistent with the established cytosolic site of PNP function.
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-74249
qualifier: located_in
review:
summary: >-
Cytosol localization from Reactome (PNP guanosine phosphorolysis); correct.
action: ACCEPT
reason: >-
Consistent with the established cytosolic site of PNP function.
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-9755044
qualifier: located_in
review:
summary: >-
Cytosol localization from Reactome (PNP-mediated ribavirin transformation);
correct core location.
action: ACCEPT
reason: >-
Consistent with the established cytosolic site of PNP function.
- term:
id: GO:0032743
label: positive regulation of interleukin-2 production
evidence_type: IMP
original_reference_id: PMID:16930574
qualifier: involved_in
review:
summary: >-
Restoring PNP in PNP-deficient T lymphocytes corrects IL-2 secretion; an
indirect, downstream immunological consequence of the metabolic enzyme.
action: KEEP_AS_NON_CORE
reason: >-
PNP does not directly regulate IL-2 transcription; loss of PNP causes
dGTP-mediated T-cell dysfunction, and enzyme replacement rescues IL-2
secretion. This is a physiological consequence, not a core molecular role.
supported_by:
- reference_id: PMID:16930574
supporting_text: "functions of PNP-deficient T lymphocytes including their response to stimulation"
- term:
id: GO:0001882
label: nucleoside binding
evidence_type: IDA
original_reference_id: PMID:9305962
qualifier: enables
review:
summary: >-
PNP binds its purine-nucleoside substrate in the active site; supporting
molecular function underlying catalysis.
action: ACCEPT
reason: >-
Structure-function studies define the purine-binding/active site of human PNP
that engages the nucleoside substrate.
supported_by:
- reference_id: PMID:9305962
supporting_text: "Purine nucleoside phosphorylase. 1. Structure-function studies."
- term:
id: GO:0002060
label: purine nucleobase binding
evidence_type: IDA
original_reference_id: PMID:9305962
qualifier: enables
review:
summary: >-
PNP binds the purine base (product/substrate) in its active site; supporting
MF consistent with structural studies.
action: ACCEPT
reason: >-
The purine base binding site (Asn243/Glu201) is defined by structure-function
mutagenesis; base binding is integral to the phosphorolysis reaction.
supported_by:
- reference_id: PMID:9305962
supporting_text: "Purine nucleoside phosphorylase. 1. Structure-function studies."
- term:
id: GO:0004731
label: purine-nucleoside phosphorylase activity
evidence_type: IDA
original_reference_id: PMID:16930574
qualifier: enables
review:
summary: >-
PNP enzymatic activity assayed in the enzyme-replacement study; supports the
core molecular function.
action: ACCEPT
reason: >-
Intracellular PNP activity is measured/restored in PNP-deficient lymphocytes,
confirming the enzyme's phosphorylase activity.
supported_by:
- reference_id: PMID:16930574
supporting_text: "Purine nucleoside phosphorylase (PNP) is an intracellular enzyme crucial for"
- term:
id: GO:0004731
label: purine-nucleoside phosphorylase activity
evidence_type: IDA
original_reference_id: PMID:18938130
qualifier: enables
review:
summary: >-
PNP enzymatic activity measured by ITC-based assay; supports the core MF.
action: ACCEPT
reason: >-
The study assays human PNP enzymatic activity (7-methylguanosine + phosphate),
confirming phosphorylase activity.
