PKM (Pyruvate Kinase M) encodes pyruvate kinase isoforms that catalyze the final step of glycolysis: conversion of phosphoenolpyruvate and ADP to pyruvate and ATP. CRITICAL ISOFORM BIOLOGY: Alternative splicing of mutually exclusive exons 9/10 produces isoforms with FUNDAMENTALLY DIFFERENT metabolic properties: (1) PKM1 (P14618-2, M1-PK) is expressed in ADULT differentiated tissues (muscle, brain, heart). It is a constitutively active homotetramer with HIGH pyruvate kinase activity, supporting efficient ATP generation via complete glycolysis and oxidative metabolism. (2) PKM2 (P14618-1, M2-PK) is expressed in EMBRYONIC tissues, PROLIFERATING cells, and nearly all CANCERS. It has LOW basal activity and is allosterically regulated by fructose-1,6-bisphosphate (FBP). PKM2 can exist as inactive monomer/dimer or active tetramer. LOW activity allows glycolytic intermediates to accumulate for biosynthetic pathways (nucleotides, amino acids, lipids) - the metabolic basis of the WARBURG EFFECT in cancer. PKM2-SPECIFIC FUNCTIONS (not shared by PKM1): - Protein kinase activity (phosphorylates histone H3 at Tyr11) - Nuclear translocation and transcription coactivator activity (with HIF-1alpha) - These non-glycolytic functions contribute to cancer cell proliferation. The PKM1-to-PKM2 switch is controlled by hnRNP splicing factors (hnRNPA1, hnRNPA2, PTBP1) and is a metabolic hallmark distinguishing differentiated vs proliferating cells.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0004743
pyruvate kinase activity
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Both PKM1 and PKM2 isoforms possess pyruvate kinase activity, catalyzing the final step of glycolysis (PEP + ADP -> pyruvate + ATP). However, these isoforms have FUNDAMENTALLY DIFFERENT enzymatic properties. PKM1 (P14618-2) is constitutively active with HIGH activity [PMID:20847263]. PKM2 (P14618-1) has LOW basal activity and requires allosteric activation by fructose-1,6-bisphosphate (FBP) to form active tetramers [PMID:15996096, PMID:18337815]. The IBA annotation is correct but does not capture this critical isoform-specific difference in activity levels.
Reason: Core function for both isoforms. Pyruvate kinase activity is the canonical function of PKM. Both isoforms catalyze this reaction, though with vastly different kinetic properties and regulation.
Supporting Evidence:
PMID:20847263
Paradoxically, decreased pyruvate kinase enzyme activity accompanies the expression of PKM2 in rapidly dividing cancer cells and tissues.
|
|
GO:0005737
cytoplasm
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Both PKM1 and PKM2 localize to the cytoplasm where they perform their glycolytic function. PKM1 is exclusively cytoplasmic [UniProt P14618]. PKM2 is predominantly cytoplasmic but can translocate to the nucleus upon specific stimuli such as EGFR activation [PMID:22056988, PMID:17308100].
Reason: Cytoplasmic localization is correct for both isoforms and represents the primary site of glycolytic function.
Supporting Evidence:
PMID:22056988
EGF treatment resulted in the nuclear accumulation of PKM2 in U87/EGFR human glioblastoma (GBM) cells... In addition, PKM1 failed to translocate into the nucleus upon EGF stimulation
|
|
GO:0006096
glycolytic process
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Both isoforms participate in glycolysis. PKM1 supports efficient glycolysis for ATP production. PKM2's low activity in cancer cells diverts glycolytic intermediates to biosynthetic pathways (the Warburg effect) [PMID:20847263].
Reason: Core function for both isoforms. Both participate in glycolysis though PKM2's low activity fundamentally alters glycolytic flux in proliferating cells.
Supporting Evidence:
PMID:20847263
The M2 isoform of pyruvate kinase (PKM2) promotes the metabolism of glucose by aerobic glycolysis and contributes to anabolic metabolism.
|
|
GO:0032869
cellular response to insulin stimulus
|
IBA
GO_REF:0000033 |
KEEP AS NON CORE |
Summary: PKM expression and activity can be regulated by insulin signaling. This is a phylogenetically conserved function supported by IBA evidence.
Reason: This represents a regulatory response rather than a core biochemical function. PKM participates in insulin-mediated metabolic regulation but this is secondary to its primary glycolytic function.
|
|
GO:0000166
nucleotide binding
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: PKM binds ADP as a substrate for the pyruvate kinase reaction. This is a correct but overly general annotation - the more specific pyruvate kinase activity annotation is more informative.
Reason: Correct parent term of ATP binding, which is required for pyruvate kinase activity. Both isoforms bind nucleotides.
|
|
GO:0000287
magnesium ion binding
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: Pyruvate kinase requires Mg2+ as a cofactor [UniProt P14618]. This applies to both isoforms.
Reason: Mg2+ is an essential cofactor for pyruvate kinase activity. Both isoforms require this ion.
|
|
GO:0003824
catalytic activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: PKM has catalytic activity. This is an overly broad parent term - the specific pyruvate kinase activity annotation is more informative.
Reason: True but uninformative parent term. Both isoforms have catalytic activity.
|
|
GO:0004674
protein serine/threonine kinase activity
|
IEA
GO_REF:0000003 |
MODIFY |
Summary: PKM2 (NOT PKM1) has protein threonine kinase activity. PKM2 phosphorylates histone H3 at Thr-11 (H3T11ph) [PMID:22901803, UniProt]. This is a PKM2-SPECIFIC function that occurs when PKM2 is in the nuclear dimeric form. PKM1 does NOT have this activity.
Reason: CRITICAL ISOFORM CONFLATION: This annotation applies ONLY to PKM2 (P14618-1), not PKM1. The IEA annotation fails to capture this isoform specificity. Should be annotated with isoform qualifier.
Proposed replacements:
protein serine/threonine kinase activity
|
|
GO:0004713
protein tyrosine kinase activity
|
IEA
GO_REF:0000116 |
MODIFY |
Summary: PKM2 (NOT PKM1) has protein tyrosine kinase activity. PKM2 phosphorylates STAT3 at Tyr-705 [PMID:22306293, UniProt]. This is a PKM2-SPECIFIC function that occurs in the nuclear dimeric form. PKM1 does NOT have this activity.
Reason: CRITICAL ISOFORM CONFLATION: This annotation applies ONLY to PKM2 (P14618-1), not PKM1. The IEA annotation fails to capture this isoform specificity. Should be annotated with isoform qualifier.
Proposed replacements:
protein tyrosine kinase activity
|
|
GO:0004715
non-membrane spanning protein tyrosine kinase activity
|
IEA
GO_REF:0000003 |
MODIFY |
Summary: PKM2 (NOT PKM1) has non-membrane spanning protein tyrosine kinase activity. This is consistent with its cytosolic/nuclear localization. PKM1 does NOT have this activity.
Reason: CRITICAL ISOFORM CONFLATION: This annotation applies ONLY to PKM2 (P14618-1), not PKM1.
Proposed replacements:
non-membrane spanning protein tyrosine kinase activity
|
|
GO:0004743
pyruvate kinase activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Duplicate of IBA annotation. Both isoforms have pyruvate kinase activity, though with vastly different kinetic properties.
Reason: Core function for both isoforms. This IEA annotation is redundant with the IBA annotation but not incorrect.
|
|
GO:0005524
ATP binding
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: PKM binds ATP/ADP as substrates for pyruvate kinase reaction. Both isoforms bind ATP.
Reason: Correct annotation for both isoforms as ATP/ADP binding is essential for pyruvate kinase activity.
|
|
GO:0005634
nucleus
|
IEA
GO_REF:0000044 |
MODIFY |
Summary: PKM2 (NOT PKM1) translocates to the nucleus upon EGFR activation and other stimuli [PMID:22056988, PMID:17308100]. PKM1 does NOT translocate to the nucleus. This is a PKM2-SPECIFIC localization.
Reason: CRITICAL ISOFORM CONFLATION: Nuclear localization applies ONLY to PKM2 (P14618-1). PMID:22056988 explicitly states "PKM1 failed to translocate into the nucleus upon EGF stimulation".
Proposed replacements:
nucleus
Supporting Evidence:
PMID:22056988
In addition, PKM1 failed to translocate into the nucleus upon EGF stimulation
|
|
GO:0005737
cytoplasm
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: Both PKM1 and PKM2 localize to the cytoplasm. This is the primary site of glycolytic function.
Reason: Correct for both isoforms. Cytoplasmic localization is the primary location for glycolytic function.
|
|
GO:0006096
glycolytic process
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Duplicate of IBA annotation. Both isoforms participate in glycolysis.
Reason: Core function for both isoforms. Redundant with IBA annotation but not incorrect.
|
|
GO:0006417
regulation of translation
|
IEA
GO_REF:0000043 |
KEEP AS NON CORE |
Summary: PKM2 may act as a translation regulator for a subset of mRNAs, associating with ER-bound ribosomes and promoting translation of ER-destined mRNAs [UniProt, by similarity]. This function is attributed to PKM2 specifically.
Reason: This is a non-canonical moonlighting function of PKM2 based on similarity evidence. Not a core function.
|
|
GO:0016301
kinase activity
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: PKM has kinase activity - pyruvate kinase activity for both isoforms, and protein kinase activity for PKM2 only. This is a broad parent term.
Reason: True but uninformative parent term encompassing both pyruvate kinase and protein kinase activities.
|
|
GO:0016740
transferase activity
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: PKM has transferase activity (phosphotransferase). This is a very broad parent term.
Reason: True but uninformative high-level parent term. Both isoforms have transferase activity.
|
|
GO:0030955
potassium ion binding
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: Pyruvate kinase requires K+ as a cofactor [UniProt P14618]. This applies to both isoforms.
Reason: K+ is an essential cofactor for pyruvate kinase activity. Both isoforms require this ion.
|
|
GO:0046872
metal ion binding
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: PKM binds metal ions (Mg2+, K+) as cofactors. Parent term of magnesium and potassium binding.
Reason: True parent term. Both isoforms bind metal ion cofactors.
|
|
GO:0005515
protein binding
|
IPI
PMID:12620389 Novel raf kinase protein-protein interactions found by an ex... |
MARK AS OVER ANNOTATED |
Summary: Yeast two-hybrid study identifying RAF kinase protein-protein interactions. PKM was identified as an interactor. This is a generic protein binding annotation from high-throughput screening.
