PCK1

Summary: Magnesium ion binding annotated from the human PCK1 crystal structure study.

Reason: PEPCK uses a divalent-metal-nucleotide complex as substrate in addition to the tightly bound Mn2+ cofactor, so Mg2+ binding is plausible and was annotated by the curator from the structural study (full text not cached). It is a mechanistic component of the PEPCK reaction rather than a separate function, so it is kept as non-core.

Summary: Generic phosphoenolpyruvate carboxykinase activity from InterPro/ortholog mapping.

Reason: Correct but general: GO:0004611 does not specify the phosphoryl donor. PCK1 is the GTP-dependent enzyme, and the review accepts the precise child term GO:0004613 on experimental evidence.

Proposed replacements: phosphoenolpyruvate carboxykinase (GTP) activity

Summary: Human PCK1 crystal structures with bound substrates define a GTP-dependent PEPCK and its GTP-specific nucleotide site.

Reason: GTP-dependent phosphoenolpyruvate carboxykinase activity (EC 4.1.1.32; oxaloacetate + GTP = PEP + GDP + CO2) is the defining, core activity of PCK1. It is supported by the human crystal structure, by kinetic studies of recombinant wild-type and patient-variant enzyme, by loss-of-function in cytosolic PEPCK deficiency, and by Reactome.

Summary: Recombinant wild-type and I45T PEPCK-C were assayed kinetically in a study of a PCK1-deficient sib pair.

Reason: GTP-dependent phosphoenolpyruvate carboxykinase activity (EC 4.1.1.32; oxaloacetate + GTP = PEP + GDP + CO2) is the defining, core activity of PCK1. It is supported by the human crystal structure, by kinetic studies of recombinant wild-type and patient-variant enzyme, by loss-of-function in cytosolic PEPCK deficiency, and by Reactome.

Summary: The PCK1 p.G309R patient variant expressed in COS-1 cells failed to produce functional PEPCK enzyme.

Reason: GTP-dependent phosphoenolpyruvate carboxykinase activity (EC 4.1.1.32; oxaloacetate + GTP = PEP + GDP + CO2) is the defining, core activity of PCK1. It is supported by the human crystal structure, by kinetic studies of recombinant wild-type and patient-variant enzyme, by loss-of-function in cytosolic PEPCK deficiency, and by Reactome.

Summary: PAINT assigns GTP-dependent PEPCK activity to the ancestral node of the GTP-PEPCK family, which includes PCK1.

Reason: GTP-dependent phosphoenolpyruvate carboxykinase activity (EC 4.1.1.32; oxaloacetate + GTP = PEP + GDP + CO2) is the defining, core activity of PCK1. It is supported by the human crystal structure, by kinetic studies of recombinant wild-type and patient-variant enzyme, by loss-of-function in cytosolic PEPCK deficiency, and by Reactome. PCK1 is a canonical member of the PEPCK [GTP] family, and its own experimental annotation is among the descendant evidence for this node.

Summary: Purified PCK1 was assayed in both the gluconeogenic (OAA to PEP) and anaplerotic (PEP to OAA) directions, with activity regulated by acetylation.

Reason: GTP-dependent phosphoenolpyruvate carboxykinase activity (EC 4.1.1.32; oxaloacetate + GTP = PEP + GDP + CO2) is the defining, core activity of PCK1. It is supported by the human crystal structure, by kinetic studies of recombinant wild-type and patient-variant enzyme, by loss-of-function in cytosolic PEPCK deficiency, and by Reactome.

Summary: Xu et al. 2020 measured PEPCK activity of PCK1 alongside its proposed protein kinase activity; AKT phosphorylation at Ser90 is reported to lower oxaloacetate binding.

Reason: GTP-dependent phosphoenolpyruvate carboxykinase activity (EC 4.1.1.32; oxaloacetate + GTP = PEP + GDP + CO2) is the defining, core activity of PCK1. It is supported by the human crystal structure, by kinetic studies of recombinant wild-type and patient-variant enzyme, by loss-of-function in cytosolic PEPCK deficiency, and by Reactome. This row is one of the eight PMID:32322062 rows; unlike the protein-kinase rows from the same paper, it restates the well-established core catalytic activity and is accepted.