- term:
id: GO:0004731
label: purine-nucleoside phosphorylase activity
evidence_type: IDA
original_reference_id: PMID:3029074
qualifier: enables
review:
summary: >-
PNP catalytic activity (and its loss in the E89K deficiency variant) directly
demonstrated; supports the core MF.
action: ACCEPT
reason: >-
Reversion of the single-base E89K mutation restores PNP catalytic activity,
directly linking the gene product to phosphorylase activity.
supported_by:
- reference_id: PMID:3029074
supporting_text: "This single base mutation alters the codon at position 89 from Glu to Lys, a"
- term:
id: GO:0004731
label: purine-nucleoside phosphorylase activity
evidence_type: IDA
original_reference_id: PMID:9305962
qualifier: enables
review:
summary: >-
Steady-state kinetics of human PNP and active-site mutants; core MF.
action: ACCEPT
reason: >-
Structure-function/mutagenesis study directly characterizes the phosphorylase
activity of human PNP.
supported_by:
- reference_id: PMID:9305962
supporting_text: "Purine nucleoside phosphorylase. 1. Structure-function studies."
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IDA
original_reference_id: PMID:16930574
qualifier: located_in
review:
summary: >-
Direct evidence that PNP is predominantly cytoplasmic; consistent with the
cytosol annotations.
action: ACCEPT
reason: >-
Endogenous and delivered PNP are predominantly distributed in the cytoplasm,
supporting the cytoplasm/cytosol localization.
supported_by:
- reference_id: PMID:16930574
supporting_text: "distributed in the cytoplasm"
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IDA
original_reference_id: PMID:3029074
qualifier: located_in
review:
summary: >-
Cytoplasmic localization of PNP; consistent with cytosolic function.
action: ACCEPT
reason: >-
Consistent with the curated cytoplasm/cytosol location of the enzyme.
- term:
id: GO:0006139
label: nucleobase-containing compound metabolic process
evidence_type: IDA
original_reference_id: PMID:3029074
qualifier: involved_in
review:
summary: >-
Very broad "nucleobase-containing compound metabolic process"; correct but far
less informative than the specific purine catabolic/salvage terms.
action: MARK_AS_OVER_ANNOTATED
reason: >-
This high-level parent term is subsumed by the specific inosine/guanosine
(deoxy)nucleoside catabolic and purine salvage terms already annotated.
- term:
id: GO:0006738
label: nicotinamide riboside catabolic process
evidence_type: IDA
original_reference_id: PMID:19001417
qualifier: involved_in
review:
summary: >-
PNP phosphorolyses nicotinamide riboside to nicotinamide, a genuine
alternative-substrate activity feeding NAD+ salvage.
action: ACCEPT
reason: >-
Mammalian PNP (not MTAP) is responsible for kinase-independent NR utilization,
cleaving NR to nicotinamide; directly demonstrated in mammalian extracts and by
Immucillin-H (PNP-specific inhibitor) sensitivity.
supported_by:
- reference_id: PMID:19001417
supporting_text: "that mammalian purine nucleoside phosphorylase but not methylthioadenosine"
- term:
id: GO:0006955
label: immune response
evidence_type: IMP
original_reference_id: PMID:16930574
qualifier: involved_in
review:
summary: >-
PNP is required for normal T-cell immune function; its deficiency causes T-cell
immunodeficiency. Indirect, downstream physiological role.
action: KEEP_AS_NON_CORE
reason: >-
"Immune response" is a broad downstream consequence of PNP's metabolic role
(dGTP toxicity to T lymphocytes on loss of function); enzyme replacement in
PNP-deficient T cells corrects their function. Not a core molecular function.
supported_by:
- reference_id: PMID:16930574
supporting_text: "functions of PNP-deficient T lymphocytes including their response to stimulation"
- term:
id: GO:0009410
label: response to xenobiotic stimulus
evidence_type: IMP
original_reference_id: PMID:15047506
qualifier: involved_in
review:
summary: >-
PNP phosphorolyses the antiviral prodrug 2',3'-dideoxyinosine (ddI), a
drug/xenobiotic-metabolism role.
action: KEEP_AS_NON_CORE
reason: >-
PNP-dependent breakdown of the xenobiotic ddI is a pharmacologically relevant
but peripheral activity reflecting its broad nucleoside-phosphorolysis
chemistry, not a core physiological process.