Reason: Generic protein binding from Y2H screen. Does not provide functional insight into PKM's core activities. More specific interaction terms would be more informative.
Supporting Evidence:
PMID:12620389
Novel raf kinase protein-protein interactions found by an exhaustive yeast two-hybrid analysis.
|
|
GO:0005515
protein binding
|
IPI
PMID:17500595 Huntingtin interacting proteins are genetic modifiers of neu... |
MARK AS OVER ANNOTATED |
Summary: PKM identified as a Huntingtin interacting protein and potential modifier of neurodegeneration. High-throughput interactome study.
Reason: Generic protein binding from interactome study. Does not distinguish between isoforms or provide functional context.
Supporting Evidence:
PMID:17500595
Huntingtin interacting proteins are genetic modifiers of neurodegeneration.
|
|
GO:0005515
protein binding
|
IPI
PMID:17620599 Functional specialization of beta-arrestin interactions reve... |
MARK AS OVER ANNOTATED |
Summary: PKM identified in beta-arrestin interactome study. High-throughput proteomics.
Reason: Generic protein binding from proteomics study. Uninformative without functional context.
Supporting Evidence:
PMID:17620599
Functional specialization of beta-arrestin interactions revealed by proteomic analysis.
|
|
GO:0005515
protein binding
|
IPI
PMID:18519040 Isoform-specific interaction of pyruvate kinase with hepatit... |
KEEP AS NON CORE |
Summary: Isoform-specific interaction of pyruvate kinase with HCV NS5B. The study specifically examines PKM2 interaction with viral protein.
Reason: Interaction with viral protein is interesting for host-pathogen biology but not a core function. Appears to be PKM2-specific based on the study context.
Supporting Evidence:
PMID:18519040
Epub 2008 Jun 2. Isoform-specific interaction of pyruvate kinase with hepatitis C virus NS5B.
|
|
GO:0005515
protein binding
|
IPI
PMID:21044950 Genome-wide YFP fluorescence complementation screen identifi... |
MARK AS OVER ANNOTATED |
Summary: PKM identified in telomere signaling regulator screen. High-throughput study.
Reason: Generic protein binding from screening study. Lacks functional specificity.
Supporting Evidence:
PMID:21044950
Epub 2010 Nov 2. Genome-wide YFP fluorescence complementation screen identifies new regulators for telomere signaling in human cells.
|
|
GO:0005515
protein binding
|
IPI
PMID:21725354 Death-associated protein kinase increases glycolytic rate th... |
KEEP AS NON CORE |
Summary: Death-associated protein kinase (DAPK) binds and activates pyruvate kinase. This is functionally relevant for PKM regulation.
Reason: Functionally relevant interaction but the generic protein binding term is uninformative. Would be better captured by a more specific term or in the regulation context.
Supporting Evidence:
PMID:21725354
Death-associated protein kinase increases glycolytic rate through binding and activation of pyruvate kinase.
|
|
GO:0005515
protein binding
|
IPI
PMID:22056988 Nuclear PKM2 regulates β-catenin transactivation upon EGFR a... |
MODIFY |
Summary: PKM2 (specifically) interacts with beta-catenin (CTNNB1) in the nucleus to regulate transcription of CCND1 [PMID:22056988]. This is a PKM2-SPECIFIC interaction that requires c-Src phosphorylation of beta-catenin at Y333.
Reason: This is a functionally significant PKM2-specific interaction. The generic protein binding term fails to capture the isoform specificity and functional significance. Should be annotated as beta-catenin binding for PKM2 specifically.
Proposed replacements:
beta-catenin binding
Supporting Evidence:
PMID:22056988
EGF stimulation resulted in an interaction between endogenous PKM2 and beta-catenin in the nuclear, but not cytosolic, fraction
|
|
GO:0005515
protein binding
|
IPI
PMID:22898364 Comparative analysis of virus-host interactomes with a mamma... |
MARK AS OVER ANNOTATED |
Summary: PKM identified in virus-host interactome study using protein complementation assay. High-throughput screening.
Reason: Generic protein binding from high-throughput viral interactome study.
Supporting Evidence:
PMID:22898364
Aug 8. Comparative analysis of virus-host interactomes with a mammalian high-throughput protein complementation assay based on Gaussia princeps luciferase.
|
|
GO:0005515
protein binding
|
IPI
PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative ... |
MARK AS OVER ANNOTATED |
Summary: PKM identified in neurodegenerative disease protein interactome mapping study.
Reason: Generic protein binding from disease-focused interactome study.
Supporting Evidence:
PMID:32814053
Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.
|
|
GO:0005515
protein binding
|
IPI
PMID:9990017 Modulation of type M2 pyruvate kinase activity by the human ... |
KEEP AS NON CORE |
Summary: HPV-16 E7 oncoprotein modulates M2-type pyruvate kinase activity. E7 binding promotes PKM2 homodimerization [UniProt].
Reason: Interaction with viral oncoprotein is relevant for understanding PKM2 in cancer but represents host-pathogen interaction rather than core function.
Supporting Evidence:
PMID:9990017
Modulation of type M2 pyruvate kinase activity by the human papillomavirus type 16 E7 oncoprotein.
|
|
GO:0003729
mRNA binding
|
IEA
GO_REF:0000107 |
KEEP AS NON CORE |
Summary: PKM2 may bind mRNAs as part of its moonlighting function in translation regulation [UniProt, by similarity]. Associates with ER-bound ribosomes.
Reason: Non-canonical moonlighting function of PKM2 based on similarity evidence. Not a core function.
|
|
GO:0005791
rough endoplasmic reticulum
|
IEA
GO_REF:0000107 |
KEEP AS NON CORE |
Summary: PKM2 may associate with rough ER as part of its translation regulation function [UniProt, by similarity].
Reason: Associated with moonlighting function in translation regulation. Not a primary localization.
|
|
GO:0005829
cytosol
|
IEA
GO_REF:0000107 |
ACCEPT |
Summary: Both PKM1 and PKM2 are cytosolic enzymes where they perform glycolysis.
Reason: Correct localization for both isoforms. Primary site of glycolytic activity.
|
|
GO:0005929
cilium
|
IEA
GO_REF:0000107 |
KEEP AS NON CORE |
Summary: PKM localization to cilium based on ortholog evidence. Limited direct evidence.
Reason: Ortholog-based evidence for specialized localization. Not a primary site of function.
|
|
GO:0061621
canonical glycolysis
|
IEA
GO_REF:0000107 |
ACCEPT |
Summary: Both isoforms participate in canonical glycolysis. PKM catalyzes the final step converting PEP to pyruvate.
Reason: Core function for both isoforms. More specific than generic glycolytic process term.
|
|
GO:2000767
positive regulation of cytoplasmic translation
|
IEA
GO_REF:0000107 |
KEEP AS NON CORE |
Summary: PKM2 may positively regulate translation of ER-destined mRNAs [UniProt, by similarity]. Moonlighting function.
Reason: Non-canonical moonlighting function based on similarity evidence. Not a core function.
|
|
GO:0005829
cytosol
|
IDA
GO_REF:0000052 |
ACCEPT |
Summary: Direct assay evidence for cytosolic localization based on immunofluorescence. Both isoforms are cytosolic.
Reason: Validated cytosolic localization. Primary site of glycolytic function for both isoforms.
|
|
GO:0004743
pyruvate kinase activity
|
IDA
PMID:20847263 Evidence for an alternative glycolytic pathway in rapidly pr... |
ACCEPT |
Summary: Direct demonstration of pyruvate kinase activity. This study examined both PKM1 and PKM2 and showed that PKM2 has lower activity and contributes to the Warburg effect by allowing glycolytic intermediates to accumulate for biosynthesis.
Reason: Core function with direct experimental evidence. Both isoforms have activity but with different kinetic properties.
Supporting Evidence:
PMID:20847263
Paradoxically, decreased pyruvate kinase enzyme activity accompanies the expression of PKM2 in rapidly dividing cancer cells and tissues.
|
|
GO:0005654
nucleoplasm
|
TAS
Reactome:R-HSA-9766062 |
MODIFY |
Summary: Reactome pathway annotation for PKM and TGIF2 binding CDH1 gene promoter. This nuclear function is PKM2-specific based on literature evidence.
Reason: ISOFORM CONFLATION: Nucleoplasm localization is PKM2-specific. PKM1 does not translocate to nucleus.
Proposed replacements:
nucleoplasm
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-9861640 |
ACCEPT |
Summary: Reactome annotation for CTLH E3 ligase ubiquitinating PKM-1. Cytosolic localization is correct for both isoforms.
Reason: Correct localization for both isoforms.
|
|
GO:0005515
protein binding
|
IPI
PMID:27573352 TSC22D2 interacts with PKM2 and inhibits cell growth in colo... |
KEEP AS NON CORE |
Summary: TSC22D2 interacts with PKM2 and inhibits cell growth in colorectal cancer. The interaction reduces nuclear PKM2 levels and represses cyclin D1 transcription.
Reason: Functionally relevant interaction specific to PKM2. Generic protein binding term lacks specificity.
Supporting Evidence:
PMID:27573352
TSC22D2 interacts with PKM2 and inhibits cell growth in colorectal cancer.
|
|
GO:0005634
nucleus
|
IDA
PMID:27573352 TSC22D2 interacts with PKM2 and inhibits cell growth in colo... |
ACCEPT |
Summary: Direct evidence for PKM nuclear localization. The study specifically examines PKM2 (isoform M2) nuclear localization and its regulation by TSC22D2.
Reason: Direct experimental evidence for nuclear localization. This is PKM2-specific function but IDA evidence is strong.
Supporting Evidence:
PMID:27573352
TSC22D2 interacts with PKM2 and inhibits cell growth in colorectal cancer.
|
|
GO:0005737
cytoplasm
|
IDA
PMID:27573352 TSC22D2 interacts with PKM2 and inhibits cell growth in colo... |
ACCEPT |
Summary: Direct evidence for PKM cytoplasmic localization. Both isoforms are cytoplasmic.
Reason: Correct for both isoforms. Primary site of glycolytic function.
Supporting Evidence:
PMID:27573352
TSC22D2 interacts with PKM2 and inhibits cell growth in colorectal cancer.
|
|
GO:0003729
mRNA binding
|
ISS
GO_REF:0000024 |
KEEP AS NON CORE |
Summary: Sequence similarity-based annotation for mRNA binding. Moonlighting function of PKM2.
