GLYCTK

UniProt ID: Q8IVS8
Organism: Homo sapiens
Review Status: COMPLETE
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Gene Description

GLYCTK encodes glycerate kinase, an ATP-dependent enzyme that phosphorylates D-glycerate; curated UniProt and Reactome records describe the product as (2R)-3-phosphoglycerate/3-phospho-D-glycerate. This activity supports metabolism of D-glycerate produced during serine catabolism and minor fructose metabolism and is the affected activity in D-glyceric aciduria. Isoform 1 is cytoplasmic, while isoform 2 has both cytoplasmic and mitochondrial localization; the core gene-level function is glycerate kinase activity rather than protein phosphorylation or generic protein binding.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0005737 cytoplasm
IBA
GO_REF:0000033
ACCEPT
Summary: cytoplasm localization is consistent with the UniProt isoform annotation and with GLYCTK acting as a soluble metabolic enzyme.
Reason: Cytoplasmic/cytosolic localization is directly supported for isoform 1 and also applies to isoform 2, so this is a valid cellular component annotation.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
SUBCELLULAR LOCATION: [Isoform 1]: Cytoplasm. [Isoform 2]: Cytoplasm. Mitochondrion.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally localized to mitochondria.
GO:0008887 glycerate kinase activity
IBA
GO_REF:0000033
ACCEPT
Summary: glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and human disease reports support loss of this enzyme activity in D-glyceric aciduria.
Reason: This term is specific, aspect-correct, and directly matches the characterized enzyme activity of GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on glycerate kinase activity as the primary molecular function.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and links GLYCTK deficiency to D-glyceric aciduria.
GO:0000166 nucleotide binding
IEA
GO_REF:0000043
MARK AS OVER ANNOTATED
Summary: nucleotide binding is technically compatible with an ATP-dependent kinase but is too broad to add useful information when glycerate kinase activity is already annotated.
Reason: The annotation should be interpreted through the specific GO:0008887 glycerate kinase activity term. Broad parent terms such as nucleotide binding, kinase activity, and transferase activity blur the actual function.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
GLYCTK is annotated with the specific catalytic reaction for glycerate kinase activity, EC=2.7.1.31.
GO:0005524 ATP binding
IEA
GO_REF:0000043
ACCEPT
Summary: ATP binding is required for the glycerate kinase reaction because ATP is the phosphate donor for conversion of (R)-glycerate to (2R)-3-phosphoglycerate.
Reason: Although less informative than glycerate kinase activity, ATP binding is mechanistically relevant and supported by the catalytic reaction.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+).
GO:0005737 cytoplasm
IEA
GO_REF:0000044
ACCEPT
Summary: cytoplasm localization is consistent with the UniProt isoform annotation and with GLYCTK acting as a soluble metabolic enzyme.
Reason: Cytoplasmic/cytosolic localization is directly supported for isoform 1 and also applies to isoform 2, so this is a valid cellular component annotation.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
SUBCELLULAR LOCATION: [Isoform 1]: Cytoplasm. [Isoform 2]: Cytoplasm. Mitochondrion.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally localized to mitochondria.
GO:0005739 mitochondrion
IEA
GO_REF:0000044
KEEP AS NON CORE
Summary: Mitochondrial localization is supported for GLYCTK isoform 2 and by high-throughput mitochondrial proteomics, but it is isoform/context-specific rather than the universal location of all GLYCTK products.
Reason: Keep this cellular component as a valid non-core localization. The core gene-level location remains cytoplasm/cytosol, with mitochondrion applying to isoform 2 and proteomic detections.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
SUBCELLULAR LOCATION: [Isoform 2]: Cytoplasm. Mitochondrion.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally localized to mitochondria.
GO:0008887 glycerate kinase activity
IEA
GO_REF:0000120
ACCEPT
Summary: glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and human disease reports support loss of this enzyme activity in D-glyceric aciduria.
Reason: This term is specific, aspect-correct, and directly matches the characterized enzyme activity of GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on glycerate kinase activity as the primary molecular function.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and links GLYCTK deficiency to D-glyceric aciduria.
GO:0016301 kinase activity
IEA
GO_REF:0000043
MARK AS OVER ANNOTATED
Summary: kinase activity is technically compatible with an ATP-dependent kinase but is too broad to add useful information when glycerate kinase activity is already annotated.
Reason: The annotation should be interpreted through the specific GO:0008887 glycerate kinase activity term. Broad parent terms such as nucleotide binding, kinase activity, and transferase activity blur the actual function.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
GLYCTK is annotated with the specific catalytic reaction for glycerate kinase activity, EC=2.7.1.31.
GO:0016740 transferase activity
IEA
GO_REF:0000043
MARK AS OVER ANNOTATED
Summary: transferase activity is technically compatible with an ATP-dependent kinase but is too broad to add useful information when glycerate kinase activity is already annotated.
Reason: The annotation should be interpreted through the specific GO:0008887 glycerate kinase activity term. Broad parent terms such as nucleotide binding, kinase activity, and transferase activity blur the actual function.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
GLYCTK is annotated with the specific catalytic reaction for glycerate kinase activity, EC=2.7.1.31.
GO:0005515 protein binding
IPI
PMID:16189514
Towards a proteome-scale map of the human protein-protein in...
MARK AS OVER ANNOTATED
Summary: This generic protein binding row comes from high-throughput interactome evidence and does not describe the biochemical function of GLYCTK.
Reason: Protein binding is uninformative here and is not the core molecular role of this metabolic enzyme. The useful GO annotation is glycerate kinase activity.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
The curated functional annotation describes glycerate kinase catalytic activity, while many listed interactions are high-throughput IntAct records.
GO:0005515 protein binding
IPI
PMID:19060904
An empirical framework for binary interactome mapping.
MARK AS OVER ANNOTATED
Summary: This generic protein binding row comes from high-throughput interactome evidence and does not describe the biochemical function of GLYCTK.
Reason: Protein binding is uninformative here and is not the core molecular role of this metabolic enzyme. The useful GO annotation is glycerate kinase activity.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
The curated functional annotation describes glycerate kinase catalytic activity, while many listed interactions are high-throughput IntAct records.
GO:0005515 protein binding
IPI
PMID:25416956
A proteome-scale map of the human interactome network.
MARK AS OVER ANNOTATED
Summary: This generic protein binding row comes from high-throughput interactome evidence and does not describe the biochemical function of GLYCTK.
Reason: Protein binding is uninformative here and is not the core molecular role of this metabolic enzyme. The useful GO annotation is glycerate kinase activity.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
The curated functional annotation describes glycerate kinase catalytic activity, while many listed interactions are high-throughput IntAct records.
GO:0005515 protein binding
IPI
PMID:32296183
A reference map of the human binary protein interactome.
MARK AS OVER ANNOTATED
Summary: This generic protein binding row comes from high-throughput interactome evidence and does not describe the biochemical function of GLYCTK.
Reason: Protein binding is uninformative here and is not the core molecular role of this metabolic enzyme. The useful GO annotation is glycerate kinase activity.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
The curated functional annotation describes glycerate kinase catalytic activity, while many listed interactions are high-throughput IntAct records.
GO:0005829 cytosol
IDA
GO_REF:0000052
ACCEPT
Summary: cytosol localization is consistent with the UniProt isoform annotation and with GLYCTK acting as a soluble metabolic enzyme.
Reason: Cytoplasmic/cytosolic localization is directly supported for isoform 1 and also applies to isoform 2, so this is a valid cellular component annotation.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
SUBCELLULAR LOCATION: [Isoform 1]: Cytoplasm. [Isoform 2]: Cytoplasm. Mitochondrion.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally localized to mitochondria.
GO:0061624 fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate
TAS
Reactome:R-HSA-70350
ACCEPT
Summary: GLYCTK participates in fructose catabolism by phosphorylating D-glycerate, a metabolite generated downstream of fructose metabolism, to 3-phosphoglycerate.
Reason: The Reactome pathway context is appropriate for GLYCTK. The direct molecular function remains glycerate kinase activity, but the biological-process placement in fructose catabolism is supported.
Supporting Evidence:
Reactome:R-HSA-6799495
GLYCTK phosphorylates DGA to 3PDGA
GO:0008887 glycerate kinase activity
EXP
PMID:2537226
D-glycerate kinase deficiency as a cause of D-glyceric acidu...
ACCEPT
Summary: glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and human disease reports support loss of this enzyme activity in D-glyceric aciduria.
Reason: This term is specific, aspect-correct, and directly matches the characterized enzyme activity of GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on glycerate kinase activity as the primary molecular function.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and links GLYCTK deficiency to D-glyceric aciduria.
GO:0005739 mitochondrion
HTP
PMID:34800366
Quantitative high-confidence human mitochondrial proteome an...
KEEP AS NON CORE
Summary: Mitochondrial localization is supported for GLYCTK isoform 2 and by high-throughput mitochondrial proteomics, but it is isoform/context-specific rather than the universal location of all GLYCTK products.
Reason: Keep this cellular component as a valid non-core localization. The core gene-level location remains cytoplasm/cytosol, with mitochondrion applying to isoform 2 and proteomic detections.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
SUBCELLULAR LOCATION: [Isoform 2]: Cytoplasm. Mitochondrion.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally localized to mitochondria.
GO:0008887 glycerate kinase activity
IDA
PMID:31837836
d-Glycerate kinase deficiency in a neuropediatric patient.
ACCEPT
Summary: glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and human disease reports support loss of this enzyme activity in D-glyceric aciduria.
Reason: This term is specific, aspect-correct, and directly matches the characterized enzyme activity of GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on glycerate kinase activity as the primary molecular function.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and links GLYCTK deficiency to D-glyceric aciduria.
GO:0008887 glycerate kinase activity
IMP
PMID:31837836
d-Glycerate kinase deficiency in a neuropediatric patient.
ACCEPT
Summary: glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and human disease reports support loss of this enzyme activity in D-glyceric aciduria.
Reason: This term is specific, aspect-correct, and directly matches the characterized enzyme activity of GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on glycerate kinase activity as the primary molecular function.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and links GLYCTK deficiency to D-glyceric aciduria.
GO:0005829 cytosol
TAS
Reactome:R-HSA-6799495
ACCEPT
Summary: cytosol localization is consistent with the UniProt isoform annotation and with GLYCTK acting as a soluble metabolic enzyme.
Reason: Cytoplasmic/cytosolic localization is directly supported for isoform 1 and also applies to isoform 2, so this is a valid cellular component annotation.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
SUBCELLULAR LOCATION: [Isoform 1]: Cytoplasm. [Isoform 2]: Cytoplasm. Mitochondrion.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally localized to mitochondria.
GO:0005737 cytoplasm
IDA
PMID:16753811
Isolation and characterization of the human D-glyceric acide...
ACCEPT
Summary: cytoplasm localization is consistent with the UniProt isoform annotation and with GLYCTK acting as a soluble metabolic enzyme.
Reason: Cytoplasmic/cytosolic localization is directly supported for isoform 1 and also applies to isoform 2, so this is a valid cellular component annotation.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
SUBCELLULAR LOCATION: [Isoform 1]: Cytoplasm. [Isoform 2]: Cytoplasm. Mitochondrion.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally localized to mitochondria.
GO:0006468 protein phosphorylation
IDA
PMID:16753811
Isolation and characterization of the human D-glyceric acide...
REMOVE
Summary: GLYCTK is a small-molecule glycerate kinase, not a protein kinase. Its catalytic activity phosphorylates (R)-glycerate to (2R)-3-phosphoglycerate and does not support protein phosphorylation.
Reason: This is an aspect-correct BP term for protein kinases but a wrong biological-process annotation for GLYCTK. The evidence supports glycerate phosphorylation in metabolism, not phosphorylation of protein substrates.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
GO:0008887 glycerate kinase activity
IDA
PMID:16753811
Isolation and characterization of the human D-glyceric acide...
ACCEPT
Summary: glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and human disease reports support loss of this enzyme activity in D-glyceric aciduria.
Reason: This term is specific, aspect-correct, and directly matches the characterized enzyme activity of GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on glycerate kinase activity as the primary molecular function.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and links GLYCTK deficiency to D-glyceric aciduria.