supported_by:
- reference_id: PMID:15047506
supporting_text: "A metabolic route for ddI clearance is its breakdown by purine nucleoside"
- term:
id: GO:0042301
label: phosphate ion binding
evidence_type: IDA
original_reference_id: PMID:18938130
qualifier: enables
review:
summary: >-
PNP binds inorganic phosphate, the co-substrate/nucleophile of phosphorolysis,
in a dedicated phosphate-binding site; supporting MF.
action: ACCEPT
reason: >-
Phosphate is the second substrate of the phosphorolysis reaction and binds a
defined active-site pocket; phosphate binding is integral to catalysis and
modulates inhibitor binding.
supported_by:
- reference_id: PMID:18938130
supporting_text: "Effect of the phosphate substrate on drug-inhibitor binding to human purine"
- term:
id: GO:0034418
label: urate biosynthetic process
evidence_type: IDA
original_reference_id: PMID:16964310
qualifier: acts_upstream_of_or_within
review:
summary: >-
PNP acts upstream in urate production (PNP -> hypoxanthine -> xanthine
oxidase -> urate); an indirect downstream pathway role.
action: KEEP_AS_NON_CORE
reason: >-
PNP generates hypoxanthine, the substrate for downstream oxidation to urate by
xanthine oxidoreductase; PNP does not itself synthesize urate, so this is a
pathway-level (acts_upstream_of_or_within) annotation.
- term:
id: GO:0042102
label: positive regulation of T cell proliferation
evidence_type: IDA
original_reference_id: PMID:16964310
qualifier: acts_upstream_of_or_within
review:
summary: >-
Restoring PNP in PNP-deficient mice corrects T-cell immunity; an indirect
downstream immunological consequence.
action: KEEP_AS_NON_CORE
reason: >-
PNP is not a direct regulator of T-cell proliferation; its loss causes
dGTP-mediated T-cell toxicity, and enzyme replacement (TAT-PNP) rescues immune
function in PNP-deficient mice. Physiological consequence, not core function.
supported_by:
- reference_id: PMID:16964310
supporting_text: "severe T cell immunodeficiency, neurological"
- term:
id: GO:0004731
label: purine-nucleoside phosphorylase activity
evidence_type: IDA
original_reference_id: PMID:16964310
qualifier: enables
review:
summary: >-
PNP catalytic activity assayed/restored in the mouse enzyme-replacement study;
supports the core MF.
action: ACCEPT
reason: >-
TAT-PNP delivery restores PNP enzymatic activity in PNP-deficient tissues,
confirming the phosphorylase activity of the enzyme.
supported_by:
- reference_id: PMID:16964310
supporting_text: "severe T cell immunodeficiency, neurological"
- term:
id: GO:0006148
label: inosine catabolic process
evidence_type: IDA
original_reference_id: PMID:16964310
qualifier: acts_upstream_of_or_within
review:
summary: >-
PNP catabolizes inosine; restoring the activity corrects nucleoside
homeostasis in PNP-deficient mice. Core catabolic role.
action: ACCEPT
reason: >-
Correction of abnormal nucleoside homeostasis on PNP replacement is consistent
with PNP's core inosine-catabolic function.
supported_by:
- reference_id: PMID:16964310
supporting_text: "abnormal nucleoside homeostasis, severe T cell immunodeficiency, neurological"
- term:
id: GO:0046638
label: positive regulation of alpha-beta T cell differentiation
evidence_type: IDA
original_reference_id: PMID:16964310
qualifier: acts_upstream_of_or_within
review:
summary: >-
Indirect downstream immunological consequence of PNP activity (T-cell
development/function rescued by enzyme replacement).
action: KEEP_AS_NON_CORE
reason: >-
PNP does not directly regulate alpha-beta T-cell differentiation; the phenotype
reflects relief of dGTP toxicity to developing/activated T cells upon restoring
enzyme activity. Non-core physiological consequence.