Reason: Non-canonical function based on similarity. Not a core function.
|
|
GO:0005791
rough endoplasmic reticulum
|
ISS
GO_REF:0000024 |
KEEP AS NON CORE |
Summary: Sequence similarity-based annotation. Associated with translation regulation moonlighting function.
Reason: Non-canonical localization associated with moonlighting function.
|
|
GO:2000767
positive regulation of cytoplasmic translation
|
ISS
GO_REF:0000024 |
KEEP AS NON CORE |
Summary: Sequence similarity-based annotation for translation regulation. Moonlighting function.
Reason: Non-canonical moonlighting function based on sequence similarity.
|
|
GO:0005515
protein binding
|
IPI
PMID:27199445 JMJD8 Regulates Angiogenic Sprouting and Cellular Metabolism... |
KEEP AS NON CORE |
Summary: JMJD8 interacts with PKM2 and regulates angiogenic sprouting and cellular metabolism.
Reason: Functionally relevant interaction but generic protein binding term is uninformative.
Supporting Evidence:
PMID:27199445
JMJD8 Regulates Angiogenic Sprouting and Cellular Metabolism by Interacting With Pyruvate Kinase M2 in Endothelial Cells.
|
|
GO:1903672
positive regulation of sprouting angiogenesis
|
IMP
PMID:27199445 JMJD8 Regulates Angiogenic Sprouting and Cellular Metabolism... |
KEEP AS NON CORE |
Summary: PKM regulates angiogenic sprouting through interaction with JMJD8 in endothelial cells. Likely PKM2-mediated based on cancer/proliferation context.
Reason: Pleiotropic downstream effect in specialized cell type context. Not a core function of PKM.
Supporting Evidence:
PMID:27199445
JMJD8 Regulates Angiogenic Sprouting and Cellular Metabolism by Interacting With Pyruvate Kinase M2 in Endothelial Cells.
|
|
GO:0045296
cadherin binding
|
HDA
PMID:25468996 E-cadherin interactome complexity and robustness resolved by... |
KEEP AS NON CORE |
Summary: High-throughput proteomics study of E-cadherin interactome. PKM identified as an interactor.
Reason: High-throughput proteomics finding. More informative than generic protein binding but not a core function.
Supporting Evidence:
PMID:25468996
E-cadherin interactome complexity and robustness resolved by quantitative proteomics.
|
|
GO:0005576
extracellular region
|
TAS
Reactome:R-HSA-6798748 |
KEEP AS NON CORE |
Summary: Reactome annotation for exocytosis of secretory granule lumen proteins. PKM found in extracellular region via secretion.
Reason: PKM can be secreted but extracellular localization is not a primary site of function.
|
|
GO:0005576
extracellular region
|
TAS
Reactome:R-HSA-6800434 |
KEEP AS NON CORE |
Summary: Reactome annotation for ficolin-rich granule exocytosis. PKM present in extracellular region.
Reason: Secondary localization from secretory process.
|
|
GO:0034774
secretory granule lumen
|
TAS
Reactome:R-HSA-6798748 |
KEEP AS NON CORE |
Summary: PKM present in secretory granule lumen per Reactome annotation.
Reason: Specialized localization related to secretory function.
|
|
GO:1904813
ficolin-1-rich granule lumen
|
TAS
Reactome:R-HSA-6800434 |
KEEP AS NON CORE |
Summary: PKM present in ficolin-1-rich granule lumen per Reactome annotation.
Reason: Specialized localization in immune cell granules.
|
|
GO:0070062
extracellular exosome
|
HDA
PMID:12519789 Proteomic and biochemical analyses of human B cell-derived e... |
KEEP AS NON CORE |
Summary: PKM detected in B cell-derived exosomes by proteomics.
Reason: Exosomal localization from proteomics study. Not primary functional location.
Supporting Evidence:
PMID:12519789
2003 Jan 7. Proteomic and biochemical analyses of human B cell-derived exosomes.
|
|
GO:0070062
extracellular exosome
|
HDA
PMID:11487543 Intestinal epithelial cells secrete exosome-like vesicles. |
KEEP AS NON CORE |
Summary: PKM detected in intestinal epithelial cell exosomes.
Reason: Exosomal cargo. Not primary functional location.
Supporting Evidence:
PMID:11487543
Intestinal epithelial cells secrete exosome-like vesicles.
|
|
GO:1903561
extracellular vesicle
|
HDA
PMID:24769233 Proteomic analysis of cerebrospinal fluid extracellular vesi... |
KEEP AS NON CORE |
Summary: PKM detected in CSF extracellular vesicles by proteomics.
Reason: Extracellular vesicle cargo from proteomics.
Supporting Evidence:
PMID:24769233
2014 Apr 24. Proteomic analysis of cerebrospinal fluid extracellular vesicles: a comprehensive dataset.
|
|
GO:0070062
extracellular exosome
|
HDA
PMID:23533145 In-depth proteomic analyses of exosomes isolated from expres... |
KEEP AS NON CORE |
Summary: PKM detected in prostatic secretion exosomes.
Reason: Exosomal cargo from proteomics.
Supporting Evidence:
PMID:23533145
2013 Apr 23. In-depth proteomic analyses of exosomes isolated from expressed prostatic secretions in urine.
|
|
GO:0031982
vesicle
|
HDA
PMID:19190083 Characterization of exosome-like vesicles released from huma... |
KEEP AS NON CORE |
Summary: PKM detected in tracheobronchial epithelial exosome-like vesicles.
Reason: Vesicular localization from proteomics.
Supporting Evidence:
PMID:19190083
Characterization of exosome-like vesicles released from human tracheobronchial ciliated epithelium: a possible role in innate defense.
|
|
GO:0005634
nucleus
|
HDA
PMID:21630459 Proteomic characterization of the human sperm nucleus. |
KEEP AS NON CORE |
Summary: PKM detected in sperm nucleus by proteomics. Supports nuclear localization capability.
Reason: Nuclear detection in specialized cell type. PKM2-specific function.
Supporting Evidence:
PMID:21630459
Jun 1. Proteomic characterization of the human sperm nucleus.
|
|
GO:0003723
RNA binding
|
HDA
PMID:22658674 Insights into RNA biology from an atlas of mammalian mRNA-bi... |
KEEP AS NON CORE |
Summary: PKM identified in mRNA-binding protein atlas. Supports moonlighting function in translation regulation.
Reason: Non-canonical moonlighting function from proteomics study.
Supporting Evidence:
PMID:22658674
May 31. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins.
|
|
GO:0005739
mitochondrion
|
HDA
PMID:20833797 Phosphoproteome analysis of functional mitochondria isolated... |
KEEP AS NON CORE |
Summary: PKM detected in mitochondrial phosphoproteome. May represent association with mitochondria or contamination.
Reason: Unexpected localization from phosphoproteomics. PKM is canonically cytosolic.
Supporting Evidence:
PMID:20833797
Epub 2010 Sep 10. Phosphoproteome analysis of functional mitochondria isolated from resting human muscle reveals extensive phosphorylation of inner membrane protein complexes and enzymes.
|
|
GO:0070062
extracellular exosome
|
HDA
PMID:19199708 Proteomic analysis of human parotid gland exosomes by multid... |
KEEP AS NON CORE |
Summary: PKM detected in parotid gland exosomes.
Reason: Exosomal cargo from proteomics.
Supporting Evidence:
PMID:19199708
Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudPIT).
|
|
GO:0070062
extracellular exosome
|
HDA
PMID:19056867 Large-scale proteomics and phosphoproteomics of urinary exos... |
KEEP AS NON CORE |
Summary: PKM detected in urinary exosomes by proteomics.
Reason: Exosomal cargo from proteomics.
Supporting Evidence:
PMID:19056867
2008 Dec 3. Large-scale proteomics and phosphoproteomics of urinary exosomes.
|
|
GO:0023026
MHC class II protein complex binding
|
HDA
PMID:20458337 MHC class II-associated proteins in B-cell exosomes and pote... |
KEEP AS NON CORE |
Summary: PKM identified as MHC class II-associated protein in B-cell exosomes.
Reason: High-throughput proteomics finding. Specialized immune function context.
Supporting Evidence:
PMID:20458337
2010 May 11. MHC class II-associated proteins in B-cell exosomes and potential functional implications for exosome biogenesis.
|
|
GO:0070062
extracellular exosome
|
HDA
PMID:20458337 MHC class II-associated proteins in B-cell exosomes and pote... |
KEEP AS NON CORE |
Summary: PKM detected in B-cell exosomes.
Reason: Exosomal cargo from proteomics.
Supporting Evidence:
PMID:20458337
2010 May 11. MHC class II-associated proteins in B-cell exosomes and potential functional implications for exosome biogenesis.
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-71670 |
ACCEPT |
Summary: Reactome annotation for pyruvate kinase reaction. Cytosolic localization correct for glycolytic function.
Reason: Core localization for glycolytic function.
|
|
GO:0004743
pyruvate kinase activity
|
IDA
PMID:20005212 Identification of small molecule inhibitors of pyruvate kina... |
ACCEPT |
Summary: Study identifying small molecule inhibitors of PKM2. Directly demonstrates pyruvate kinase activity.
Reason: Core function with direct experimental evidence.
Supporting Evidence:
PMID:20005212
Epub 2009 Dec 11. Identification of small molecule inhibitors of pyruvate kinase M2.
|
|
GO:0070062
extracellular exosome
|
HDA
PMID:21362503 Protein profile of exosomes from trabecular meshwork cells. |
KEEP AS NON CORE |
Summary: PKM detected in trabecular meshwork cell exosomes.
Reason: Exosomal cargo from proteomics.
Supporting Evidence:
PMID:21362503
Epub 2011 Mar 8. Protein profile of exosomes from trabecular meshwork cells.
|
|
GO:0005737
cytoplasm
|
IDA
GO_REF:0000054 |
ACCEPT |
Summary: Direct assay evidence for cytoplasmic localization from fusion protein studies.
Reason: Core localization for both isoforms.
|
|
GO:0005634
nucleus
|
IDA
PMID:18191611 Pyruvate kinase isozyme type M2 (PKM2) interacts and coopera... |
ACCEPT |
Summary: PKM2 interacts with Oct-4 in the nucleus and cooperates in regulating transcription. This is PKM2-SPECIFIC nuclear function.