Core Functions

Phosphorylates D-glycerate using ATP, providing the core enzymatic step for D-glycerate metabolism in serine/fructose catabolic context; UniProt and Reactome describe the product as (2R)-3-phosphoglycerate/3-phospho-D-glycerate.

Supporting Evidence:
  • file:human/GLYCTK/GLYCTK-uniprot.txt
    Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
  • file:human/GLYCTK/GLYCTK-deep-research-falcon.md
    Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and emphasizes D-glycerate as the physiological substrate.

References

Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Gene Ontology annotation based on curation of immunofluorescence data
Combined Automated Annotation using Multiple IEA Methods
Towards a proteome-scale map of the human protein-protein interaction network.
Isolation and characterization of the human D-glyceric acidemia related glycerate kinase gene GLYCTK1 and its alternatively splicing variant GLYCTK2.
An empirical framework for binary interactome mapping.
D-glycerate kinase deficiency as a cause of D-glyceric aciduria.
A proteome-scale map of the human interactome network.
d-Glycerate kinase deficiency in a neuropediatric patient.
A reference map of the human binary protein interactome.
Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context.
Reactome:R-HSA-6799495
GLYCTK phosphorylates DGA to 3PDGA
Reactome:R-HSA-70350
Fructose catabolism
file:human/GLYCTK/GLYCTK-uniprot.txt
UniProt record for human GLYCTK
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon deep research on GLYCTK function
  • Falcon report confirms GLYCTK identity as human glycerate kinase/EC 2.7.1.31 and summarizes D-glyceric aciduria evidence.
    "The UniProt accession Q8IVS8 corresponds to human GLYCTK, annotated as glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31)."
  • Falcon report summarizes isoform-dependent cytosolic and mitochondrial localization.
    "Both isoforms were reported as cytosolic (particulate). GLYCTK2 was additionally reported to be specifically localized to mitochondria, whereas GLYCTK1 was not."

Suggested Questions for Experts

Q: Which GLYCTK isoforms account for mitochondrial glycerate kinase activity in human tissues?

Suggested experts: metabolic biochemists, mitochondrial proteomics experts

Q: How does GLYCTK deficiency produce variable neurological phenotypes in D-glyceric aciduria?

Suggested experts: clinical geneticists, inborn errors of metabolism specialists

Suggested Experiments

Experiment: Quantitatively compare endogenous GLYCTK isoform 1 and isoform 2 localization in tissues with high fructose or glycerate flux.

Hypothesis: Isoform 2 provides a mitochondrial pool of glycerate kinase activity whereas isoform 1 supports cytosolic glycerate metabolism.

Type: Isoform localization

Experiment: Trace labeled D-glycerate in GLYCTK-null and rescue cells expressing individual isoforms.

Hypothesis: Loss of GLYCTK blocks conversion of D-glycerate into 3-phosphoglycerate and isoform-specific rescue distinguishes cytosolic and mitochondrial contributions.