supported_by:
- reference_id: PMID:16964310
supporting_text: "severe T cell immunodeficiency, neurological"
core_functions:
- description: >-
Phosphorolytic cleavage of the N-glycosidic bond of 6-oxopurine
(deoxy)ribonucleosides (inosine, guanosine, 2'-deoxyinosine, 2'-deoxyguanosine),
using inorganic phosphate to produce the free purine base (hypoxanthine or
guanine) plus (2'-deoxy)-alpha-D-ribose-1-phosphate.
molecular_function:
id: GO:0004731
label: purine-nucleoside phosphorylase activity
directly_involved_in:
- id: GO:0006148
label: inosine catabolic process
supported_by:
- reference_id: PMID:6771276
supporting_text: "the phosphorolysis of inosine, deoxyinosine, guanosine, and deoxyguanosine with"
- reference_id: PMID:23438750
supporting_text: "catalyzes the reversible phosphorolysis of purine (deoxy)-ribonucleosides to the corresponding purine base"
- description: >-
Generation of free purine bases (hypoxanthine, guanine) from purine nucleosides,
supplying the purine salvage pathway; the reversible reaction also contributes to
nucleoside interconversion in purine-containing compound salvage.
molecular_function:
id: GO:0004731
label: purine-nucleoside phosphorylase activity
directly_involved_in:
- id: GO:0043101
label: purine-containing compound salvage
locations:
- id: GO:0005829
label: cytosol
supported_by:
- reference_id: PMID:9305964
supporting_text: "highly specific for 6-oxopurine"
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:0000052
title: Gene Ontology annotation based on curation of immunofluorescence data
findings: []
- id: GO_REF:0000116
title: Automatic Gene Ontology annotation based on Rhea mapping
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: PMID:15047506
title: Role of purine nucleoside phosphorylase in interactions between 2',3'-dideoxyinosine
and allopurinol, ganciclovir, or tenofovir.
findings: []
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: >-
Full text cached; establishes PNP-dependent phosphorolysis/clearance of the
antiviral ddI, supporting the response-to-xenobiotic annotation.
- id: PMID:16930574
title: Intracellular delivery of purine nucleoside phosphorylase (PNP) fused to
protein transduction domain corrects PNP deficiency in vitro.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Enzyme-replacement study confirming PNP activity, cytoplasmic localization, and
correction of T-lymphocyte function/IL-2 in PNP-deficient cells.
- id: PMID:16964310
title: TAT-mediated intracellular delivery of purine nucleoside phosphorylase corrects
its deficiency in mice.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
In vivo mouse enzyme replacement; ties PNP activity to correction of nucleoside
homeostasis and T-cell immunodeficiency (downstream immune/urate annotations).
- id: PMID:18938130
title: Effect of the phosphate substrate on drug-inhibitor binding to human purine
nucleoside phosphorylase.
findings: []
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: >-
ITC study of human PNP; supports phosphate-ion binding and enzymatic activity;
confirms trimer with catalytic sites at subunit interfaces.
- id: PMID:19001417
title: Nicotinamide riboside and nicotinic acid riboside salvage in fungi and mammals.
Quantitative basis for Urh1 and purine nucleoside phosphorylase function in NAD+
metabolism.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Full text cached; demonstrates mammalian PNP (not MTAP) as the NR phosphorylase
feeding NAD+ salvage; supports NR catabolism annotation.
- id: PMID:19056867
title: Large-scale proteomics and phosphoproteomics of urinary exosomes.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: >-
High-throughput exosome proteomics; supports incidental exosome detection, not
a functional localization.
- id: PMID:20212140
title: Four generations of transition-state analogues for human purine nucleoside
phosphorylase.
findings: []
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: >-
Structural study of human PNP transition-state analogue inhibitors; used here
as an IntAct self-interaction source consistent with the homotrimer.
- 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: >-
High-throughput exosome proteomics; incidental detection of a cytosolic enzyme.