Summary: Combined automated annotation (InterPro PEPCK [GTP] signature, Rhea:10388/EC 4.1.1.32, mouse ortholog).

Reason: GTP-dependent phosphoenolpyruvate carboxykinase activity (EC 4.1.1.32; oxaloacetate + GTP = PEP + GDP + CO2) is the defining, core activity of PCK1. It is supported by the human crystal structure, by kinetic studies of recombinant wild-type and patient-variant enzyme, by loss-of-function in cytosolic PEPCK deficiency, and by Reactome. The automated mapping is correct for this family member.

Summary: A homozygous PCK1 deletion in a patient with liver failure was confirmed pathogenic by enzymatic studies.

Reason: GTP-dependent phosphoenolpyruvate carboxykinase activity (EC 4.1.1.32; oxaloacetate + GTP = PEP + GDP + CO2) is the defining, core activity of PCK1. It is supported by the human crystal structure, by kinetic studies of recombinant wild-type and patient-variant enzyme, by loss-of-function in cytosolic PEPCK deficiency, and by Reactome.

Summary: Transferred from rat Pck1 (P07379).

Reason: GTP-dependent phosphoenolpyruvate carboxykinase activity (EC 4.1.1.32; oxaloacetate + GTP = PEP + GDP + CO2) is the defining, core activity of PCK1. It is supported by the human crystal structure, by kinetic studies of recombinant wild-type and patient-variant enzyme, by loss-of-function in cytosolic PEPCK deficiency, and by Reactome. The rat ortholog transfer agrees with direct human evidence.

Summary: The human PCK1 structure revealed a novel GTP-binding site with a phenylalanine-lined guanine pocket that confers GTP specificity.

Reason: GTP binding is directly demonstrated, but GTP is the phosphoryl-donor substrate of the core PEPCK (GTP) reaction, so the binding term is kept as a non-core component of that activity.

Summary: InterPro (IPR008209, PEPCK [GTP]) mapping to GTP binding.

Reason: Correct and consistent with the structural evidence; kept as non-core because GTP is a substrate of the core PEPCK activity.

Summary: Cytoplasm, transferred from rat Pck1.

Reason: Correct but general. PCK1 is the cytosolic PEPCK isozyme, and the review accepts GO:0005829 cytosol on experimental, phylogenetic and Reactome evidence.

Proposed replacements: cytosol

Summary: PAINT 'is_active_in mitochondrion' from node PTN000169230, with donors PCK2 (human Q16822, mouse Pck2).

Reason: Over-propagated IBA. Mitochondrial PEPCK activity belongs to the paralog PCK2 (PEPCK-M), the only donors cited. PCK1 is the cytosolic isozyme, has no mitochondrial targeting presequence, and is experimentally cytosolic, with a conditional ER pool. The mitochondrial location was acquired on the PCK2 branch and does not apply to PCK1.

Summary: pSer90-PCK1 translocates to the endoplasmic reticulum in HCC cells.

Reason: Per PMID:32322062, a pool of PCK1 relocates to the ER only after AKT phosphorylates Ser90, where it is proposed to phosphorylate INSIG1/2. The localisation is conditional and tied to the non-core moonlighting kinase function, so it is kept as non-core. The GTP-dependent protein serine kinase activity of PCK1 rests on a single study in human hepatocellular carcinoma cells (PMID:32322062; our cached copy is abstract-only, so the curator's IDA, made from the full text, is retained). The only follow-up found (PMID:39433189, PRRSV-infected MARC-145 monkey cells) invokes the same AKT/PCK1/INSIG/SREBP axis but is not an independent reconstitution with purified enzyme, and no other laboratory has separated the proposed kinase activity from PEPCK catalysis with kinase-dead/PEPCK-competent mutants. The activity is therefore kept as a non-core, conditional (pSer90-dependent) moonlighting function; the core function of PCK1 is GTP-dependent PEP carboxykinase activity in gluconeogenesis, glyceroneogenesis and cataplerosis. ORGANELLES check (2026-11-05). PCK1 is a soluble cytosolic enzyme with no signal peptide or transmembrane segment, so the pSer90 pool is recruited to the ER surface and stays at the root (no membrane or lumen row). The cached copy of PMID:32322062 is abstract-only, so the ER marker and fractionation controls behind the curated ECO:0000269 UniProt line cannot be checked here; the row is kept on curator deference. Marker-controlled fractionation or co-staining of endogenous pSer90-PCK1 with an ER membrane marker would settle it.