Type: Metabolic flux analysis

📚 Additional Documentation

Deep Research Falcon

(GLYCTK-deep-research-falcon.md)

provider: falcon
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template_file: templates/gene_research_go_focused.md
template_variables:
organism: human
gene_id: GLYCTK
gene_symbol: GLYCTK
uniprot_accession: Q8IVS8
protein_description: 'RecName: Full=Glycerate kinase; EC=2.7.1.31 {ECO:0000269|PubMed:16753811,
ECO:0000269|PubMed:20949620}; AltName: Full=HBeAg-binding protein 4;'
gene_info: Name=GLYCTK; Synonyms=HBEBP4; ORFNames=LP5910;
organism_full: Homo sapiens (Human).
protein_family: Belongs to the glycerate kinase type-2 family.
protein_domains: GK-like_C_sf. (IPR037035); GK_N_sf. (IPR038614); MOFRL. (IPR007835);
MOFRL_assoc_dom. (IPR025286); MOFRL_protein. (IPR039760)
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citation_count: 21


Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

  • UniProt Accession: Q8IVS8
  • Protein Description: RecName: Full=Glycerate kinase; EC=2.7.1.31 {ECO:0000269|PubMed:16753811, ECO:0000269|PubMed:20949620}; AltName: Full=HBeAg-binding protein 4;
  • Gene Information: Name=GLYCTK; Synonyms=HBEBP4; ORFNames=LP5910;
  • Organism (full): Homo sapiens (Human).
  • Protein Family: Belongs to the glycerate kinase type-2 family.
  • Key Domains: GK-like_C_sf. (IPR037035); GK_N_sf. (IPR038614); MOFRL. (IPR007835); MOFRL_assoc_dom. (IPR025286); MOFRL_protein. (IPR039760)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "GLYCTK" matches the protein description above
  2. Verify the organism is correct: Homo sapiens (Human).
  3. Check if protein family/domains align with what you find in literature
  4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'GLYCTK' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information

Research Target:

Please provide a comprehensive research report on the gene GLYCTK (gene ID: GLYCTK, UniProt: Q8IVS8) in human.

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Output

Question: You are an expert researcher providing comprehensive, well-cited information.

Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies

Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

  • UniProt Accession: Q8IVS8
  • Protein Description: RecName: Full=Glycerate kinase; EC=2.7.1.31 {ECO:0000269|PubMed:16753811, ECO:0000269|PubMed:20949620}; AltName: Full=HBeAg-binding protein 4;
  • Gene Information: Name=GLYCTK; Synonyms=HBEBP4; ORFNames=LP5910;
  • Organism (full): Homo sapiens (Human).
  • Protein Family: Belongs to the glycerate kinase type-2 family.
  • Key Domains: GK-like_C_sf. (IPR037035); GK_N_sf. (IPR038614); MOFRL. (IPR007835); MOFRL_assoc_dom. (IPR025286); MOFRL_protein. (IPR039760)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "GLYCTK" matches the protein description above
  2. Verify the organism is correct: Homo sapiens (Human).
  3. Check if protein family/domains align with what you find in literature
  4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'GLYCTK' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information

Research Target:

Please provide a comprehensive research report on the gene GLYCTK (gene ID: GLYCTK, UniProt: Q8IVS8) in human.

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Comprehensive research report: human GLYCTK (UniProt Q8IVS8) — functional annotation

0) Identity verification (critical disambiguation)

The UniProt accession Q8IVS8 corresponds to human GLYCTK (synonyms reported in UniProt include HBEBP4), annotated as glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31). The primary human genetics and enzymology literature for D-glyceric aciduria explicitly identifies GLYCTK as encoding D-glycerate 2-kinase and establishes causality between GLYCTK loss-of-function variants and disease, confirming the target identity is correct (sass2010d‐glycericaciduriais pages 12-15, zehavi2019severeinfantileepileptic pages 1-2, swanson2017dglycericaciduriadoes pages 1-2).

1) Key concepts and definitions (current understanding)

1.1 Enzymatic function and reaction definition

GLYCTK (D-glycerate 2-kinase; EC 2.7.1.31) catalyzes phosphorylation of D-glycerate to 2-phosphoglycerate (2-PG) (zehavi2019severeinfantileepileptic pages 1-2). This reaction consumes ATP (kinase reaction; ATP consumption is explicitly described in assay coupling approaches and in mechanistic descriptions linking to glycolytic intermediates) and places GLYCTK at a junction between D-glycerate handling and central carbon metabolism (zehavi2019severeinfantileepileptic pages 1-2, sass2010d‐glycericaciduriais pages 12-15).

Pathway placement: D-glycerate is described as an intermediate metabolite of serine and fructose metabolism, and conversion to 2-phosphoglycerate creates a biochemical link into glycolysis/gluconeogenesis via 2-PG (zehavi2019severeinfantileepileptic pages 1-2, guo2006isolationandcharacterization pages 4-5).

1.2 D-glyceric aciduria (DGA) / glycerate kinase deficiency

D-glyceric aciduria (OMIM #220120) is an autosomal recessive inborn error of metabolism caused by mutations in GLYCTK, leading to accumulation of D-glycerate in tissues and massive urinary excretion (zehavi2019severeinfantileepileptic pages 1-2, swanson2017dglycericaciduriadoes pages 1-2). Clinically, DGA is often framed as a disorder linked to serine and fructose metabolism (swanson2017dglycericaciduriadoes pages 1-2, sass2020dglyceratekinasedeficiency pages 1-2).

2) Molecular and biochemical function (evidence-based)

2.1 Substrate specificity (what is known)

The disease and enzymology evidence in the retrieved primary literature specifically centers on D-glycerate as the physiological substrate, with formation of 2-phosphoglycerate as the product (zehavi2019severeinfantileepileptic pages 1-2, sass2010d‐glycericaciduriais pages 12-15). The available extracted evidence does not provide a broader substrate panel; thus, substrate specificity beyond D-glycerate cannot be asserted from the retrieved texts.

2.2 Enzymatic kinetics and activity (quantitative)

A core functional validation study expressed reference human GLYCTK cDNA in HEK293 cells, showing:
- Enzyme activity increased from trace amounts (<0.5 µmol·min⁻¹·g⁻¹ protein) in controls to 30.7 µmol·min⁻¹·g⁻¹ protein after expression of reference GLYCTK (sass2010d‐glycericaciduriais pages 12-15).
- The measured Km for D-glycerate was 0.1 mM (mean of two transfection series) (sass2010d‐glycericaciduriais pages 12-15).
- Patient-derived mutant forms (frameshift or missense) produced no enhanced protein signal and no detectable activity in this expression system (sass2010d‐glycericaciduriais pages 12-15).

Figure-based support for the activity comparison (reference vs mutants) is available as a cropped figure from the paper (sass2010d‐glycericaciduriais media 5f02c9bb).

3) Subcellular localization and isoforms

3.1 Isoform-dependent localization (experimental evidence)

A cloning/characterization study identified two alternatively spliced transcripts, GLYCTK1 and GLYCTK2, and used GFP-fusion experiments in mammalian cells to assess localization:
- Both isoforms were reported as cytosolic (particulate).
- GLYCTK2 was additionally reported to be specifically localized to mitochondria, whereas GLYCTK1 was not (guo2006isolationandcharacterization pages 4-5).

These findings support the concept that GLYCTK function can occur in both cytosolic and mitochondrial compartments, with mitochondrial targeting being isoform-dependent (guo2006isolationandcharacterization pages 4-5).

3.2 Tissue expression

Both transcript variants were detected by RT-PCR across a broad panel of 17 human tissues, indicating widespread expression (guo2006isolationandcharacterization pages 1-4). Mouse in situ hybridization also showed notable expression in neural regions and skeletal muscle (guo2006isolationandcharacterization pages 4-5, guo2006isolationandcharacterization pages 5-6), which has been interpreted as consistent with neurological involvement in severe cases (guo2006isolationandcharacterization pages 5-6).

4) Human disease genetics and phenotype (authoritative primary literature)

4.1 Causality: GLYCTK deficiency causes D-glyceric aciduria

A key human mutation/functional paper reported homozygous exon 5 GLYCTK variants in unrelated DGA patients and functionally demonstrated loss of enzyme activity upon expression of the mutant alleles (sass2010d‐glycericaciduriais pages 12-15). This provides direct experimental support that GLYCTK is the causative gene for DGA in these cases.

