GLDC is the P protein (glycine decarboxylase) of the mitochondrial glycine cleavage system (GCS), a pyridoxal-5'-phosphate (PLP)-dependent homodimeric enzyme (EC 1.4.4.2) encoded on human chromosome 9. It catalyses the first, committed step of glycine catabolism: it binds the alpha-amino group of glycine through its PLP cofactor (covalently attached as a Schiff base to Lys754), decarboxylates the glycine to release CO2, and transfers the residual aminomethyl moiety to the lipoic-acid (lipoamide) arm of the H protein (GCSH) rather than releasing free methylamine. Together with the T protein (AMT), the L protein (DLD) and the H protein (GCSH), GLDC forms the glycine cleavage system, the major route of glycine degradation, which links glycine to one-carbon/folate metabolism and serine biosynthesis. The mature protein localises to the mitochondrial matrix after cleavage of an N-terminal transit peptide. Loss-of-function variants in GLDC are the most common cause (~80% of cases) of nonketotic hyperglycinemia (glycine encephalopathy), an autosomal recessive disorder characterised by accumulation of glycine in body fluids, neonatal seizures and severe encephalopathy.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0004375
glycine dehydrogenase (decarboxylating) activity
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Core molecular function. The phylogenetic (IBA) annotation to glycine dehydrogenase (decarboxylating) activity is the correct, informative MF for the GCS P protein and is corroborated by experimental and TAS evidence in this same gene.
Reason: GLDC is the P protein of the glycine cleavage system and catalyses the PLP-dependent decarboxylation of glycine (EC 1.4.4.2). This IBA is concordant with the EXP, IDA and TAS annotations to the same term.
Supporting Evidence:
file:human/GLDC/GLDC-uniprot.txt
The P protein (GLDC) binds the alpha-amino group of glycine
|
|
GO:0019464
glycine decarboxylation via glycine cleavage system
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Core biological process. This is the most specific process term for GLDC: glycine decarboxylation carried out as the P-protein step of the glycine cleavage system.
Reason: Matches the experimentally established role of GLDC as the P protein of the GCS and is the preferred, most-informative process term for this gene.
Supporting Evidence:
file:human/GLDC/GLDC-uniprot.txt
remaining methylamine moiety is then transferred to the lipoamide
|
|
GO:0005739
mitochondrion
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Correct subcellular localisation. GLDC acts in the mitochondrion (matrix). This IBA is consistent with IDA, HTP and TAS localisation evidence.
Reason: GLDC carries an N-terminal mitochondrial transit peptide and the GCS operates in the mitochondrial matrix; mitochondrion is the correct compartment, though the matrix (GO:0005759) is more precise.
Supporting Evidence:
file:human/GLDC/GLDC-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion
|
|
GO:0004375
glycine dehydrogenase (decarboxylating) activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Electronic assignment of the core catalytic MF via EC 1.4.4.2 / RHEA:24304 and InterPro. Correct and concordant with experimental evidence.
Reason: The EC/RHEA and InterPro mappings correctly capture the glycine dehydrogenase (decarboxylating) activity of the P protein.
Supporting Evidence:
file:human/GLDC/GLDC-uniprot.txt
EC=1.4.4.2
|
|
GO:0005739
mitochondrion
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: Electronic localisation from the UniProt Subcellular Location vocabulary (SL-0173, Mitochondrion). Correct.
Reason: Consistent with the curated UniProt subcellular location and with IDA/HTP/TAS evidence.
Supporting Evidence:
file:human/GLDC/GLDC-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion
|
|
GO:0006520
amino acid metabolic process
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: Very general parent process. GLDC does participate in amino acid metabolism, but this is far broader than its actual role in glycine cleavage.
Reason: Correct as a broad InterPro-based grouping term; the informative process is the more specific GO:0019464 (glycine decarboxylation via glycine cleavage system). Broad IEA parents may be retained.
Supporting Evidence:
file:human/GLDC/GLDC-uniprot.txt
The glycine cleavage system catalyzes the degradation of
|
|
GO:0006544
glycine metabolic process
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: Broad but correct grouping term. GLDC is central to glycine metabolism; GO:0019464 is the more specific catabolic term.
Reason: Accurate InterPro-based parent term consistent with the enzyme acting on glycine.
Supporting Evidence:
file:human/GLDC/GLDC-uniprot.txt
The glycine cleavage system catalyzes the degradation of
|
|
GO:0006546
glycine catabolic process
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: Correct process: GLDC catalyses the first step of glycine degradation. This is the direct parent of the more specific GO:0019464.