- id: PMID:23438750
title: Catalytic site conformations in human PNP by 19F-NMR and crystallography.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Full text cached; establishes reversible phosphorolysis of purine
(deoxy)ribonucleosides, homotrimeric structure, and catalytic mechanism.
- id: PMID:23533145
title: In-depth proteomic analyses of exosomes isolated from expressed prostatic
secretions in urine.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: >-
High-throughput exosome proteomics; incidental detection.
- id: PMID:25502805
title: A massively parallel pipeline to clone DNA variants and examine molecular
phenotypes of human disease mutations.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: >-
Large-scale variant/interaction pipeline; used as an IntAct self-interaction
source consistent with the homotrimer.
- id: PMID:31515488
title: Extensive disruption of protein interactions by genetic variants across the
allele frequency spectrum in human populations.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: >-
Large-scale interactome-perturbation study; IntAct self-interaction source.
- id: PMID:32296183
title: A reference map of the human binary protein interactome.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: >-
Binary interactome map (HuRI); IntAct self-interaction source consistent with
homotrimer.
- id: PMID:32814053
title: Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins
and Uncovers Widespread Protein Aggregation in Affected Brains.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: >-
Y2H neurodegenerative-disease interactome; source of non-specific protein
binding IPIs flagged as over-annotation.
- id: PMID:3029074
title: A human purine nucleoside phosphorylase deficiency caused by a single base
change.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Identifies the E89K deficiency mutation abolishing PNP activity; supports
catalytic activity, cytoplasmic localization, and PNP-deficiency biology.
- id: PMID:5056638
title: Purine nucleoside phosphorylase activity of human erythrocytes in iron deficiency
anaemia.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: >-
Abstract-only cache; human erythrocyte PNP activity assay supporting the
catalytic-activity annotation.
- id: PMID:6771276
title: Characterization of purine nucleoside phosphorylase from human granulocytes
and its metabolism of deoxyribonucleosides.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Key experimental characterization: purified human PNP is a trimer and
phosphorolyses inosine, deoxyinosine, guanosine and deoxyguanosine; adenine and
pyrimidine (deoxy)nucleosides are not substrates.
- id: PMID:9305962
title: Purine nucleoside phosphorylase. 1. Structure-function studies.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Active-site mutagenesis (Asn243, Glu201, His86) defining substrate/base binding
and catalysis; supports nucleoside and purine-nucleobase binding.
- id: PMID:9305964
title: Purine nucleoside phosphorylase. 3. Reversal of purine base specificity by
site-directed mutagenesis.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Establishes 6-oxopurine specificity (inosine kcat/KM ~350,000-fold over
adenosine) and kinetic parameters; N243D reverses specificity to 6-aminopurines.
- id: Reactome:R-HSA-112033
title: PNP catalyzes the conversion of hypoxanthine and (deoxy)ribose-1-phosphate
to (deoxy)inosine
findings: []
- id: Reactome:R-HSA-112034
title: PNP catalyzes the conversion of guanine and (deoxy)ribose-1-phosphate to
(deoxy)guanosine
findings: []
- id: Reactome:R-HSA-6798748
title: Exocytosis of secretory granule lumen proteins
findings: []
- id: Reactome:R-HSA-6800434
title: Exocytosis of ficolin-rich granule lumen proteins
findings: []
- id: Reactome:R-HSA-74242
title: PNP catalyzes the conversion of (deoxy)inosine to hypoxanthine and (deoxy)ribose
findings: []
- id: Reactome:R-HSA-74249
title: PNP catalyzes the conversion of (deoxy)guanosine to guanine and (deoxy)ribose
findings: []
- id: Reactome:R-HSA-9735775
title: Defective PNP does not convert (deoxy)inosine to hypoxanthine and (deoxy)ribose
findings: []
- id: Reactome:R-HSA-9735789
title: Defective PNP does not convert (deoxy)guanosine to guanine and (deoxy)ribose
findings: []
- id: Reactome:R-HSA-9755044
title: PNP trimer transforms RBV to T-CONH2
findings: []