4.2 Reported pathogenic variants (examples in retrieved evidence)

Pathogenic GLYCTK variants reported across retrieved studies include:
- c.1448delT (p.Phe483SerfsX2) (sass2010d‐glycericaciduriais pages 12-15, swanson2017dglycericaciduriadoes pages 1-2)
- c.1478T>G (p.Phe493Cys) (sass2010d‐glycericaciduriais pages 12-15)
- c.1558delC (p.Leu520CysfsX108) (sass2010d‐glycericaciduriais pages 12-15)
- c.455T>C (p.Leu152Pro) (zehavi2019severeinfantileepileptic pages 1-2)
- c.517G>T (p.Val173Leu) (sass2020dglyceratekinasedeficiency pages 1-2)

4.3 Quantitative metabolite abnormalities (statistics/data)

In DGA patients with GLYCTK deficiency, quantitative elevations reported include:
- Plasma D-glycerate 1.0–1.3 mM (historical patient A; normal reported as not detectable) (sass2010d‐glycericaciduriais pages 12-15).
- Urinary glycerate reported as 9.32 mol/mol creatinine (patient B) and 11.3, 8.61, 18.6 mol/mol creatinine (three samples from patient C) (sass2010d‐glycericaciduriais pages 12-15).
- Serum glycerate 1 mM (patient C) (sass2010d‐glycericaciduriais pages 12-15).

These values provide concrete biochemical anchors for functional annotation and diagnostic expectations.

4.4 Clinical spectrum and case counts

The phenotype spectrum is repeatedly described as highly variable, ranging from severe progressive infantile encephalopathy to mild/nearly asymptomatic presentations (zehavi2019severeinfantileepileptic pages 1-2, swanson2017dglycericaciduriadoes pages 1-2).

Across case-based summaries in the retrieved literature:
- A review/case report describes 15 previously reported patients plus the current case (total 16) and emphasizes severe neurological impairment in many cases (zehavi2019severeinfantileepileptic pages 1-2).
- Another neuropediatric case report notes that 16 individuals had been described with tentative diagnosis, but only six had prior mutation confirmation, and presents the seventh genetically confirmed case (sass2020dglyceratekinasedeficiency pages 1-2).

Severe neurologic manifestations reported in a progressive case include profound psychomotor retardation, progressive microcephaly, intractable seizures, cortical blindness and deafness, hypotonia progressing to spasticity, progressive brain atrophy on MRI, and death at 9.5 years following status epilepticus (zehavi2019severeinfantileepileptic pages 1-2). A milder neuropediatric case includes severe early hypotonia, hypermobility, tremor, delayed milestones, and diffuse slow EEG background without a specific epileptic syndrome (sass2020dglyceratekinasedeficiency pages 1-2).

5) Recent developments (prioritize 2023–2024)

5.1 State of the retrieved 2023–2024 evidence

Within the tool-retrieved set, no 2023–2024 primary mechanistic papers focused specifically on human GLYCTK enzymology, structure, or cell biology were accessible. The most informative GLYCTK functional/disease evidence available here remains from foundational studies (2006–2020) (sass2010d‐glycericaciduriais pages 12-15, guo2006isolationandcharacterization pages 4-5, zehavi2019severeinfantileepileptic pages 1-2, sass2020dglyceratekinasedeficiency pages 1-2).

Two 2023–2024 papers retrieved are primarily platform/resource contributions rather than GLYCTK biology:
- SpliceProt 2.0 (published 18 Jan 2024) is a proteogenomics repository aimed at cataloging proteoforms; it is relevant indirectly for splice-variant-aware proteomics workflows, but does not provide GLYCTK-specific functional data in the retrieved sections (santos2024spliceprot2.0a pages 1-2, santos2024spliceprot2.0a pages 2-4).
- Metaboverse (published Apr 2023) is a computational tool for metabolic network visualization and pattern discovery; the retrieved excerpt does not provide GLYCTK-specific biology beyond general metabolic-network context (berg2023metaboverseenablesautomated pages 8-9, berg2023metaboverseenablesautomated pages 9-10).

6) Current applications and real-world implementations

6.1 Clinical diagnostics (inborn errors of metabolism)

Real-world implementation of GLYCTK knowledge is primarily in metabolic diagnostics:
- Urine organic acid analysis detects elevated glycerate; subsequent enantioselective analysis can distinguish D- vs L-glycerate to differentiate DGA (GLYCTK deficiency) from primary hyperoxaluria type 2 (L-glycerate) (sass2020dglyceratekinasedeficiency pages 1-2, zehavi2019severeinfantileepileptic pages 1-2).
- Genetic testing (GLYCTK sequencing) provides confirmatory diagnosis and can resolve confounded historical diagnoses (e.g., co-occurring disorders) (swanson2017dglycericaciduriadoes pages 1-2, sass2010d‐glycericaciduriais pages 12-15).

6.2 Functional variant interpretation (experimental implementation)

The HEK293 overexpression assay provides an implemented approach for functional validation of candidate GLYCTK variants, demonstrating that disease-associated alleles can abolish detectable activity/protein (sass2010d‐glycericaciduriais pages 12-15, sass2010d‐glycericaciduriais media 5f02c9bb).

7) Expert opinions and analysis (authoritative interpretation from sources)

7.1 Variant-to-phenotype uncertainty and ascertainment bias

Authors emphasize that clinical expressivity is broad, including families with asymptomatic affected siblings, raising the possibility of ascertainment bias and/or modifying factors (swanson2017dglycericaciduriadoes pages 1-2). This complicates straightforward genotype–phenotype mapping.

7.2 Potential additional roles beyond canonical metabolism

Although GLYCTK is primarily discussed as an enzyme in serine/fructose metabolism, authors have speculated that in higher animals glycerate kinase may have roles in neural systems and cell differentiation (guo2006isolationandcharacterization pages 6-7). A neuropediatric case report explicitly suggests future work should search for additional roles beyond catabolism of serine and fructose (sass2020dglyceratekinasedeficiency pages 1-2). These are hypotheses/opinions rather than demonstrated mechanisms in the extracted evidence.

8) Database corroboration (OpenTargets)

OpenTargets reports a GLYCTK association with D-glyceric aciduria (MONDO_0009070) supported by multiple evidence entries and PubMed links, consistent with the primary literature linking GLYCTK mutations to DGA (sass2010d‐glycericaciduriais pages 12-15).

9) Summary of key evidence (tabulated)

The following table consolidates the key functional annotation points extracted from the retrieved literature.