Reason: Direct experimental evidence for PKM2 nuclear localization and function.
Supporting Evidence:
PMID:18191611
PKM2 is an isozyme of pyruvate kinase that is specifically expressed in proliferating cells, such as embryonic stem cells, embryonic carcinoma cells, as well as cancer cells.
|
|
GO:0005737
cytoplasm
|
IDA
PMID:18298799 Modulation of M2-type pyruvate kinase activity by the cytopl... |
ACCEPT |
Summary: Study showing cytoplasmic PML modulates PKM2 activity. Confirms cytoplasmic localization.
Reason: Core localization confirmed by direct evidence.
Supporting Evidence:
PMID:18298799
cytoplasmic PML (cPML) directly interacts with M2-type pyruvate kinase (PKM2)
|
|
GO:0005515
protein binding
|
IPI
PMID:18191611 Pyruvate kinase isozyme type M2 (PKM2) interacts and coopera... |
MODIFY |
Summary: PKM2 interacts with Oct-4 transcription factor. The interaction enhances Oct-4 transcriptional activity. PKM2-SPECIFIC interaction.
Reason: Functionally significant interaction with transcription factor. Generic protein binding term is uninformative. Should be more specific (e.g., transcription factor binding).
Proposed replacements:
DNA-binding transcription factor binding
Supporting Evidence:
PMID:18191611
ectopic expression of the PKM2 enhanced Oct-4-mediated transcription
|
|
GO:0005515
protein binding
|
IPI
PMID:18298799 Modulation of M2-type pyruvate kinase activity by the cytopl... |
KEEP AS NON CORE |
Summary: PKM2 interacts with PML tumor suppressor. PML modulates PKM2 tetrameric activity.
Reason: Functionally relevant interaction for PKM2 regulation but generic protein binding term is uninformative.
Supporting Evidence:
PMID:18298799
cytoplasmic PML (cPML) directly interacts with M2-type pyruvate kinase (PKM2)
|
|
GO:0005634
nucleus
|
IDA
PMID:17308100 Nuclear translocation of the tumor marker pyruvate kinase M2... |
ACCEPT |
Summary: PKM2 translocates to nucleus in response to apoptotic stimuli and TT-232. Nuclear translocation induces cell death. PKM2-SPECIFIC function.
Reason: Direct experimental evidence for PKM2-specific nuclear translocation.
Supporting Evidence:
PMID:17308100
Nuclear translocation of PKM2 is sufficient to induce cell death that is caspase independent, isoform specific, and independent of its enzymatic activity.
|
|
GO:0012501
programmed cell death
|
IDA
PMID:17308100 Nuclear translocation of the tumor marker pyruvate kinase M2... |
KEEP AS NON CORE |
Summary: Nuclear PKM2 translocation induces programmed cell death. This is a PKM2-SPECIFIC function that is caspase-independent and independent of pyruvate kinase activity.
Reason: PKM2-specific non-metabolic function. Not a core function but well-documented.
Supporting Evidence:
PMID:17308100
Nuclear translocation of PKM2 is sufficient to induce cell death that is caspase independent, isoform specific, and independent of its enzymatic activity.
|
|
GO:0004743
pyruvate kinase activity
|
TAS
PMID:2854097 Human M2-type pyruvate kinase: cDNA cloning, chromosomal ass... |
ACCEPT |
Summary: Original cloning of human M2-type pyruvate kinase cDNA. Establishes pyruvate kinase activity as core function.
Reason: Core function from original characterization of PKM2.
Supporting Evidence:
PMID:2854097
Human M2-type pyruvate kinase: cDNA cloning, chromosomal assignment and expression in hepatoma.
|
|
GO:0004743
pyruvate kinase activity
|
TAS
PMID:2040271 Isolation and characterization of the human pyruvate kinase ... |
ACCEPT |
Summary: Isolation and characterization of human pyruvate kinase M gene.
Reason: Core function from gene characterization.
Supporting Evidence:
PMID:2040271
Isolation and characterization of the human pyruvate kinase M gene.
|
|
GO:0004743
pyruvate kinase activity
|
TAS
PMID:2813362 Cytosolic thyroid hormone-binding protein is a monomer of py... |
ACCEPT |
Summary: Demonstrates PKM is a cytosolic thyroid hormone-binding protein that is a monomer of pyruvate kinase with enzymatic activity.
Reason: Core function established in characterization study.
Supporting Evidence:
PMID:2813362
Cytosolic thyroid hormone-binding protein is a monomer of pyruvate kinase.
|
|
GO:0005829
cytosol
|
NAS
PMID:2813362 Cytosolic thyroid hormone-binding protein is a monomer of py... |
ACCEPT |
Summary: PKM identified as cytosolic thyroid hormone-binding protein.
Reason: Core localization established in early characterization.
Supporting Evidence:
PMID:2813362
Cytosolic thyroid hormone-binding protein is a monomer of pyruvate kinase.
|
PKM encodes pyruvate kinase isoforms with fundamentally different metabolic properties - the M1/M2 switch is a hallmark of the Warburg effect in cancer.
| Isoform | UniProt ID | Synonym | Activity | Regulation | Expression |
|---|---|---|---|---|---|
| PKM1 | P14618-2 | M1-PK | HIGH constitutive | Not allosteric | ADULT muscle, brain, heart |
| PKM2 | P14618-1 | M2-PK | LOW basal, activatable | Allosteric (FBP) | EMBRYONIC, proliferating, CANCER |
Alternative splicing of mutually exclusive exons 9 and 10:
- Exon 9 → PKM1 (adult)
- Exon 10 → PKM2 (embryonic/cancer)
Controlled by hnRNP splicing factors (hnRNPA1, hnRNPA2, PTB).
PKM1 (isoform 2):
- Constitutively active homotetramer
- High pyruvate kinase activity
- Efficient ATP generation via glycolysis
- Normal oxidative metabolism
PKM2 (isoform 1):
- Allosterically regulated by fructose-1,6-bisphosphate (FBP)
- Can exist as inactive monomer/dimer or active tetramer
- LOW activity allows glycolytic intermediates to accumulate
- Supports biosynthetic pathways (nucleotides, amino acids, lipids)
- Nuclear translocation: Can act as transcription coactivator
Cancer cells switch from PKM1 to PKM2:
- LOW PKM2 activity → glycolytic intermediates diverted to biosynthesis
- Supports rapid proliferation
- PKM2 is nearly universal in cancer
PKM2 has functions ABSENT from PKM1:
- Protein kinase activity - phosphorylates histones (H3Y11)
- Transcription coactivation - interacts with HIF-1α
- Nuclear functions - regulates gene expression
id: P14618
gene_symbol: PKM
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: >-
PKM (Pyruvate Kinase M) encodes pyruvate kinase isoforms that catalyze the final
step of glycolysis: conversion of phosphoenolpyruvate and ADP to pyruvate and ATP.
CRITICAL ISOFORM BIOLOGY: Alternative splicing of mutually exclusive exons 9/10
produces isoforms with FUNDAMENTALLY DIFFERENT metabolic properties:
(1) PKM1 (P14618-2, M1-PK) is expressed in ADULT differentiated tissues (muscle,
brain, heart). It is a constitutively active homotetramer with HIGH pyruvate kinase
activity, supporting efficient ATP generation via complete glycolysis and oxidative
metabolism.
(2) PKM2 (P14618-1, M2-PK) is expressed in EMBRYONIC tissues, PROLIFERATING cells,
and nearly all CANCERS. It has LOW basal activity and is allosterically regulated
by fructose-1,6-bisphosphate (FBP). PKM2 can exist as inactive monomer/dimer or
active tetramer. LOW activity allows glycolytic intermediates to accumulate for
biosynthetic pathways (nucleotides, amino acids, lipids) - the metabolic basis
of the WARBURG EFFECT in cancer.
PKM2-SPECIFIC FUNCTIONS (not shared by PKM1):
- Protein kinase activity (phosphorylates histone H3 at Tyr11)
- Nuclear translocation and transcription coactivator activity (with HIF-1alpha)
- These non-glycolytic functions contribute to cancer cell proliferation.
The PKM1-to-PKM2 switch is controlled by hnRNP splicing factors (hnRNPA1, hnRNPA2,
PTBP1) and is a metabolic hallmark distinguishing differentiated vs proliferating
cells.
alternative_products:
- name: M2 {ECO:0000303|PubMed:2854097} (M2-PK, PKM2)
id: P14618-1
- name: M1 {ECO:0000303|PubMed:2854097} (M1-PK, PKM1)
id: P14618-2, P14786-1
sequence_note: VSP_011101
- name: '3'
id: P14618-3
sequence_note: VSP_043370
existing_annotations:
- term:
id: GO:0004743
label: pyruvate kinase activity
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
Both PKM1 and PKM2 isoforms possess pyruvate kinase activity, catalyzing the
final step of glycolysis
(PEP + ADP -> pyruvate + ATP). However, these isoforms have FUNDAMENTALLY
DIFFERENT enzymatic properties.
PKM1 (P14618-2) is constitutively active with HIGH activity [PMID:20847263].
PKM2 (P14618-1) has LOW basal
activity and requires allosteric activation by fructose-1,6-bisphosphate (FBP)
to form active tetramers
[PMID:15996096, PMID:18337815]. The IBA annotation is correct but does not
capture this critical
isoform-specific difference in activity levels.
action: ACCEPT
reason: >-
Core function for both isoforms. Pyruvate kinase activity is the canonical
function of PKM.
Both isoforms catalyze this reaction, though with vastly different kinetic
properties and regulation.
supported_by:
- reference_id: PMID:20847263
supporting_text: "Paradoxically, decreased pyruvate kinase enzyme activity
accompanies the expression of PKM2 in rapidly dividing cancer cells and
tissues."
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
Both PKM1 and PKM2 localize to the cytoplasm where they perform their glycolytic
function.