Summary: Automated mapping from UniProt subcellular location (SL-0095 endoplasmic reticulum), itself based on PMID:32322062.

Reason: Restates the UniProt subcellular location curated from PMID:32322062, so it receives the same action as the IDA row. Per PMID:32322062, a pool of PCK1 relocates to the ER only after AKT phosphorylates Ser90, where it is proposed to phosphorylate INSIG1/2. The localisation is conditional and tied to the non-core moonlighting kinase function, so it is kept as non-core. ORGANELLES check (2026-11-05). PCK1 is a soluble cytosolic enzyme with no signal peptide or transmembrane segment, so the pSer90 pool is recruited to the ER surface and stays at the root (no membrane or lumen row). The cached copy of PMID:32322062 is abstract-only, so the ER marker and fractionation controls behind the curated ECO:0000269 UniProt line cannot be checked here; the row is kept on curator deference. Marker-controlled fractionation or co-staining of endogenous pSer90-PCK1 with an ER membrane marker would settle it.

Summary: PAINT assignment of cytosol to the PCK1 (cytosolic PEPCK) clade.

Reason: PCK1 is the cytosolic PEPCK isozyme (PEPCK-C) and carries out its gluconeogenic reaction in the cytosol; this is the correct and core location.

Summary: PCK1 detected in the cytosol of HCC cells, translocating to ER upon AKT phosphorylation.

Reason: PCK1 is the cytosolic PEPCK isozyme (PEPCK-C) and carries out its gluconeogenic reaction in the cytosol; this is the correct and core location. This PMID:32322062 row is accepted because cytosolic localisation is independently well established.

Summary: Automated mapping from UniProt subcellular location (SL-0091 cytosol).

Reason: PCK1 is the cytosolic PEPCK isozyme (PEPCK-C) and carries out its gluconeogenic reaction in the cytosol; this is the correct and core location.

Summary: Reactome expression event places PEPCK-C protein in the cytosol.

Reason: PCK1 is the cytosolic PEPCK isozyme (PEPCK-C) and carries out its gluconeogenic reaction in the cytosol; this is the correct and core location. The Reactome event is a gene-expression event, but the protein product location it asserts is correct.

Summary: Reactome reaction: PCK1 converts OA to PEP in the cytosol.

Reason: PCK1 is the cytosolic PEPCK isozyme (PEPCK-C) and carries out its gluconeogenic reaction in the cytosol; this is the correct and core location.

Summary: Reactome expression event (NR1H3-regulated) places PCK1 protein in the cytosol.

Reason: PCK1 is the cytosolic PEPCK isozyme (PEPCK-C) and carries out its gluconeogenic reaction in the cytosol; this is the correct and core location. The Reactome event is a gene-expression event, but the protein product location it asserts is correct.

Summary: Reactome event on TCF19:NuRD repression of PCK1 expression, with PCK1 protein in the cytosol.

Reason: PCK1 is the cytosolic PEPCK isozyme (PEPCK-C) and carries out its gluconeogenic reaction in the cytosol; this is the correct and core location. The Reactome event concerns transcriptional repression, but the protein product location it asserts is correct.

Summary: Annotated from a study of a PCK1 promoter SNP associated with type 2 diabetes.

Reason: Correct but general. PCK1's role in glucose metabolism is gluconeogenesis (GO:0006094, an is_a descendant via glucose biosynthesis), accepted in this review. The cited study concerns promoter variation and reporter expression, which supports the general claim only.

Proposed replacements: gluconeogenesis

Summary: PAINT assignment of gluconeogenesis to the PEPCK [GTP] family.

Reason: PCK1 catalyses the committed, rate-limiting conversion of oxaloacetate to PEP in hepatic and renal gluconeogenesis; PCK1 deficiency causes hypoglycemia. Core process.