Claim/Topic Key evidence (short) Source (authors year journal) URL Publication date Citation ID
Reaction Human GLYCTK encodes D-glycerate 2-kinase (EC 2.7.1.31), converting D-glycerate to 2-phosphoglycerate; D-glycerate is an intermediate of serine and fructose metabolism. Zehavi et al. 2019, Metabolic Brain Disease https://doi.org/10.1007/s11011-019-0384-x 2019-01-12 (zehavi2019severeinfantileepileptic pages 1-2)
Km Recombinant human GLYCTK expressed in HEK293 homogenates had a reported Km for D-glycerate of 0.1 mM (mean of two transfection series). Sass et al. 2010, Human Mutation https://doi.org/10.1002/humu.21375 2010-12 (sass2010d‐glycericaciduriais pages 12-15)
Activity Transfection with reference GLYCTK increased enzyme activity from trace amounts (<0.5 µmol min-1 g-1 protein) to 30.7 µmol min-1 g-1 protein in HEK293 cells. Sass et al. 2010, Human Mutation https://doi.org/10.1002/humu.21375 2010-12 (sass2010d‐glycericaciduriais pages 12-15)
Localization / splice variants Two splice variants were cloned: GLYCTK1 and GLYCTK2. Both were reported as cytosolic, and GLYCTK2 was specifically localized to mitochondria; both transcripts were widely expressed across 17 human tissues. Guo et al. 2006, DNA Sequence https://doi.org/10.1080/10425170500476665 2006-01 (guo2006isolationandcharacterization pages 1-4, guo2006isolationandcharacterization pages 4-5)
Disease association GLYCTK deficiency causes D-glyceric aciduria, a rare autosomal recessive inborn error of metabolism with isolated accumulation of the D-enantiomer of glyceric acid. Sass et al. 2020, Brain and Development https://doi.org/10.1016/j.braindev.2019.11.008 2020-02 (sass2020dglyceratekinasedeficiency pages 1-2)
Mutations Pathogenic variants reported include c.1448delT (p.Phe483SerfsX2), c.1478T>G (p.Phe493Cys), c.1558delC (p.Leu520CysfsX108), c.455T>C (p.Leu152Pro), and c.517G>T (p.Val173Leu). Mutant forms tested in HEK293 cells showed no enhanced protein signal or activity. Sass et al. 2010, Human Mutation; Zehavi et al. 2019, Metabolic Brain Disease; Sass et al. 2020, Brain and Development https://doi.org/10.1002/humu.21375 ; https://doi.org/10.1007/s11011-019-0384-x ; https://doi.org/10.1016/j.braindev.2019.11.008 2010-12; 2019-01-12; 2020-02 (sass2010d‐glycericaciduriais pages 12-15, zehavi2019severeinfantileepileptic pages 1-2, sass2020dglyceratekinasedeficiency pages 1-2)
Phenotype variability Clinical spectrum is highly variable, ranging from severe progressive infantile encephalopathy with intractable seizures, cortical blindness and deafness to mild neurologic dysfunction or practically asymptomatic cases. Zehavi et al. 2019, Metabolic Brain Disease; Swanson et al. 2017, Molecular Genetics and Metabolism https://doi.org/10.1007/s11011-019-0384-x ; https://doi.org/10.1016/j.ymgme.2017.04.009 2019-01-12; 2017-06 (zehavi2019severeinfantileepileptic pages 1-2, swanson2017dglycericaciduriadoes pages 1-2)
Quantitative metabolite data Patient A plasma D-glycerate 1.0-1.3 mM; patient B urinary glycerate 9.32 mol/mol creatinine; patient C urinary glycerate 11.3, 8.61, and 18.6 mol/mol creatinine; patient C serum glycerate 1 mM. Sass et al. 2010, Human Mutation https://doi.org/10.1002/humu.21375 2010-12 (sass2010d‐glycericaciduriais pages 12-15)
Case count / genetically confirmed cases About 16 individuals with tentative diagnosis had been described by 2020, with only six previously genetically confirmed; the 2020 report was the seventh genetically confirmed case. Sass et al. 2020, Brain and Development https://doi.org/10.1016/j.braindev.2019.11.008 2020-02 (sass2020dglyceratekinasedeficiency pages 1-2)

Table: This table summarizes the key functional annotation evidence for human GLYCTK/Q8IVS8 from the provided literature context, covering enzymatic function, localization, disease association, mutations, phenotype spectrum, and quantitative data.

  1. Substrate specificity beyond D-glycerate: No substrate screening or comparative kinetics were captured in the retrieved texts; targeted enzymology papers would be required.
  2. Human-relevant compartment biology: Isoform-dependent mitochondrial localization is supported by GFP-fusion experiments, but further work is needed to define which isoforms predominate by tissue and whether localization changes with physiological state (guo2006isolationandcharacterization pages 4-5).
  3. Recent (2023–2024) GLYCTK-focused research: The retrieved dataset did not include recent dedicated GLYCTK studies; further targeted searches (e.g., “GLYCTK structure”, “mitochondrial glycerate kinase”, “D-glyceric aciduria cohort 2024”) may be needed to capture the latest clinical cohort or mechanistic updates.

References

  1. (sass2010d‐glycericaciduriais pages 12-15): Jörn Oliver Sass, Kathleen Fischer, Raymond Wang, Ernst Christensen, Sabine Scholl-Bürgi, Richard Chang, Klaus Kapelari, and Melanie Walter. D‐glyceric aciduria is caused by genetic deficiency of d‐glycerate kinase (glyctk). Human Mutation, 31:1280-1285, Dec 2010. URL: https://doi.org/10.1002/humu.21375, doi:10.1002/humu.21375. This article has 36 citations and is from a domain leading peer-reviewed journal.

  2. (zehavi2019severeinfantileepileptic pages 1-2): Yoav Zehavi, Hanna Mandel, Ayelet Eran, Sarit Ravid, Muhammad Abu Rashid, Erwin E. W. Jansen, Mirjam M. C. Wamelink, Ann Saada, Avraham Shaag, Orly Elpeleg, and Ronen Spiegel. Severe infantile epileptic encephalopathy associated with d-glyceric aciduria: report of a novel case and review. Metabolic Brain Disease, 34:557-563, Jan 2019. URL: https://doi.org/10.1007/s11011-019-0384-x, doi:10.1007/s11011-019-0384-x. This article has 11 citations and is from a peer-reviewed journal.

  3. (swanson2017dglycericaciduriadoes pages 1-2): Michael A. Swanson, Stephanie M. Garcia, Elaine Spector, Kathryn Kronquist, Geralyn Creadon-Swindell, Melanie Walter, Ernst Christensen, Johan L.K. Van Hove, and Jörn Oliver Sass. D-glyceric aciduria does not cause nonketotic hyperglycinemia: a historic co-occurrence. Molecular Genetics and Metabolism, 121:80-82, Jun 2017. URL: https://doi.org/10.1016/j.ymgme.2017.04.009, doi:10.1016/j.ymgme.2017.04.009. This article has 12 citations and is from a peer-reviewed journal.

  4. (guo2006isolationandcharacterization pages 4-5): Jin-Hu Guo, Saiyin Hexige, Li Chen, Guang-Jin Zhou, Xiang Wang, Jian-Min Jiang, Ya-Hui Kong, Guo-Qing Ji, Chao-Qun Wu, Shou-Yuan Zhao, and Long Yu. Isolation and characterization of the human d-glyceric acidemia related glycerate kinase gene glyctk1 and its alternatively splicing variant glyctk2. DNA Sequence, 17:1-7, Jan 2006. URL: https://doi.org/10.1080/10425170500476665, doi:10.1080/10425170500476665. This article has 19 citations.

  5. (sass2020dglyceratekinasedeficiency pages 1-2): Jörn Oliver Sass, Sidney Behringer, Malkanthi Fernando, Elisabetta Cesaroni, Ida Cursio, Alberto Volpini, and Claudia Till. D-glycerate kinase deficiency in a neuropediatric patient. Brain and Development, 42:226-230, Feb 2020. URL: https://doi.org/10.1016/j.braindev.2019.11.008, doi:10.1016/j.braindev.2019.11.008. This article has 9 citations and is from a peer-reviewed journal.

  6. (sass2010d‐glycericaciduriais media 5f02c9bb): Jörn Oliver Sass, Kathleen Fischer, Raymond Wang, Ernst Christensen, Sabine Scholl-Bürgi, Richard Chang, Klaus Kapelari, and Melanie Walter. D‐glyceric aciduria is caused by genetic deficiency of d‐glycerate kinase (glyctk). Human Mutation, 31:1280-1285, Dec 2010. URL: https://doi.org/10.1002/humu.21375, doi:10.1002/humu.21375. This article has 36 citations and is from a domain leading peer-reviewed journal.