PKM1 is exclusively cytoplasmic [UniProt P14618]. PKM2 is predominantly cytoplasmic
but can
translocate to the nucleus upon specific stimuli such as EGFR activation [PMID:22056988,
PMID:17308100].
action: ACCEPT
reason: >-
Cytoplasmic localization is correct for both isoforms and represents the primary
site of
glycolytic function.
supported_by:
- reference_id: PMID:22056988
supporting_text: "EGF treatment resulted in the nuclear accumulation of
PKM2 in U87/EGFR human glioblastoma (GBM) cells... In addition, PKM1 failed
to translocate into the nucleus upon EGF stimulation"
- term:
id: GO:0006096
label: glycolytic process
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
Both isoforms participate in glycolysis. PKM1 supports efficient glycolysis
for ATP production.
PKM2's low activity in cancer cells diverts glycolytic intermediates to biosynthetic
pathways
(the Warburg effect) [PMID:20847263].
action: ACCEPT
reason: >-
Core function for both isoforms. Both participate in glycolysis though PKM2's
low activity
fundamentally alters glycolytic flux in proliferating cells.
supported_by:
- reference_id: PMID:20847263
supporting_text: "The M2 isoform of pyruvate kinase (PKM2) promotes the
metabolism of glucose by aerobic glycolysis and contributes to anabolic
metabolism."
- term:
id: GO:0032869
label: cellular response to insulin stimulus
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
PKM expression and activity can be regulated by insulin signaling. This is
a phylogenetically
conserved function supported by IBA evidence.
action: KEEP_AS_NON_CORE
reason: >-
This represents a regulatory response rather than a core biochemical function.
PKM participates
in insulin-mediated metabolic regulation but this is secondary to its primary
glycolytic function.
- term:
id: GO:0000166
label: nucleotide binding
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
PKM binds ADP as a substrate for the pyruvate kinase reaction. This is a correct
but overly general annotation - the more specific pyruvate kinase activity
annotation
is more informative.
action: ACCEPT
reason: >-
Correct parent term of ATP binding, which is required for pyruvate kinase
activity.
Both isoforms bind nucleotides.
- term:
id: GO:0000287
label: magnesium ion binding
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
Pyruvate kinase requires Mg2+ as a cofactor [UniProt P14618]. This applies
to both isoforms.
action: ACCEPT
reason: >-
Mg2+ is an essential cofactor for pyruvate kinase activity. Both isoforms
require this ion.
- term:
id: GO:0003824
label: catalytic activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
PKM has catalytic activity. This is an overly broad parent term - the specific
pyruvate kinase activity annotation is more informative.
action: ACCEPT
reason: >-
True but uninformative parent term. Both isoforms have catalytic activity.
- term:
id: GO:0004674
label: protein serine/threonine kinase activity
evidence_type: IEA
original_reference_id: GO_REF:0000003
review:
summary: >-
PKM2 (NOT PKM1) has protein threonine kinase activity. PKM2 phosphorylates
histone H3 at
Thr-11 (H3T11ph) [PMID:22901803, UniProt]. This is a PKM2-SPECIFIC function
that occurs
when PKM2 is in the nuclear dimeric form. PKM1 does NOT have this activity.
action: MODIFY
reason: >-
CRITICAL ISOFORM CONFLATION: This annotation applies ONLY to PKM2 (P14618-1),
not PKM1.
The IEA annotation fails to capture this isoform specificity. Should be annotated
with
isoform qualifier.
proposed_replacement_terms:
- id: GO:0004674
label: protein serine/threonine kinase activity
additional_reference_ids:
- UniProt:P14618
- term:
id: GO:0004713
label: protein tyrosine kinase activity
evidence_type: IEA
original_reference_id: GO_REF:0000116
review:
summary: >-
PKM2 (NOT PKM1) has protein tyrosine kinase activity. PKM2 phosphorylates
STAT3 at Tyr-705
[PMID:22306293, UniProt]. This is a PKM2-SPECIFIC function that occurs in
the nuclear dimeric
form. PKM1 does NOT have this activity.
action: MODIFY
reason: >-
CRITICAL ISOFORM CONFLATION: This annotation applies ONLY to PKM2 (P14618-1),
not PKM1.
The IEA annotation fails to capture this isoform specificity. Should be annotated
with
isoform qualifier.
proposed_replacement_terms:
- id: GO:0004713
label: protein tyrosine kinase activity
- term:
id: GO:0004715
label: non-membrane spanning protein tyrosine kinase activity
evidence_type: IEA
original_reference_id: GO_REF:0000003
review:
summary: >-
PKM2 (NOT PKM1) has non-membrane spanning protein tyrosine kinase activity.
This is
consistent with its cytosolic/nuclear localization. PKM1 does NOT have this
activity.
action: MODIFY
reason: >-
CRITICAL ISOFORM CONFLATION: This annotation applies ONLY to PKM2 (P14618-1),
not PKM1.
proposed_replacement_terms:
- id: GO:0004715
label: non-membrane spanning protein tyrosine kinase activity
- term:
id: GO:0004743
label: pyruvate kinase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
Duplicate of IBA annotation. Both isoforms have pyruvate kinase activity,
though with
vastly different kinetic properties.
action: ACCEPT
reason: >-
Core function for both isoforms. This IEA annotation is redundant with the
IBA annotation
but not incorrect.
- term:
id: GO:0005524
label: ATP binding
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
PKM binds ATP/ADP as substrates for pyruvate kinase reaction. Both isoforms
bind ATP.
action: ACCEPT
reason: >-
Correct annotation for both isoforms as ATP/ADP binding is essential for pyruvate
kinase activity.
- term:
id: GO:0005634
label: nucleus
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: >-
PKM2 (NOT PKM1) translocates to the nucleus upon EGFR activation and other
stimuli
[PMID:22056988, PMID:17308100]. PKM1 does NOT translocate to the nucleus.
This is a
PKM2-SPECIFIC localization.
action: MODIFY
reason: >-
CRITICAL ISOFORM CONFLATION: Nuclear localization applies ONLY to PKM2 (P14618-1).
PMID:22056988 explicitly states "PKM1 failed to translocate into the nucleus
upon EGF stimulation".
proposed_replacement_terms:
- id: GO:0005634
label: nucleus
supported_by:
- reference_id: PMID:22056988
supporting_text: "In addition, PKM1 failed to translocate into the nucleus
upon EGF stimulation"
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: >-
Both PKM1 and PKM2 localize to the cytoplasm. This is the primary site of
glycolytic function.
action: ACCEPT
reason: >-
Correct for both isoforms. Cytoplasmic localization is the primary location
for glycolytic function.
- term:
id: GO:0006096
label: glycolytic process
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
Duplicate of IBA annotation. Both isoforms participate in glycolysis.
action: ACCEPT
reason: >-
Core function for both isoforms. Redundant with IBA annotation but not incorrect.
- term:
id: GO:0006417
label: regulation of translation
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
PKM2 may act as a translation regulator for a subset of mRNAs, associating
with ER-bound
ribosomes and promoting translation of ER-destined mRNAs [UniProt, by similarity].
This
function is attributed to PKM2 specifically.
action: KEEP_AS_NON_CORE
reason: >-
This is a non-canonical moonlighting function of PKM2 based on similarity
evidence.
Not a core function.
- term:
id: GO:0016301
label: kinase activity
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
PKM has kinase activity - pyruvate kinase activity for both isoforms, and
protein kinase
activity for PKM2 only. This is a broad parent term.
action: ACCEPT
reason: >-
True but uninformative parent term encompassing both pyruvate kinase and protein
kinase activities.
- term:
id: GO:0016740
label: transferase activity
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
PKM has transferase activity (phosphotransferase). This is a very broad parent
term.
action: ACCEPT
reason: >-
True but uninformative high-level parent term. Both isoforms have transferase
activity.
- term:
id: GO:0030955
label: potassium ion binding
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
Pyruvate kinase requires K+ as a cofactor [UniProt P14618]. This applies to
both isoforms.
action: ACCEPT
reason: >-
K+ is an essential cofactor for pyruvate kinase activity. Both isoforms require
this ion.
- term:
id: GO:0046872
label: metal ion binding
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
PKM binds metal ions (Mg2+, K+) as cofactors. Parent term of magnesium and
potassium binding.
action: ACCEPT
reason: >-
True parent term. Both isoforms bind metal ion cofactors.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:12620389
review:
summary: >-
Yeast two-hybrid study identifying RAF kinase protein-protein interactions.
PKM was
identified as an interactor. This is a generic protein binding annotation
from
high-throughput screening.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Generic protein binding from Y2H screen. Does not provide functional insight
into
PKM's core activities. More specific interaction terms would be more informative.
supported_by:
- reference_id: PMID:12620389
supporting_text: Novel raf kinase protein-protein interactions found
by an exhaustive yeast two-hybrid analysis.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:17500595
review:
summary: >-
PKM identified as a Huntingtin interacting protein and potential modifier
of
neurodegeneration. High-throughput interactome study.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Generic protein binding from interactome study. Does not distinguish between
isoforms or provide functional context.
supported_by:
- reference_id: PMID:17500595
supporting_text: Huntingtin interacting proteins are genetic modifiers
of neurodegeneration.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:17620599
review:
summary: >-
PKM identified in beta-arrestin interactome study. High-throughput proteomics.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Generic protein binding from proteomics study. Uninformative without functional
context.
supported_by:
- reference_id: PMID:17620599
supporting_text: Functional specialization of beta-arrestin
interactions revealed by proteomic analysis.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:18519040
review:
summary: >-
Isoform-specific interaction of pyruvate kinase with HCV NS5B. The study specifically
examines PKM2 interaction with viral protein.
action: KEEP_AS_NON_CORE
reason: >-
Interaction with viral protein is interesting for host-pathogen biology but
not a
core function. Appears to be PKM2-specific based on the study context.
supported_by:
- reference_id: PMID:18519040
supporting_text: Epub 2008 Jun 2. Isoform-specific interaction of
pyruvate kinase with hepatitis C virus NS5B.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:21044950
review:
summary: >-
PKM identified in telomere signaling regulator screen. High-throughput study.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Generic protein binding from screening study. Lacks functional specificity.
supported_by:
- reference_id: PMID:21044950
supporting_text: Epub 2010 Nov 2. Genome-wide YFP fluorescence
complementation screen identifies new regulators for telomere
signaling in human cells.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:21725354
review:
summary: >-
Death-associated protein kinase (DAPK) binds and activates pyruvate kinase.
This is functionally relevant for PKM regulation.
action: KEEP_AS_NON_CORE
reason: >-
Functionally relevant interaction but the generic protein binding term is
uninformative.