Summary: Deacetylated PCK1 carries out the gluconeogenic OAA to PEP reaction.

Reason: PCK1 catalyses the committed, rate-limiting conversion of oxaloacetate to PEP in hepatic and renal gluconeogenesis; PCK1 deficiency causes hypoglycemia. Core process.

Summary: InterPro/UniPathway mapping to gluconeogenesis.

Reason: PCK1 catalyses the committed, rate-limiting conversion of oxaloacetate to PEP in hepatic and renal gluconeogenesis; PCK1 deficiency causes hypoglycemia. Core process.

Summary: Patient with homozygous PCK1 deletion and acute liver failure / fasting intolerance.

Reason: PCK1 catalyses the committed, rate-limiting conversion of oxaloacetate to PEP in hepatic and renal gluconeogenesis; PCK1 deficiency causes hypoglycemia. Core process.

Summary: Transferred from rat Pck1.

Reason: PCK1 catalyses the committed, rate-limiting conversion of oxaloacetate to PEP in hepatic and renal gluconeogenesis; PCK1 deficiency causes hypoglycemia. Core process.

Summary: Reactome gluconeogenesis pathway includes cytosolic PEPCK.

Reason: PCK1 catalyses the committed, rate-limiting conversion of oxaloacetate to PEP in hepatic and renal gluconeogenesis; PCK1 deficiency causes hypoglycemia. Core process.

Summary: PAINT assignment of oxaloacetate metabolic process.

Reason: Oxaloacetate is the direct substrate (gluconeogenic/cataplerotic direction) or product (anaplerotic direction) of PCK1; oxaloacetate metabolism is a core process for the enzyme.

Summary: PCK1 interconverts oxaloacetate and PEP in both directions depending on its acetylation state.

Reason: Oxaloacetate is the direct substrate (gluconeogenic/cataplerotic direction) or product (anaplerotic direction) of PCK1; oxaloacetate metabolism is a core process for the enzyme.

Summary: Ensembl Compara transfer from mouse Pck1.

Reason: Oxaloacetate is the direct substrate (gluconeogenic/cataplerotic direction) or product (anaplerotic direction) of PCK1; oxaloacetate metabolism is a core process for the enzyme.

Summary: Glycerol biosynthetic process, transferred from rat Pck1 (glyceroneogenesis in adipose tissue and liver).

Reason: PCK1 is the key enzyme of glyceroneogenesis, the synthesis of glycerol-3-phosphate from pyruvate/lactate precursors for fatty-acid re-esterification in adipose tissue and liver. GO folded glyceroneogenesis into this term when it obsoleted GO:0046327 'glycerol biosynthetic process from pyruvate' (exact synonym 'glyceroneogenesis', replaced_by GO:0006114), so this is the term GO intends for glyceroneogenesis even though the pathway's product is glycerol-3-phosphate rather than free glycerol. Kept consistent with the mouse Pck1 review, where the same term rests on IMP evidence.

Summary: InterPro mapping to purine nucleotide binding.

Reason: True but uninformative: GO:0005525 GTP binding, a descendant of purine nucleotide binding, is supported experimentally for PCK1 and kept in this review.

Summary: PCK1 phosphorylates INSIG1 Ser207 and INSIG2 Ser151 (peptidyl-serine phosphorylation of substrate proteins).

Reason: Follows directly from the GO:0106264 claim and carries the same caveat. The GTP-dependent protein serine kinase activity of PCK1 rests on a single study in human hepatocellular carcinoma cells (PMID:32322062; our cached copy is abstract-only, so the curator's IDA, made from the full text, is retained). The only follow-up found (PMID:39433189, PRRSV-infected MARC-145 monkey cells) invokes the same AKT/PCK1/INSIG/SREBP axis but is not an independent reconstitution with purified enzyme, and no other laboratory has separated the proposed kinase activity from PEPCK catalysis with kinase-dead/PEPCK-competent mutants. The activity is therefore kept as a non-core, conditional (pSer90-dependent) moonlighting function; the core function of PCK1 is GTP-dependent PEP carboxykinase activity in gluconeogenesis, glyceroneogenesis and cataplerosis.