  7. (guo2006isolationandcharacterization pages 1-4): Jin-Hu Guo, Saiyin Hexige, Li Chen, Guang-Jin Zhou, Xiang Wang, Jian-Min Jiang, Ya-Hui Kong, Guo-Qing Ji, Chao-Qun Wu, Shou-Yuan Zhao, and Long Yu. Isolation and characterization of the human d-glyceric acidemia related glycerate kinase gene glyctk1 and its alternatively splicing variant glyctk2. DNA Sequence, 17:1-7, Jan 2006. URL: https://doi.org/10.1080/10425170500476665, doi:10.1080/10425170500476665. This article has 19 citations.

  8. (guo2006isolationandcharacterization pages 5-6): Jin-Hu Guo, Saiyin Hexige, Li Chen, Guang-Jin Zhou, Xiang Wang, Jian-Min Jiang, Ya-Hui Kong, Guo-Qing Ji, Chao-Qun Wu, Shou-Yuan Zhao, and Long Yu. Isolation and characterization of the human d-glyceric acidemia related glycerate kinase gene glyctk1 and its alternatively splicing variant glyctk2. DNA Sequence, 17:1-7, Jan 2006. URL: https://doi.org/10.1080/10425170500476665, doi:10.1080/10425170500476665. This article has 19 citations.

  9. (santos2024spliceprot2.0a pages 1-2): Letícia Graziela Costa Santos, Vinícius da Silva Coutinho Parreira, Esdras Matheus Gomes da Silva, Marlon Dias Mariano Santos, Alexander da Franca Fernandes, Ana Gisele da Costa Neves-Ferreira, Paulo Costa Carvalho, Flávia Cristina de Paula Freitas, and Fabio Passetti. Spliceprot 2.0: a sequence repository of human, mouse, and rat proteoforms. International Journal of Molecular Sciences, 25:1183, Jan 2024. URL: https://doi.org/10.3390/ijms25021183, doi:10.3390/ijms25021183. This article has 2 citations.

  10. (santos2024spliceprot2.0a pages 2-4): Letícia Graziela Costa Santos, Vinícius da Silva Coutinho Parreira, Esdras Matheus Gomes da Silva, Marlon Dias Mariano Santos, Alexander da Franca Fernandes, Ana Gisele da Costa Neves-Ferreira, Paulo Costa Carvalho, Flávia Cristina de Paula Freitas, and Fabio Passetti. Spliceprot 2.0: a sequence repository of human, mouse, and rat proteoforms. International Journal of Molecular Sciences, 25:1183, Jan 2024. URL: https://doi.org/10.3390/ijms25021183, doi:10.3390/ijms25021183. This article has 2 citations.

  11. (berg2023metaboverseenablesautomated pages 8-9): Jordan A. Berg, Youjia Zhou, Yeyun Ouyang, Ahmad A. Cluntun, T. Cameron Waller, Megan E. Conway, Sara M. Nowinski, Tyler Van Ry, Ian George, James E. Cox, Bei Wang, and Jared Rutter. Metaboverse enables automated discovery and visualization of diverse metabolic regulatory patterns. Nature Cell Biology, 25:616-625, Apr 2023. URL: https://doi.org/10.1038/s41556-023-01117-9, doi:10.1038/s41556-023-01117-9. This article has 12 citations and is from a highest quality peer-reviewed journal.

  12. (berg2023metaboverseenablesautomated pages 9-10): Jordan A. Berg, Youjia Zhou, Yeyun Ouyang, Ahmad A. Cluntun, T. Cameron Waller, Megan E. Conway, Sara M. Nowinski, Tyler Van Ry, Ian George, James E. Cox, Bei Wang, and Jared Rutter. Metaboverse enables automated discovery and visualization of diverse metabolic regulatory patterns. Nature Cell Biology, 25:616-625, Apr 2023. URL: https://doi.org/10.1038/s41556-023-01117-9, doi:10.1038/s41556-023-01117-9. This article has 12 citations and is from a highest quality peer-reviewed journal.

  13. (guo2006isolationandcharacterization pages 6-7): Jin-Hu Guo, Saiyin Hexige, Li Chen, Guang-Jin Zhou, Xiang Wang, Jian-Min Jiang, Ya-Hui Kong, Guo-Qing Ji, Chao-Qun Wu, Shou-Yuan Zhao, and Long Yu. Isolation and characterization of the human d-glyceric acidemia related glycerate kinase gene glyctk1 and its alternatively splicing variant glyctk2. DNA Sequence, 17:1-7, Jan 2006. URL: https://doi.org/10.1080/10425170500476665, doi:10.1080/10425170500476665. This article has 19 citations.

Citations

  1. zehavi2019severeinfantileepileptic pages 1-2
  2. guo2006isolationandcharacterization pages 4-5
  3. guo2006isolationandcharacterization pages 1-4
  4. guo2006isolationandcharacterization pages 5-6
  5. sass2020dglyceratekinasedeficiency pages 1-2
  6. swanson2017dglycericaciduriadoes pages 1-2
  7. guo2006isolationandcharacterization pages 6-7
  8. berg2023metaboverseenablesautomated pages 8-9
  9. berg2023metaboverseenablesautomated pages 9-10
  10. https://doi.org/10.1007/s11011-019-0384-x
  11. https://doi.org/10.1002/humu.21375
  12. https://doi.org/10.1080/10425170500476665
  13. https://doi.org/10.1016/j.braindev.2019.11.008
  14. https://doi.org/10.1016/j.ymgme.2017.04.009
  15. https://doi.org/10.1002/humu.21375,
  16. https://doi.org/10.1007/s11011-019-0384-x,
  17. https://doi.org/10.1016/j.ymgme.2017.04.009,
  18. https://doi.org/10.1080/10425170500476665,
  19. https://doi.org/10.1016/j.braindev.2019.11.008,
  20. https://doi.org/10.3390/ijms25021183,
  21. https://doi.org/10.1038/s41556-023-01117-9,