Reason: Glycine catabolic process accurately describes the pathway GLDC initiates; concordant with IDA and TAS annotations to the same term.
Supporting Evidence:
file:human/GLDC/GLDC-uniprot.txt
The glycine cleavage system catalyzes the degradation of
|
|
GO:0016829
lyase activity
|
IEA
GO_REF:0000002 |
REMOVE |
Summary: Wrong-branch electronic mapping. GLDC is classified EC 1.4.4.2, an oxidoreductase acting on the CH-NH2 group of donors (glycine dehydrogenase (decarboxylating)); it is not a lyase. The lyase term derives from the broad PLP-fold InterPro signature IPR001597 (aromatic-amino-acid beta-eliminating lyase / threonine aldolase), which over-generalises to a lyase MF that does not apply to this enzyme.
Reason: This is a demonstrably incorrect electronic (IEA/InterPro) MF inference: the enzyme's molecular function is glycine dehydrogenase (decarboxylating) activity (GO:0004375, an oxidoreductase, EC 1.4.4.2), captured accurately by other annotations. Lyase activity is the wrong ontology branch for this protein and is safe to remove per the IEA-mis-mapping criterion.
Supporting Evidence:
file:human/GLDC/GLDC-uniprot.txt
EC=1.4.4.2
|
|
GO:0005960
glycine cleavage complex
|
NAS
PMID:28244183 Nonketotic hyperglycinemia: Functional assessment of missens... |
ACCEPT |
Summary: Correct complex membership. GLDC is the P protein subunit of the four-protein glycine cleavage system (P/GLDC, T/AMT, L/DLD, H/GCSH).
Reason: Well-established: GLDC is a bona fide subunit of the glycine cleavage complex. Curated by ComplexPortal.
Supporting Evidence:
file:human/GLDC/GLDC-uniprot.txt
P (GLDC), T (GCST), L (DLD) and H (GCSH)
|
|
GO:0019464
glycine decarboxylation via glycine cleavage system
|
NAS
PMID:24467211 Glycine decarboxylase is an unusual amino acid decarboxylase... |
ACCEPT |
Summary: Core process, independently supported by the mechanistic study of Go et al. (2014), which shows GLDC decarboxylates glycine and hands the aminomethyl group to the H protein within the GCS.
Reason: The cited mechanistic paper directly characterises GLDC-catalysed glycine decarboxylation as the P-protein step of the glycine cleavage system.
Supporting Evidence:
PMID:24467211
aminomethyl moiety is instead transferred to an accessory H-protein
|
|
GO:0005739
mitochondrion
|
IDA
GO_REF:0000052 |
ACCEPT |
Summary: Immunofluorescence (HPA) localisation to mitochondrion. Consistent with all other localisation evidence.
Reason: Direct immunofluorescence evidence supports mitochondrial localisation, concordant with the transit peptide and matrix localisation.
Supporting Evidence:
file:human/GLDC/GLDC-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion
|
|
GO:0004375
glycine dehydrogenase (decarboxylating) activity
|
EXP
PMID:1993704 The glycine cleavage system. Molecular cloning of the chicke... |
ACCEPT |
Summary: Experimental support for the core catalytic function. Kume et al. cloned the human glycine decarboxylase cDNA and characterised the PLP-binding active-site region essential for enzyme activity.
Reason: Direct experimental characterisation of human glycine decarboxylase, including the PLP-binding lysine and glycine-rich phosphate-binding region that organise the active site.
Supporting Evidence:
PMID:1993704
The pyridoxal phosphate binding site lysine and a glycine-rich region
|
|
GO:0005739
mitochondrion
|
HTP
PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... |
ACCEPT |
Summary: High-throughput mitochondrial proteomics localises GLDC to mitochondria, concordant with all other localisation evidence.
Reason: GLDC was identified in a high-confidence quantitative human mitochondrial proteome; this HTP evidence agrees with the transit peptide, IDA immunofluorescence and matrix TAS annotations.
Supporting Evidence:
file:human/GLDC/GLDC-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion
|
|
GO:0005759
mitochondrial matrix
|
TAS
Reactome:R-HSA-5693967 |
ACCEPT |
Summary: Most precise localisation: the glycine decarboxylation reaction occurs in the mitochondrial matrix. Retained as the informative compartment.