Would be better captured by a more specific term or in the regulation context.
supported_by:
- reference_id: PMID:21725354
supporting_text: Death-associated protein kinase increases glycolytic
rate through binding and activation of pyruvate kinase.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:22056988
review:
summary: >-
PKM2 (specifically) interacts with beta-catenin (CTNNB1) in the nucleus to
regulate
transcription of CCND1 [PMID:22056988]. This is a PKM2-SPECIFIC interaction
that
requires c-Src phosphorylation of beta-catenin at Y333.
action: MODIFY
reason: >-
This is a functionally significant PKM2-specific interaction. The generic
protein binding
term fails to capture the isoform specificity and functional significance.
Should be
annotated as beta-catenin binding for PKM2 specifically.
proposed_replacement_terms:
- id: GO:0008013
label: beta-catenin binding
supported_by:
- reference_id: PMID:22056988
supporting_text: "EGF stimulation resulted in an interaction between endogenous
PKM2 and beta-catenin in the nuclear, but not cytosolic, fraction"
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:22898364
review:
summary: >-
PKM identified in virus-host interactome study using protein complementation
assay.
High-throughput screening.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Generic protein binding from high-throughput viral interactome study.
supported_by:
- reference_id: PMID:22898364
supporting_text: Aug 8. Comparative analysis of virus-host
interactomes with a mammalian high-throughput protein
complementation assay based on Gaussia princeps luciferase.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:32814053
review:
summary: >-
PKM identified in neurodegenerative disease protein interactome mapping study.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Generic protein binding from disease-focused interactome study.
supported_by:
- reference_id: PMID:32814053
supporting_text: Interactome Mapping Provides a Network of
Neurodegenerative Disease Proteins and Uncovers Widespread Protein
Aggregation in Affected Brains.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:9990017
review:
summary: >-
HPV-16 E7 oncoprotein modulates M2-type pyruvate kinase activity. E7 binding
promotes
PKM2 homodimerization [UniProt].
action: KEEP_AS_NON_CORE
reason: >-
Interaction with viral oncoprotein is relevant for understanding PKM2 in cancer
but represents host-pathogen interaction rather than core function.
supported_by:
- reference_id: PMID:9990017
supporting_text: Modulation of type M2 pyruvate kinase activity by the
human papillomavirus type 16 E7 oncoprotein.
- term:
id: GO:0003729
label: mRNA binding
evidence_type: IEA
original_reference_id: GO_REF:0000107
review:
summary: >-
PKM2 may bind mRNAs as part of its moonlighting function in translation regulation
[UniProt, by similarity]. Associates with ER-bound ribosomes.
action: KEEP_AS_NON_CORE
reason: >-
Non-canonical moonlighting function of PKM2 based on similarity evidence.
Not a core function.
- term:
id: GO:0005791
label: rough endoplasmic reticulum
evidence_type: IEA
original_reference_id: GO_REF:0000107
review:
summary: >-
PKM2 may associate with rough ER as part of its translation regulation function
[UniProt, by similarity].
action: KEEP_AS_NON_CORE
reason: >-
Associated with moonlighting function in translation regulation. Not a primary
localization.
- term:
id: GO:0005829
label: cytosol
evidence_type: IEA
original_reference_id: GO_REF:0000107
review:
summary: >-
Both PKM1 and PKM2 are cytosolic enzymes where they perform glycolysis.
action: ACCEPT
reason: >-
Correct localization for both isoforms. Primary site of glycolytic activity.
- term:
id: GO:0005929
label: cilium
evidence_type: IEA
original_reference_id: GO_REF:0000107
review:
summary: >-
PKM localization to cilium based on ortholog evidence. Limited direct evidence.
action: KEEP_AS_NON_CORE
reason: >-
Ortholog-based evidence for specialized localization. Not a primary site of
function.
- term:
id: GO:0061621
label: canonical glycolysis
evidence_type: IEA
original_reference_id: GO_REF:0000107
review:
summary: >-
Both isoforms participate in canonical glycolysis. PKM catalyzes the final
step
converting PEP to pyruvate.
action: ACCEPT
reason: >-
Core function for both isoforms. More specific than generic glycolytic process
term.
- term:
id: GO:2000767
label: positive regulation of cytoplasmic translation
evidence_type: IEA
original_reference_id: GO_REF:0000107
review:
summary: >-
PKM2 may positively regulate translation of ER-destined mRNAs [UniProt, by
similarity].
Moonlighting function.
action: KEEP_AS_NON_CORE
reason: >-
Non-canonical moonlighting function based on similarity evidence. Not a core
function.
- term:
id: GO:0005829
label: cytosol
evidence_type: IDA
original_reference_id: GO_REF:0000052
review:
summary: >-
Direct assay evidence for cytosolic localization based on immunofluorescence.
Both isoforms are cytosolic.
action: ACCEPT
reason: >-
Validated cytosolic localization. Primary site of glycolytic function for
both isoforms.
- term:
id: GO:0004743
label: pyruvate kinase activity
evidence_type: IDA
original_reference_id: PMID:20847263
review:
summary: >-
Direct demonstration of pyruvate kinase activity. This study examined both
PKM1 and PKM2
and showed that PKM2 has lower activity and contributes to the Warburg effect
by allowing
glycolytic intermediates to accumulate for biosynthesis.
action: ACCEPT
reason: >-
Core function with direct experimental evidence. Both isoforms have activity
but with
different kinetic properties.
supported_by:
- reference_id: PMID:20847263
supporting_text: "Paradoxically, decreased pyruvate kinase enzyme activity
accompanies the expression of PKM2 in rapidly dividing cancer cells and
tissues."
- term:
id: GO:0005654
label: nucleoplasm
evidence_type: TAS
original_reference_id: Reactome:R-HSA-9766062
review:
summary: >-
Reactome pathway annotation for PKM and TGIF2 binding CDH1 gene promoter.
This nuclear
function is PKM2-specific based on literature evidence.
action: MODIFY
reason: >-
ISOFORM CONFLATION: Nucleoplasm localization is PKM2-specific. PKM1 does not
translocate
to nucleus.
proposed_replacement_terms:
- id: GO:0005654
label: nucleoplasm
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-9861640
review:
summary: >-
Reactome annotation for CTLH E3 ligase ubiquitinating PKM-1. Cytosolic localization
is correct for both isoforms.
action: ACCEPT
reason: >-
Correct localization for both isoforms.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:27573352
review:
summary: >-
TSC22D2 interacts with PKM2 and inhibits cell growth in colorectal cancer.
The interaction reduces nuclear PKM2 levels and represses cyclin D1 transcription.
action: KEEP_AS_NON_CORE
reason: >-
Functionally relevant interaction specific to PKM2. Generic protein binding
term
lacks specificity.
supported_by:
- reference_id: PMID:27573352
supporting_text: TSC22D2 interacts with PKM2 and inhibits cell growth
in colorectal cancer.
- term:
id: GO:0005634
label: nucleus
evidence_type: IDA
original_reference_id: PMID:27573352
review:
summary: >-
Direct evidence for PKM nuclear localization. The study specifically examines
PKM2
(isoform M2) nuclear localization and its regulation by TSC22D2.
action: ACCEPT
reason: >-
Direct experimental evidence for nuclear localization. This is PKM2-specific
function
but IDA evidence is strong.
supported_by:
- reference_id: PMID:27573352
supporting_text: TSC22D2 interacts with PKM2 and inhibits cell growth
in colorectal cancer.
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IDA
original_reference_id: PMID:27573352
review:
summary: >-
Direct evidence for PKM cytoplasmic localization. Both isoforms are cytoplasmic.
action: ACCEPT
reason: >-
Correct for both isoforms. Primary site of glycolytic function.
supported_by:
- reference_id: PMID:27573352
supporting_text: TSC22D2 interacts with PKM2 and inhibits cell growth
in colorectal cancer.
- term:
id: GO:0003729
label: mRNA binding
evidence_type: ISS
original_reference_id: GO_REF:0000024
review:
summary: >-
Sequence similarity-based annotation for mRNA binding. Moonlighting function
of PKM2.
action: KEEP_AS_NON_CORE
reason: >-
Non-canonical function based on similarity. Not a core function.
- term:
id: GO:0005791
label: rough endoplasmic reticulum
evidence_type: ISS
original_reference_id: GO_REF:0000024
review:
summary: >-
Sequence similarity-based annotation. Associated with translation regulation
moonlighting function.
action: KEEP_AS_NON_CORE
reason: >-
Non-canonical localization associated with moonlighting function.
- term:
id: GO:2000767
label: positive regulation of cytoplasmic translation
evidence_type: ISS
original_reference_id: GO_REF:0000024
review:
summary: >-
Sequence similarity-based annotation for translation regulation. Moonlighting
function.
action: KEEP_AS_NON_CORE
reason: >-
Non-canonical moonlighting function based on sequence similarity.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:27199445
review:
summary: >-
JMJD8 interacts with PKM2 and regulates angiogenic sprouting and cellular
metabolism.
action: KEEP_AS_NON_CORE
reason: >-
Functionally relevant interaction but generic protein binding term is uninformative.
supported_by:
- reference_id: PMID:27199445
supporting_text: JMJD8 Regulates Angiogenic Sprouting and Cellular
Metabolism by Interacting With Pyruvate Kinase M2 in Endothelial
Cells.
- term:
id: GO:1903672
label: positive regulation of sprouting angiogenesis
evidence_type: IMP
original_reference_id: PMID:27199445
review:
summary: >-
PKM regulates angiogenic sprouting through interaction with JMJD8 in endothelial
cells.
Likely PKM2-mediated based on cancer/proliferation context.
action: KEEP_AS_NON_CORE
reason: >-
Pleiotropic downstream effect in specialized cell type context. Not a core
function
of PKM.
supported_by:
- reference_id: PMID:27199445
supporting_text: JMJD8 Regulates Angiogenic Sprouting and Cellular
Metabolism by Interacting With Pyruvate Kinase M2 in Endothelial
Cells.
- term:
id: GO:0045296
label: cadherin binding
evidence_type: HDA
original_reference_id: PMID:25468996
review:
summary: >-
High-throughput proteomics study of E-cadherin interactome. PKM identified
as
an interactor.
action: KEEP_AS_NON_CORE
reason: >-
High-throughput proteomics finding. More informative than generic protein
binding
but not a core function.
supported_by:
- reference_id: PMID:25468996
supporting_text: E-cadherin interactome complexity and robustness
resolved by quantitative proteomics.