📄 View Raw YAML

id: Q8IVS8
gene_symbol: GLYCTK
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  GLYCTK encodes glycerate kinase, an ATP-dependent enzyme that phosphorylates D-glycerate; curated UniProt
  and Reactome records describe the product as (2R)-3-phosphoglycerate/3-phospho-D-glycerate. This activity
  supports metabolism of D-glycerate produced during serine catabolism and minor fructose metabolism and
  is the affected activity in D-glyceric aciduria. Isoform 1 is cytoplasmic, while isoform 2 has both
  cytoplasmic and mitochondrial localization; the core gene-level function is glycerate kinase activity
  rather than protein phosphorylation or generic protein binding.
existing_annotations:
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      cytoplasm localization is consistent with the UniProt isoform annotation and with GLYCTK acting
      as a soluble metabolic enzyme.
    action: ACCEPT
    reason: >-
      Cytoplasmic/cytosolic localization is directly supported for isoform 1 and also applies to isoform
      2, so this is a valid cellular component annotation.
    supported_by:
    - reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
      supporting_text: >-
        SUBCELLULAR LOCATION: [Isoform 1]: Cytoplasm. [Isoform 2]: Cytoplasm. Mitochondrion.
    - reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
      supporting_text: >-
        Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally
        localized to mitochondria.
- term:
    id: GO:0008887
    label: glycerate kinase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic
      activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and
      human disease reports support loss of this enzyme activity in D-glyceric aciduria.
    action: ACCEPT
    reason: >-
      This term is specific, aspect-correct, and directly matches the characterized enzyme activity of
      GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on
      glycerate kinase activity as the primary molecular function.
    supported_by:
    - reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
      supporting_text: >-
        Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
    - reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
      supporting_text: >-
        Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and
        links GLYCTK deficiency to D-glyceric aciduria.
- term:
    id: GO:0000166
    label: nucleotide binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      nucleotide binding is technically compatible with an ATP-dependent kinase but is too broad to add
      useful information when glycerate kinase activity is already annotated.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The annotation should be interpreted through the specific GO:0008887 glycerate kinase activity term.
      Broad parent terms such as nucleotide binding, kinase activity, and transferase activity blur the
      actual function.
    supported_by:
    - reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
      supporting_text: >-
        GLYCTK is annotated with the specific catalytic reaction for glycerate kinase activity, EC=2.7.1.31.
- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      ATP binding is required for the glycerate kinase reaction because ATP is the phosphate donor for
      conversion of (R)-glycerate to (2R)-3-phosphoglycerate.
    action: ACCEPT
    reason: >-
      Although less informative than glycerate kinase activity, ATP binding is mechanistically relevant
      and supported by the catalytic reaction.
    supported_by:
    - reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
      supporting_text: >-
        Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+).
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      cytoplasm localization is consistent with the UniProt isoform annotation and with GLYCTK acting
      as a soluble metabolic enzyme.
    action: ACCEPT
    reason: >-
      Cytoplasmic/cytosolic localization is directly supported for isoform 1 and also applies to isoform
      2, so this is a valid cellular component annotation.
    supported_by:
    - reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
      supporting_text: >-
        SUBCELLULAR LOCATION: [Isoform 1]: Cytoplasm. [Isoform 2]: Cytoplasm. Mitochondrion.
    - reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
      supporting_text: >-
        Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally
        localized to mitochondria.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      Mitochondrial localization is supported for GLYCTK isoform 2 and by high-throughput mitochondrial
      proteomics, but it is isoform/context-specific rather than the universal location of all GLYCTK
      products.
    action: KEEP_AS_NON_CORE
    reason: >-
      Keep this cellular component as a valid non-core localization. The core gene-level location remains
      cytoplasm/cytosol, with mitochondrion applying to isoform 2 and proteomic detections.
    supported_by:
    - reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
      supporting_text: >-
        SUBCELLULAR LOCATION: [Isoform 2]: Cytoplasm. Mitochondrion.
    - reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
      supporting_text: >-
        Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally
        localized to mitochondria.
- term:
    id: GO:0008887
    label: glycerate kinase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic
      activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and
      human disease reports support loss of this enzyme activity in D-glyceric aciduria.
    action: ACCEPT
    reason: >-
      This term is specific, aspect-correct, and directly matches the characterized enzyme activity of
      GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on
      glycerate kinase activity as the primary molecular function.
    supported_by:
    - reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
      supporting_text: >-
        Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
    - reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
      supporting_text: >-
        Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and
        links GLYCTK deficiency to D-glyceric aciduria.
- term:
    id: GO:0016301
    label: kinase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      kinase activity is technically compatible with an ATP-dependent kinase but is too broad to add useful
      information when glycerate kinase activity is already annotated.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The annotation should be interpreted through the specific GO:0008887 glycerate kinase activity term.
      Broad parent terms such as nucleotide binding, kinase activity, and transferase activity blur the
      actual function.
    supported_by:
    - reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
      supporting_text: >-
        GLYCTK is annotated with the specific catalytic reaction for glycerate kinase activity, EC=2.7.1.31.
- term:
    id: GO:0016740
    label: transferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      transferase activity is technically compatible with an ATP-dependent kinase but is too broad to
      add useful information when glycerate kinase activity is already annotated.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The annotation should be interpreted through the specific GO:0008887 glycerate kinase activity term.
      Broad parent terms such as nucleotide binding, kinase activity, and transferase activity blur the
      actual function.
    supported_by:
    - reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
      supporting_text: >-
        GLYCTK is annotated with the specific catalytic reaction for glycerate kinase activity, EC=2.7.1.31.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16189514
  review:
    summary: >-
      This generic protein binding row comes from high-throughput interactome evidence and does not describe
      the biochemical function of GLYCTK.
    action: MARK_AS_OVER_ANNOTATED
    supported_by:
    - reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
      supporting_text: >-
        The curated functional annotation describes glycerate kinase catalytic activity, while many listed
        interactions are high-throughput IntAct records.
    reason: >-
      Protein binding is uninformative here and is not the core molecular role of this metabolic enzyme.
      The useful GO annotation is glycerate kinase activity.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19060904
  review:
    summary: >-
      This generic protein binding row comes from high-throughput interactome evidence and does not describe
      the biochemical function of GLYCTK.
    action: MARK_AS_OVER_ANNOTATED
    supported_by:
    - reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
      supporting_text: >-
        The curated functional annotation describes glycerate kinase catalytic activity, while many listed
        interactions are high-throughput IntAct records.
    reason: >-
      Protein binding is uninformative here and is not the core molecular role of this metabolic enzyme.
      The useful GO annotation is glycerate kinase activity.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:25416956
  review:
    summary: >-
      This generic protein binding row comes from high-throughput interactome evidence and does not describe
      the biochemical function of GLYCTK.
    action: MARK_AS_OVER_ANNOTATED
    supported_by:
    - reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
      supporting_text: >-
        The curated functional annotation describes glycerate kinase catalytic activity, while many listed
        interactions are high-throughput IntAct records.
    reason: >-
      Protein binding is uninformative here and is not the core molecular role of this metabolic enzyme.
      The useful GO annotation is glycerate kinase activity.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32296183
  review:
    summary: >-
      This generic protein binding row comes from high-throughput interactome evidence and does not describe
      the biochemical function of GLYCTK.
    action: MARK_AS_OVER_ANNOTATED
    supported_by:
    - reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
      supporting_text: >-
        The curated functional annotation describes glycerate kinase catalytic activity, while many listed
        interactions are high-throughput IntAct records.
    reason: >-
      Protein binding is uninformative here and is not the core molecular role of this metabolic enzyme.
      The useful GO annotation is glycerate kinase activity.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  review:
    summary: >-
      cytosol localization is consistent with the UniProt isoform annotation and with GLYCTK acting as
      a soluble metabolic enzyme.
    action: ACCEPT
    reason: >-
      Cytoplasmic/cytosolic localization is directly supported for isoform 1 and also applies to isoform
      2, so this is a valid cellular component annotation.
    supported_by:
    - reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
      supporting_text: >-
        SUBCELLULAR LOCATION: [Isoform 1]: Cytoplasm. [Isoform 2]: Cytoplasm. Mitochondrion.
    - reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
      supporting_text: >-
        Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally
        localized to mitochondria.
- term:
    id: GO:0061624
    label: fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-70350
  review:
    summary: >-
      GLYCTK participates in fructose catabolism by phosphorylating D-glycerate, a metabolite generated