Summary: PAINT assignment of manganese ion binding to the PEPCK [GTP] family.

Reason: PCK1 binds one Mn2+ per subunit as an essential catalytic cofactor (structures of human PCK1). Correct, but cofactor binding is a component of the core PEPCK activity rather than a function in its own right.

Summary: Mn2+ observed in the active site of human PCK1 crystal structures.

Reason: PCK1 binds one Mn2+ per subunit as an essential catalytic cofactor. Correct, but cofactor binding is a component of the core PEPCK activity rather than a function in its own right.

Summary: ARBA machine-learning prediction of manganese ion binding.

Reason: Consistent with the experimentally determined Mn2+ cofactor site of PCK1; kept as non-core for the same reason as the IDA and IBA rows.

Summary: Crystal structures of PCK1 with bound substrates (oxaloacetate/PEP).

Reason: Binding of the carboxylic-acid substrates oxaloacetate and PEP is real but is simply substrate binding by the PEPCK active site; it is kept as a non-core facet of the core catalytic activity.

Summary: Insulin down-regulated a PCK1 promoter-luciferase reporter, and the -232G allele abolished this.

Reason: PCK1 is a classic hormone-responsive gene: glucocorticoids and glucagon/cAMP induce its transcription and insulin represses it. The enzyme does not transduce these signals. Its regulated expression is, however, how the gluconeogenic arm of the fasting and insulin responses is carried out in liver and kidney, so the term is retained as non-core rather than marked as over-annotation. Same verdict as the mouse Pck1 review for these response terms. This row's assay measures insulin repression of the PCK1 promoter driving a luciferase reporter.

Summary: PAINT assignment of cellular response to insulin stimulus (node PTN000169232).

Reason: Insulin represses PCK1 transcription, and per PMID:32322062 insulin/AKT signalling phosphorylates PCK1 Ser90. PCK1 is therefore an insulin-responsive enzyme, but this is regulation of PCK1 rather than PCK1 executing the insulin response, so it is kept as non-core.

Summary: Annotated from the AKT-PCK1-INSIG study; AKT-dependent PCK1 Ser90 phosphorylation lies downstream of insulin/growth-factor signalling.

Reason: Consistent with the IBA row. PCK1 is a downstream target of insulin/AKT signalling (Ser90 phosphorylation), which links insulin signalling to its proposed kinase function. This is peripheral to the core gluconeogenic function. The GTP-dependent protein serine kinase activity of PCK1 rests on a single study in human hepatocellular carcinoma cells (PMID:32322062; our cached copy is abstract-only, so the curator's IDA, made from the full text, is retained). The only follow-up found (PMID:39433189, PRRSV-infected MARC-145 monkey cells) invokes the same AKT/PCK1/INSIG/SREBP axis but is not an independent reconstitution with purified enzyme, and no other laboratory has separated the proposed kinase activity from PEPCK catalysis with kinase-dead/PEPCK-competent mutants. The activity is therefore kept as a non-core, conditional (pSer90-dependent) moonlighting function; the core function of PCK1 is GTP-dependent PEP carboxykinase activity in gluconeogenesis, glyceroneogenesis and cataplerosis.

Summary: Glucose homeostasis, transferred from rat Pck1.

Reason: PCK1-driven gluconeogenesis contributes to whole-body glucose homeostasis, and loss of PCK1 causes fasting hypoglycemia. This is a systemic, organism-level consequence of the core gluconeogenic activity, so it is kept as non-core.

Summary: PAINT assignment of response to starvation.

Reason: PCK1 is induced during fasting, and the gluconeogenesis it catalyses is the physiological response that maintains blood glucose in starvation. This is reasonable but non-core.

Summary: Ensembl Compara transfer from mouse Pck1.

Reason: Based on mouse studies (UniProt: By similarity, from Q9Z2V4), PCK1-derived PEP feeds glycogen synthesis and the pentose phosphate pathway, which memory CD8+ T cells need for homeostasis. PCK1 is a metabolic requirement for those cells rather than a regulator of the differentiation program, and the evidence is not human. Over-annotation. The mouse Pck1 review keeps the same term as non-core, because there it rests on direct mouse IMP evidence (PMID:29230018). The role-conflation caveat applies to that row too; here the row is also only a transfer.