- term:
id: GO:0005576
label: extracellular region
evidence_type: TAS
original_reference_id: Reactome:R-HSA-6798748
review:
summary: >-
Reactome annotation for exocytosis of secretory granule lumen proteins. PKM
found
in extracellular region via secretion.
action: KEEP_AS_NON_CORE
reason: >-
PKM can be secreted but extracellular localization is not a primary site of
function.
- term:
id: GO:0005576
label: extracellular region
evidence_type: TAS
original_reference_id: Reactome:R-HSA-6800434
review:
summary: >-
Reactome annotation for ficolin-rich granule exocytosis. PKM present in extracellular
region.
action: KEEP_AS_NON_CORE
reason: >-
Secondary localization from secretory process.
- term:
id: GO:0034774
label: secretory granule lumen
evidence_type: TAS
original_reference_id: Reactome:R-HSA-6798748
review:
summary: >-
PKM present in secretory granule lumen per Reactome annotation.
action: KEEP_AS_NON_CORE
reason: >-
Specialized localization related to secretory function.
- term:
id: GO:1904813
label: ficolin-1-rich granule lumen
evidence_type: TAS
original_reference_id: Reactome:R-HSA-6800434
review:
summary: >-
PKM present in ficolin-1-rich granule lumen per Reactome annotation.
action: KEEP_AS_NON_CORE
reason: >-
Specialized localization in immune cell granules.
- term:
id: GO:0070062
label: extracellular exosome
evidence_type: HDA
original_reference_id: PMID:12519789
review:
summary: >-
PKM detected in B cell-derived exosomes by proteomics.
action: KEEP_AS_NON_CORE
reason: >-
Exosomal localization from proteomics study. Not primary functional location.
supported_by:
- reference_id: PMID:12519789
supporting_text: 2003 Jan 7. Proteomic and biochemical analyses of
human B cell-derived exosomes.
- term:
id: GO:0070062
label: extracellular exosome
evidence_type: HDA
original_reference_id: PMID:11487543
review:
summary: >-
PKM detected in intestinal epithelial cell exosomes.
action: KEEP_AS_NON_CORE
reason: >-
Exosomal cargo. Not primary functional location.
supported_by:
- reference_id: PMID:11487543
supporting_text: Intestinal epithelial cells secrete exosome-like
vesicles.
- term:
id: GO:1903561
label: extracellular vesicle
evidence_type: HDA
original_reference_id: PMID:24769233
review:
summary: >-
PKM detected in CSF extracellular vesicles by proteomics.
action: KEEP_AS_NON_CORE
reason: >-
Extracellular vesicle cargo from proteomics.
supported_by:
- reference_id: PMID:24769233
supporting_text: '2014 Apr 24. Proteomic analysis of cerebrospinal fluid
extracellular vesicles: a comprehensive dataset.'
- term:
id: GO:0070062
label: extracellular exosome
evidence_type: HDA
original_reference_id: PMID:23533145
review:
summary: >-
PKM detected in prostatic secretion exosomes.
action: KEEP_AS_NON_CORE
reason: >-
Exosomal cargo from proteomics.
supported_by:
- reference_id: PMID:23533145
supporting_text: 2013 Apr 23. In-depth proteomic analyses of exosomes
isolated from expressed prostatic secretions in urine.
- term:
id: GO:0031982
label: vesicle
evidence_type: HDA
original_reference_id: PMID:19190083
review:
summary: >-
PKM detected in tracheobronchial epithelial exosome-like vesicles.
action: KEEP_AS_NON_CORE
reason: >-
Vesicular localization from proteomics.
supported_by:
- reference_id: PMID:19190083
supporting_text: 'Characterization of exosome-like vesicles released from
human tracheobronchial ciliated epithelium: a possible role in innate
defense.'
- term:
id: GO:0005634
label: nucleus
evidence_type: HDA
original_reference_id: PMID:21630459
review:
summary: >-
PKM detected in sperm nucleus by proteomics. Supports nuclear localization
capability.
action: KEEP_AS_NON_CORE
reason: >-
Nuclear detection in specialized cell type. PKM2-specific function.
supported_by:
- reference_id: PMID:21630459
supporting_text: Jun 1. Proteomic characterization of the human sperm
nucleus.
- term:
id: GO:0003723
label: RNA binding
evidence_type: HDA
original_reference_id: PMID:22658674
review:
summary: >-
PKM identified in mRNA-binding protein atlas. Supports moonlighting function
in
translation regulation.
action: KEEP_AS_NON_CORE
reason: >-
Non-canonical moonlighting function from proteomics study.
supported_by:
- reference_id: PMID:22658674
supporting_text: May 31. Insights into RNA biology from an atlas of
mammalian mRNA-binding proteins.
- term:
id: GO:0005739
label: mitochondrion
evidence_type: HDA
original_reference_id: PMID:20833797
review:
summary: >-
PKM detected in mitochondrial phosphoproteome. May represent association with
mitochondria or contamination.
action: KEEP_AS_NON_CORE
reason: >-
Unexpected localization from phosphoproteomics. PKM is canonically cytosolic.
supported_by:
- reference_id: PMID:20833797
supporting_text: Epub 2010 Sep 10. Phosphoproteome analysis of
functional mitochondria isolated from resting human muscle reveals
extensive phosphorylation of inner membrane protein complexes and
enzymes.
- term:
id: GO:0070062
label: extracellular exosome
evidence_type: HDA
original_reference_id: PMID:19199708
review:
summary: >-
PKM detected in parotid gland exosomes.
action: KEEP_AS_NON_CORE
reason: >-
Exosomal cargo from proteomics.
supported_by:
- reference_id: PMID:19199708
supporting_text: Proteomic analysis of human parotid gland exosomes by
multidimensional protein identification technology (MudPIT).
- term:
id: GO:0070062
label: extracellular exosome
evidence_type: HDA
original_reference_id: PMID:19056867
review:
summary: >-
PKM detected in urinary exosomes by proteomics.
action: KEEP_AS_NON_CORE
reason: >-
Exosomal cargo from proteomics.
supported_by:
- reference_id: PMID:19056867
supporting_text: 2008 Dec 3. Large-scale proteomics and
phosphoproteomics of urinary exosomes.
- term:
id: GO:0023026
label: MHC class II protein complex binding
evidence_type: HDA
original_reference_id: PMID:20458337
review:
summary: >-
PKM identified as MHC class II-associated protein in B-cell exosomes.
action: KEEP_AS_NON_CORE
reason: >-
High-throughput proteomics finding. Specialized immune function context.
supported_by:
- reference_id: PMID:20458337
supporting_text: 2010 May 11. MHC class II-associated proteins in
B-cell exosomes and potential functional implications for exosome
biogenesis.
- term:
id: GO:0070062
label: extracellular exosome
evidence_type: HDA
original_reference_id: PMID:20458337
review:
summary: >-
PKM detected in B-cell exosomes.
action: KEEP_AS_NON_CORE
reason: >-
Exosomal cargo from proteomics.
supported_by:
- reference_id: PMID:20458337
supporting_text: 2010 May 11. MHC class II-associated proteins in
B-cell exosomes and potential functional implications for exosome
biogenesis.
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-71670
review:
summary: >-
Reactome annotation for pyruvate kinase reaction. Cytosolic localization correct
for glycolytic function.
action: ACCEPT
reason: >-
Core localization for glycolytic function.
- term:
id: GO:0004743
label: pyruvate kinase activity
evidence_type: IDA
original_reference_id: PMID:20005212
review:
summary: >-
Study identifying small molecule inhibitors of PKM2. Directly demonstrates
pyruvate kinase activity.
action: ACCEPT
reason: >-
Core function with direct experimental evidence.
supported_by:
- reference_id: PMID:20005212
supporting_text: Epub 2009 Dec 11. Identification of small molecule
inhibitors of pyruvate kinase M2.
- term:
id: GO:0070062
label: extracellular exosome
evidence_type: HDA
original_reference_id: PMID:21362503
review:
summary: >-
PKM detected in trabecular meshwork cell exosomes.
action: KEEP_AS_NON_CORE
reason: >-
Exosomal cargo from proteomics.
supported_by:
- reference_id: PMID:21362503
supporting_text: Epub 2011 Mar 8. Protein profile of exosomes from
trabecular meshwork cells.
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IDA
original_reference_id: GO_REF:0000054
review:
summary: >-
Direct assay evidence for cytoplasmic localization from fusion protein studies.
action: ACCEPT
reason: >-
Core localization for both isoforms.
- term:
id: GO:0005634
label: nucleus
evidence_type: IDA
original_reference_id: PMID:18191611
review:
summary: >-
PKM2 interacts with Oct-4 in the nucleus and cooperates in regulating transcription.
This is PKM2-SPECIFIC nuclear function.
action: ACCEPT
reason: >-
Direct experimental evidence for PKM2 nuclear localization and function.
supported_by:
- reference_id: PMID:18191611
supporting_text: "PKM2 is an isozyme of pyruvate kinase that is specifically
expressed in proliferating cells, such as embryonic stem cells, embryonic
carcinoma cells, as well as cancer cells."
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IDA
original_reference_id: PMID:18298799
review:
summary: >-
Study showing cytoplasmic PML modulates PKM2 activity. Confirms cytoplasmic
localization.
action: ACCEPT
reason: >-
Core localization confirmed by direct evidence.
supported_by:
- reference_id: PMID:18298799
supporting_text: "cytoplasmic PML (cPML) directly interacts with M2-type
pyruvate kinase (PKM2)"
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:18191611
review:
summary: >-
PKM2 interacts with Oct-4 transcription factor. The interaction enhances Oct-4
transcriptional activity. PKM2-SPECIFIC interaction.
action: MODIFY
reason: >-
Functionally significant interaction with transcription factor. Generic protein
binding
term is uninformative. Should be more specific (e.g., transcription factor
binding).
proposed_replacement_terms:
- id: GO:0140297
label: DNA-binding transcription factor binding
supported_by:
- reference_id: PMID:18191611
supporting_text: "ectopic expression of the PKM2 enhanced Oct-4-mediated
transcription"
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:18298799
review:
summary: >-
PKM2 interacts with PML tumor suppressor. PML modulates PKM2 tetrameric activity.
action: KEEP_AS_NON_CORE
reason: >-
Functionally relevant interaction for PKM2 regulation but generic protein
binding
term is uninformative.
supported_by:
- reference_id: PMID:18298799
supporting_text: "cytoplasmic PML (cPML) directly interacts with M2-type
pyruvate kinase (PKM2)"
- term:
id: GO:0005634
label: nucleus
evidence_type: IDA
original_reference_id: PMID:17308100
review:
summary: >-
PKM2 translocates to nucleus in response to apoptotic stimuli and TT-232.