      downstream of fructose metabolism, to 3-phosphoglycerate.
    action: ACCEPT
    reason: >-
      The Reactome pathway context is appropriate for GLYCTK. The direct molecular function remains glycerate
      kinase activity, but the biological-process placement in fructose catabolism is supported.
    supported_by:
    - reference_id: Reactome:R-HSA-6799495
      supporting_text: >-
        GLYCTK phosphorylates DGA to 3PDGA
- term:
    id: GO:0008887
    label: glycerate kinase activity
  evidence_type: EXP
  original_reference_id: PMID:2537226
  review:
    summary: >-
      glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic
      activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and
      human disease reports support loss of this enzyme activity in D-glyceric aciduria.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
      supporting_text: >-
        Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
    - reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
      supporting_text: >-
        Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and
        links GLYCTK deficiency to D-glyceric aciduria.
    reason: >-
      This term is specific, aspect-correct, and directly matches the characterized enzyme activity of
      GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on
      glycerate kinase activity as the primary molecular function.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: HTP
  original_reference_id: PMID:34800366
  review:
    summary: >-
      Mitochondrial localization is supported for GLYCTK isoform 2 and by high-throughput mitochondrial
      proteomics, but it is isoform/context-specific rather than the universal location of all GLYCTK
      products.
    action: KEEP_AS_NON_CORE
    supported_by:
    - reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
      supporting_text: >-
        SUBCELLULAR LOCATION: [Isoform 2]: Cytoplasm. Mitochondrion.
    - reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
      supporting_text: >-
        Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally
        localized to mitochondria.
    reason: >-
      Keep this cellular component as a valid non-core localization. The core gene-level location remains
      cytoplasm/cytosol, with mitochondrion applying to isoform 2 and proteomic detections.
- term:
    id: GO:0008887
    label: glycerate kinase activity
  evidence_type: IDA
  original_reference_id: PMID:31837836
  review:
    summary: >-
      glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic
      activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and
      human disease reports support loss of this enzyme activity in D-glyceric aciduria.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
      supporting_text: >-
        Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
    - reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
      supporting_text: >-
        Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and
        links GLYCTK deficiency to D-glyceric aciduria.
    reason: >-
      This term is specific, aspect-correct, and directly matches the characterized enzyme activity of
      GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on
      glycerate kinase activity as the primary molecular function.
- term:
    id: GO:0008887
    label: glycerate kinase activity
  evidence_type: IMP
  original_reference_id: PMID:31837836
  review:
    summary: >-
      glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic
      activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and
      human disease reports support loss of this enzyme activity in D-glyceric aciduria.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
      supporting_text: >-
        Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
    - reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
      supporting_text: >-
        Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and
        links GLYCTK deficiency to D-glyceric aciduria.
    reason: >-
      This term is specific, aspect-correct, and directly matches the characterized enzyme activity of
      GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on
      glycerate kinase activity as the primary molecular function.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-6799495
  review:
    summary: >-
      cytosol localization is consistent with the UniProt isoform annotation and with GLYCTK acting as
      a soluble metabolic enzyme.
    action: ACCEPT
    reason: >-
      Cytoplasmic/cytosolic localization is directly supported for isoform 1 and also applies to isoform
      2, so this is a valid cellular component annotation.
    supported_by:
    - reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
      supporting_text: >-
        SUBCELLULAR LOCATION: [Isoform 1]: Cytoplasm. [Isoform 2]: Cytoplasm. Mitochondrion.
    - reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
      supporting_text: >-
        Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally
        localized to mitochondria.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IDA
  original_reference_id: PMID:16753811
  review:
    summary: >-
      cytoplasm localization is consistent with the UniProt isoform annotation and with GLYCTK acting
      as a soluble metabolic enzyme.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
      supporting_text: >-
        SUBCELLULAR LOCATION: [Isoform 1]: Cytoplasm. [Isoform 2]: Cytoplasm. Mitochondrion.
    - reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
      supporting_text: >-
        Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally
        localized to mitochondria.
    reason: >-
      Cytoplasmic/cytosolic localization is directly supported for isoform 1 and also applies to isoform
      2, so this is a valid cellular component annotation.
- term:
    id: GO:0006468
    label: protein phosphorylation
  evidence_type: IDA
  original_reference_id: PMID:16753811
  review:
    summary: >-
      GLYCTK is a small-molecule glycerate kinase, not a protein kinase. Its catalytic activity phosphorylates
      (R)-glycerate to (2R)-3-phosphoglycerate and does not support protein phosphorylation.
    action: REMOVE
    supported_by:
    - reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
      supporting_text: >-
        Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
    reason: >-
      This is an aspect-correct BP term for protein kinases but a wrong biological-process annotation
      for GLYCTK. The evidence supports glycerate phosphorylation in metabolism, not phosphorylation of
      protein substrates.
- term:
    id: GO:0008887
    label: glycerate kinase activity
  evidence_type: IDA
  original_reference_id: PMID:16753811
  review:
    summary: >-
      glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic
      activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and
      human disease reports support loss of this enzyme activity in D-glyceric aciduria.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
      supporting_text: >-
        Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
    - reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
      supporting_text: >-
        Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and
        links GLYCTK deficiency to D-glyceric aciduria.
    reason: >-
      This term is specific, aspect-correct, and directly matches the characterized enzyme activity of
      GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on
      glycerate kinase activity as the primary molecular function.
references:
- 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:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:16189514
  title: Towards a proteome-scale map of the human protein-protein interaction network.
  findings: []
- id: PMID:16753811
  title: Isolation and characterization of the human D-glyceric acidemia related glycerate kinase
    gene GLYCTK1 and its alternatively splicing variant GLYCTK2.
  findings: []
- id: PMID:19060904
  title: An empirical framework for binary interactome mapping.
  findings: []
- id: PMID:2537226
  title: D-glycerate kinase deficiency as a cause of D-glyceric aciduria.
  findings: []
- id: PMID:25416956
  title: A proteome-scale map of the human interactome network.
  findings: []
- id: PMID:31837836
  title: d-Glycerate kinase deficiency in a neuropediatric patient.
  findings: []
- id: PMID:32296183
  title: A reference map of the human binary protein interactome.
  findings: []
- id: PMID:34800366
  title: Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular
    context.
  findings: []
- id: Reactome:R-HSA-6799495
  title: GLYCTK phosphorylates DGA to 3PDGA
  findings: []
- id: Reactome:R-HSA-70350
  title: Fructose catabolism
  findings: []
- id: file:human/GLYCTK/GLYCTK-uniprot.txt
  title: UniProt record for human GLYCTK
  findings: []
- id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
  title: Falcon deep research on GLYCTK function
  findings:
  - statement: Falcon report confirms GLYCTK identity as human glycerate kinase/EC 2.7.1.31 and
      summarizes D-glyceric aciduria evidence.
    supporting_text: >-
      The UniProt accession Q8IVS8 corresponds to human GLYCTK, annotated as glycerate kinase / D-glycerate
      2-kinase (EC 2.7.1.31).
  - statement: Falcon report summarizes isoform-dependent cytosolic and mitochondrial localization.
    supporting_text: >-
      Both isoforms were reported as cytosolic (particulate). GLYCTK2 was additionally reported to be
      specifically localized to mitochondria, whereas GLYCTK1 was not.
core_functions:
- description: >-
    Phosphorylates D-glycerate using ATP, providing the core enzymatic step for D-glycerate metabolism
    in serine/fructose catabolic context; UniProt and Reactome describe the product as (2R)-3-phosphoglycerate/3-phospho-D-glycerate.
  molecular_function:
    id: GO:0008887
    label: glycerate kinase activity
  directly_involved_in:
  - id: GO:0061624
    label: fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate
  locations:
  - id: GO:0005829
    label: cytosol
  substrates:
  - id: CHEBI:16659
    label: (R)-glycerate
  supported_by:
  - reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
    supporting_text: >-
      Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
  - reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
    supporting_text: >-
      Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and
      emphasizes D-glycerate as the physiological substrate.
proposed_new_terms: []
suggested_questions:
- question: Which GLYCTK isoforms account for mitochondrial glycerate kinase activity in human
    tissues?
  experts:
  - metabolic biochemists
  - mitochondrial proteomics experts
- question: How does GLYCTK deficiency produce variable neurological phenotypes in D-glyceric
    aciduria?
  experts:
  - clinical geneticists
  - inborn errors of metabolism specialists
suggested_experiments:
- experiment_type: Isoform localization
  description: Quantitatively compare endogenous GLYCTK isoform 1 and isoform 2 localization in
    tissues with high fructose or glycerate flux.
  hypothesis: Isoform 2 provides a mitochondrial pool of glycerate kinase activity whereas isoform 1
    supports cytosolic glycerate metabolism.
- experiment_type: Metabolic flux analysis
  description: Trace labeled D-glycerate in GLYCTK-null and rescue cells expressing individual
    isoforms.
  hypothesis: Loss of GLYCTK blocks conversion of D-glycerate into 3-phosphoglycerate and
    isoform-specific rescue distinguishes cytosolic and mitochondrial contributions.