Summary: Manual transfer from mouse Pck1 (Q9Z2V4).

Reason: Based on mouse studies (UniProt: By similarity, from Q9Z2V4), PCK1-derived PEP feeds glycogen synthesis and the pentose phosphate pathway, which memory CD8+ T cells need for homeostasis. PCK1 is a metabolic requirement for those cells rather than a regulator of the differentiation program, and the evidence is not human. Over-annotation. The mouse Pck1 review keeps the same term as non-core, because there it rests on direct mouse IMP evidence (PMID:29230018). The role-conflation caveat applies to that row too; here the row is also only a transfer.

Summary: Glyceraldehyde-3-phosphate biosynthetic process, transferred from mouse Pck1 by Ensembl Compara.

Reason: PCK1 catalyses the committed step of the route by which oxaloacetate is carried, via PEP and the reversible lower gluconeogenic reactions, to glyceraldehyde-3-phosphate/DHAP, the precursor of glycerol-3-phosphate in glyceroneogenesis. GO curators model mouse Pck1 PEPCK activity in this process in GO-CAM gomodel:6494e2e900002018 ('Glyceraldehyde-3-phosphate biosynthetic process 1 (Mouse)'), and the source mouse row is IMP. Accepted for consistency with the mouse Pck1 review.

Summary: PCK1-mediated INSIG phosphorylation releases SCAP-SREBP to the Golgi, activating SREBP target genes and lipogenesis in HCC cells.

Reason: The sign is correct: per PMID:32322062, INSIG phosphorylation by PCK1 reduces sterol binding and INSIG-SCAP interaction, so PCK1 opposes SREBP-SCAP retention in the ER and promotes lipid synthesis. This is also how GO-CAM gomodel:6205c24300000880 models it (GO:0106264 part_of GO:0046889, negatively regulating INSIG activities). PCK1 is not part of the retention machinery, so acts_upstream_of_or_within GO:0036316 'SREBP-SCAP complex retention in endoplasmic reticulum' (as propagated to mouse Pck1 by ISO) would be an over-annotation of the wrong sign; no such term is proposed here. The GTP-dependent protein serine kinase activity of PCK1 rests on a single study in human hepatocellular carcinoma cells (PMID:32322062; our cached copy is abstract-only, so the curator's IDA, made from the full text, is retained). The only follow-up found (PMID:39433189, PRRSV-infected MARC-145 monkey cells) invokes the same AKT/PCK1/INSIG/SREBP axis but is not an independent reconstitution with purified enzyme, and no other laboratory has separated the proposed kinase activity from PEPCK catalysis with kinase-dead/PEPCK-competent mutants. The activity is therefore kept as a non-core, conditional (pSer90-dependent) moonlighting function; the core function of PCK1 is GTP-dependent PEP carboxykinase activity in gluconeogenesis, glyceroneogenesis and cataplerosis.

Summary: Regulation of lipid biosynthetic process from the same PCK1-INSIG study.

Reason: Entailed by GO:0046889 positive regulation of lipid biosynthetic process from the same paper, which is kept (as non-core) in this review and specifies the direction of the effect.

Summary: PCK1 identified in a large-scale proteomic survey of human urinary exosomes.

Reason: High-throughput detection of an abundant renal proximal-tubule cytosolic enzyme in urinary exosomes; plausible as cargo but not a site of PCK1 function.

Summary: PAINT assignment of hepatocyte differentiation (node PTN000169232).

Reason: PCK1 is a marker of differentiated, gluconeogenic hepatocytes, not a driver of hepatocyte differentiation, and no PCK1-specific evidence shows the enzyme does any of the work of that process. PCK1-deficient patients present with metabolic (hypoglycemia, liver dysfunction) rather than developmental liver phenotypes. The IBA node's donors (rat and human Pck1/PCK1) reflect marker expression. Marked over-annotated rather than removed, to defer to the PAINT node placement, and to match the mouse Pck1 verdict on the same node.