Nuclear
translocation induces cell death. PKM2-SPECIFIC function.
action: ACCEPT
reason: >-
Direct experimental evidence for PKM2-specific nuclear translocation.
supported_by:
- reference_id: PMID:17308100
supporting_text: "Nuclear translocation of PKM2 is sufficient to induce
cell death that is caspase independent, isoform specific, and independent
of its enzymatic activity."
- term:
id: GO:0012501
label: programmed cell death
evidence_type: IDA
original_reference_id: PMID:17308100
review:
summary: >-
Nuclear PKM2 translocation induces programmed cell death. This is a PKM2-SPECIFIC
function that is caspase-independent and independent of pyruvate kinase activity.
action: KEEP_AS_NON_CORE
reason: >-
PKM2-specific non-metabolic function. Not a core function but well-documented.
supported_by:
- reference_id: PMID:17308100
supporting_text: "Nuclear translocation of PKM2 is sufficient to induce
cell death that is caspase independent, isoform specific, and independent
of its enzymatic activity."
- term:
id: GO:0004743
label: pyruvate kinase activity
evidence_type: TAS
original_reference_id: PMID:2854097
review:
summary: >-
Original cloning of human M2-type pyruvate kinase cDNA. Establishes pyruvate
kinase
activity as core function.
action: ACCEPT
reason: >-
Core function from original characterization of PKM2.
supported_by:
- reference_id: PMID:2854097
supporting_text: 'Human M2-type pyruvate kinase: cDNA cloning, chromosomal
assignment and expression in hepatoma.'
- term:
id: GO:0004743
label: pyruvate kinase activity
evidence_type: TAS
original_reference_id: PMID:2040271
review:
summary: >-
Isolation and characterization of human pyruvate kinase M gene.
action: ACCEPT
reason: >-
Core function from gene characterization.
supported_by:
- reference_id: PMID:2040271
supporting_text: Isolation and characterization of the human pyruvate
kinase M gene.
- term:
id: GO:0004743
label: pyruvate kinase activity
evidence_type: TAS
original_reference_id: PMID:2813362
review:
summary: >-
Demonstrates PKM is a cytosolic thyroid hormone-binding protein that is a
monomer
of pyruvate kinase with enzymatic activity.
action: ACCEPT
reason: >-
Core function established in characterization study.
supported_by:
- reference_id: PMID:2813362
supporting_text: Cytosolic thyroid hormone-binding protein is a
monomer of pyruvate kinase.
- term:
id: GO:0005829
label: cytosol
evidence_type: NAS
original_reference_id: PMID:2813362
review:
summary: >-
PKM identified as cytosolic thyroid hormone-binding protein.
action: ACCEPT
reason: >-
Core localization established in early characterization.
supported_by:
- reference_id: PMID:2813362
supporting_text: Cytosolic thyroid hormone-binding protein is a
monomer of pyruvate kinase.
core_functions:
- molecular_function:
id: GO:0004743
label: pyruvate kinase activity
description: >-
PKM catalyzes the final rate-limiting step of glycolysis, transferring a phosphoryl
group
from phosphoenolpyruvate (PEP) to ADP to generate pyruvate and ATP. CRITICAL
ISOFORM
DISTINCTION: PKM1 (P14618-2) is constitutively active with HIGH activity in
adult tissues
(muscle, brain, heart). PKM2 (P14618-1) has LOW basal activity requiring allosteric
activation by fructose-1,6-bisphosphate, and is expressed in embryonic tissues
and cancer
cells. PKM2's low activity allows glycolytic intermediates to accumulate for
biosynthetic
pathways - the metabolic basis of the Warburg effect.
- molecular_function:
id: GO:0004713
label: protein tyrosine kinase activity
description: >-
PKM2-SPECIFIC FUNCTION (not present in PKM1): Nuclear dimeric PKM2 acts as a
protein
tyrosine kinase, phosphorylating STAT3 at Tyr-705 to activate transcription.
This
non-metabolic moonlighting function contributes to cancer cell proliferation
and
tumorigenesis. PKM1 does NOT have this activity.
- molecular_function:
id: GO:0004674
label: protein serine/threonine kinase activity
description: >-
PKM2-SPECIFIC FUNCTION (not present in PKM1): Nuclear dimeric PKM2 phosphorylates
histone H3 at Thr-11 (H3T11ph), promoting gene transcription and tumorigenesis.
This protein kinase activity requires nuclear translocation and dimerization,
distinct from its cytoplasmic glycolytic function. PKM1 does NOT have this activity.
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with
GO terms
findings: []
- id: GO_REF:0000003
title: Gene Ontology annotation based on Enzyme Commission mapping
findings: []
- id: GO_REF:0000024
title: Manual transfer of experimentally-verified manual GO annotation data
to orthologs by curator judgment of sequence similarity
findings: []
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings: []
- id: GO_REF:0000043
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword
mapping
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:0000054
title: Gene Ontology annotation based on curation of intracellular
localizations of expressed fusion proteins in living cells
findings: []
- id: GO_REF:0000107
title: Automatic transfer of experimentally verified manual GO annotation
data to orthologs using Ensembl Compara
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:11487543
title: Intestinal epithelial cells secrete exosome-like vesicles.
findings: []
- id: PMID:12519789
title: Proteomic and biochemical analyses of human B cell-derived exosomes.
Potential implications for their function and multivesicular body
formation.
findings: []
- id: PMID:12620389
title: Novel raf kinase protein-protein interactions found by an exhaustive
yeast two-hybrid analysis.
findings: []
- id: PMID:17308100
title: Nuclear translocation of the tumor marker pyruvate kinase M2 induces
programmed cell death.
findings: []
- id: PMID:17500595
title: Huntingtin interacting proteins are genetic modifiers of
neurodegeneration.
findings: []
- id: PMID:17620599
title: Functional specialization of beta-arrestin interactions revealed by
proteomic analysis.
findings: []
- id: PMID:18191611
title: Pyruvate kinase isozyme type M2 (PKM2) interacts and cooperates with
Oct-4 in regulating transcription.
findings: []
- id: PMID:18298799
title: Modulation of M2-type pyruvate kinase activity by the cytoplasmic PML
tumor suppressor protein.
findings: []
- id: PMID:18519040
title: Isoform-specific interaction of pyruvate kinase with hepatitis C
virus NS5B.
findings: []
- id: PMID:19056867
title: Large-scale proteomics and phosphoproteomics of urinary exosomes.
findings: []
- id: PMID:19190083
title: 'Characterization of exosome-like vesicles released from human tracheobronchial
ciliated epithelium: a possible role in innate defense.'
findings: []
- id: PMID:19199708
title: Proteomic analysis of human parotid gland exosomes by
multidimensional protein identification technology (MudPIT).
findings: []
- id: PMID:20005212
title: Identification of small molecule inhibitors of pyruvate kinase M2.
findings: []
- id: PMID:2040271
title: Isolation and characterization of the human pyruvate kinase M gene.
findings: []
- id: PMID:20458337
title: MHC class II-associated proteins in B-cell exosomes and potential
functional implications for exosome biogenesis.
findings: []
- id: PMID:20833797
title: Phosphoproteome analysis of functional mitochondria isolated from
resting human muscle reveals extensive phosphorylation of inner membrane
protein complexes and enzymes.
findings: []
- id: PMID:20847263
title: Evidence for an alternative glycolytic pathway in rapidly
proliferating cells.
findings: []
- id: PMID:21044950
title: Genome-wide YFP fluorescence complementation screen identifies new
regulators for telomere signaling in human cells.
findings: []
- id: PMID:21362503
title: Protein profile of exosomes from trabecular meshwork cells.
findings: []
- id: PMID:21630459
title: Proteomic characterization of the human sperm nucleus.
findings: []
- id: PMID:21725354
title: Death-associated protein kinase increases glycolytic rate through
binding and activation of pyruvate kinase.
findings: []
- id: PMID:22056988
title: Nuclear PKM2 regulates β-catenin transactivation upon EGFR
activation.
findings: []
- id: PMID:22658674
title: Insights into RNA biology from an atlas of mammalian mRNA-binding
proteins.
findings: []
- id: PMID:22898364
title: Comparative analysis of virus-host interactomes with a mammalian
high-throughput protein complementation assay based on Gaussia princeps
luciferase.
findings: []
- id: PMID:23533145
title: In-depth proteomic analyses of exosomes isolated from expressed
prostatic secretions in urine.
findings: []
- id: PMID:24769233
title: 'Proteomic analysis of cerebrospinal fluid extracellular vesicles: a comprehensive
dataset.'
findings: []
- id: PMID:25468996
title: E-cadherin interactome complexity and robustness resolved by
quantitative proteomics.
findings: []
- id: PMID:27199445
title: JMJD8 Regulates Angiogenic Sprouting and Cellular Metabolism by
Interacting With Pyruvate Kinase M2 in Endothelial Cells.
findings: []
- id: PMID:27573352
title: TSC22D2 interacts with PKM2 and inhibits cell growth in colorectal
cancer.
findings: []
- id: PMID:2813362
title: Cytosolic thyroid hormone-binding protein is a monomer of pyruvate
kinase.
findings: []
- id: PMID:2854097
title: 'Human M2-type pyruvate kinase: cDNA cloning, chromosomal assignment and
expression in hepatoma.'
findings: []
- id: PMID:32814053
title: Interactome Mapping Provides a Network of Neurodegenerative Disease
Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.
findings: []
- id: PMID:9990017
title: Modulation of type M2 pyruvate kinase activity by the human
papillomavirus type 16 E7 oncoprotein.
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-71670
title: Pyruvate kinase dephosphorylates PEP to PYR
findings: []
- id: Reactome:R-HSA-9766062
title: PKM and TGIF2 bind CDH1 gene promoter
findings: []
- id: Reactome:R-HSA-9861640
title: CTLH E3 ligase ubiquitinates PKM-1
findings: []