Summary: PAINT assignment of cellular response to glucose stimulus.

Reason: High glucose triggers p300-dependent acetylation of PCK1 at Lys91, which switches the enzyme toward the anaplerotic direction. PCK1 is transcriptionally repressed by high glucose (TCF19:NuRD). PCK1 activity and expression therefore respond to glucose. This is regulatory context, not core function.

Summary: High glucose increased PCK1 acetylation and its anaplerotic (PEP to OAA) activity.

Reason: PCK1 changes its catalytic direction in response to glucose via acetylation. This is genuine but regulatory context for the core enzyme activity, so it is kept as non-core.

Summary: PAINT assignment of cellular response to dexamethasone stimulus (node PTN000169232).

Reason: PCK1 is a classic hormone-responsive gene: glucocorticoids and glucagon/cAMP induce its transcription and insulin represses it. The enzyme does not transduce these signals. Its regulated expression is, however, how the gluconeogenic arm of the fasting and insulin responses is carried out in liver and kidney, so the term is retained as non-core rather than marked as over-annotation. Same verdict as the mouse Pck1 review for these response terms. This row is an IBA from the same PAINT node as the mouse Pck1 row and is judged on the same basis: glucocorticoid induction of the PCK1 gene, not glucocorticoid signalling by the enzyme.

Summary: Annotated from the PCK1 acetylation study describing cataplerotic/anaplerotic flux of TCA-cycle intermediates.

Reason: The intent (PCK1 controls the flux of TCA-cycle intermediates by cataplerosis/anaplerosis) is sound, but GO:0072350 is defined as metabolism of acids with three carboxyl groups (e.g. citrate). PCK1 acts on oxaloacetate (a dicarboxylic acid) and PEP, not on tricarboxylic acids. The accurate term, GO:0006107 oxaloacetate metabolic process, is already carried by PCK1 from the same paper (IDA) and from IBA.

Proposed replacements: oxaloacetate metabolic process

Summary: Xu et al. 2020 report that AKT-phosphorylated (pSer90) PCK1 uses GTP to phosphorylate INSIG1 Ser207 and INSIG2 Ser151 at the ER in human HCC cells.

Reason: The GTP-dependent protein serine kinase activity of PCK1 rests on a single study in human hepatocellular carcinoma cells (PMID:32322062; our cached copy is abstract-only, so the curator's IDA, made from the full text, is retained). The only follow-up found (PMID:39433189, PRRSV-infected MARC-145 monkey cells) invokes the same AKT/PCK1/INSIG/SREBP axis but is not an independent reconstitution with purified enzyme, and no other laboratory has separated the proposed kinase activity from PEPCK catalysis with kinase-dead/PEPCK-competent mutants. The activity is therefore kept as a non-core, conditional (pSer90-dependent) moonlighting function; the core function of PCK1 is GTP-dependent PEP carboxykinase activity in gluconeogenesis, glyceroneogenesis and cataplerosis.

Summary: Rhea-based mapping from the UniProt catalytic-activity annotation RHEA:64020 (L-seryl-[protein] + GTP = O-phospho-L-seryl-[protein] + GDP + H+).

Reason: This IEA is not independent evidence: the Rhea:64020 reaction in the UniProt entry is itself curated solely from PMID:32322062, so this row restates the IDA row and receives the same action. The mapping from that reaction to GO:0106264 is technically correct. The GTP-dependent protein serine kinase activity of PCK1 rests on a single study in human hepatocellular carcinoma cells (PMID:32322062; our cached copy is abstract-only, so the curator's IDA, made from the full text, is retained). The only follow-up found (PMID:39433189, PRRSV-infected MARC-145 monkey cells) invokes the same AKT/PCK1/INSIG/SREBP axis but is not an independent reconstitution with purified enzyme, and no other laboratory has separated the proposed kinase activity from PEPCK catalysis with kinase-dead/PEPCK-competent mutants. The activity is therefore kept as a non-core, conditional (pSer90-dependent) moonlighting function; the core function of PCK1 is GTP-dependent PEP carboxykinase activity in gluconeogenesis, glyceroneogenesis and cataplerosis.