Reason: The GCS operates in the mitochondrial matrix; Reactome places the GLDC-catalysed decarboxylation there. This is the preferred, more specific cellular-component term.
Supporting Evidence:
file:human/GLDC/GLDC-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion
|
|
GO:0036255
response to methylamine
|
ISS
GO_REF:0000024 |
KEEP AS NON CORE |
Summary: Peripheral regulatory response inferred by similarity from rat (P15505). Reflects that GCS P-protein activity is inhibited in the presence of methylamine, not a distinct biological role of GLDC.
Reason: Derived from an activity-regulation observation (methylamine inhibits the enzyme). It is a plausible ISS-transferred response but does not represent a core function of GLDC; retained as non-core.
Supporting Evidence:
file:human/GLDC/GLDC-uniprot.txt
Inhibited in presence
|
|
GO:0042803
protein homodimerization activity
|
ISS
GO_REF:0000024 |
KEEP AS NON CORE |
Summary: Supported: the functional P protein is a homodimer. Retained as a supporting (non-core) molecular function underpinning the catalytic unit.
Reason: UniProt records GLDC as a homodimer (by similarity to rat P15505), and the PLP-dependent active site is formed in the dimer. Real but ancillary to the catalytic MF.
Supporting Evidence:
file:human/GLDC/GLDC-uniprot.txt
Homodimer (By similarity)
|
|
GO:0070280
pyridoxal binding
|
ISS
GO_REF:0000024 |
MODIFY |
Summary: The cofactor is pyridoxal 5'-phosphate (PLP), covalently bound as a Schiff base at Lys754, not free pyridoxal. The more accurate MF is pyridoxal phosphate binding (GO:0030170), which UniProt itself also carries.
Reason: GLDC binds pyridoxal 5'-phosphate (the phosphorylated, active cofactor), attached as N6-(pyridoxal phosphate)lysine at Lys754; the specific, accurate term is GO:0030170 pyridoxal phosphate binding rather than the more general pyridoxal binding.
Proposed replacements:
pyridoxal phosphate binding
Supporting Evidence:
file:human/GLDC/GLDC-uniprot.txt
Name=pyridoxal 5'-phosphate
file:human/GLDC/GLDC-uniprot.txt
N6-(pyridoxal phosphate)lysine
|
|
GO:1903442
response to lipoic acid
|
ISS
GO_REF:0000024 |
KEEP AS NON CORE |
Summary: Peripheral regulatory response inferred by similarity from rat (P15505), reflecting that P-protein activity is stimulated by lipoic acid (the lipoamide arm of the H protein is the physiological acceptor).
Reason: Derived from an activity-regulation observation (lipoic acid stimulates the enzyme). Consistent with the mechanism but not a core function; retained as non-core.
Supporting Evidence:
file:human/GLDC/GLDC-uniprot.txt
Stimulated by lipoic acid
|
|
GO:0004375
glycine dehydrogenase (decarboxylating) activity
|
IDA
PMID:28244183 Nonketotic hyperglycinemia: Functional assessment of missens... |
ACCEPT |
Summary: Direct experimental support for the core catalytic MF: enzymatic assays of GCS P-protein activity for wild-type and NKH missense variants expressed in COS7 cells.
Reason: Bravo-Alonso et al. measured residual GCS P-protein (glycine decarboxylase) activity for GLDC constructs, directly assaying this molecular function.
Supporting Evidence:
PMID:28244183
assess the residual activity and mutant protein stability
|
|
GO:0005739
mitochondrion
|
IDA
PMID:28244183 Nonketotic hyperglycinemia: Functional assessment of missens... |
ACCEPT |
Summary: Direct evidence of mitochondrial localisation; the same study also reported NKH variants with altered (partially cytosolic) localisation, confirming the wild-type mitochondrial targeting.
Reason: Localisation of GLDC to mitochondria was directly assessed; consistent with the transit peptide and all other localisation evidence.
Supporting Evidence:
file:human/GLDC/GLDC-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion
|
|
GO:0006546
glycine catabolic process
|
IDA
PMID:28244183 Nonketotic hyperglycinemia: Functional assessment of missens... |
ACCEPT |
Summary: Direct evidence linking GLDC to glycine catabolism: NKH variants cause loss or reduction of glycine catabolic process, as characterised functionally in this study.
Reason: The functional assessment demonstrates that pathogenic GLDC variants impair the glycine catabolic process, confirming GLDC's role in it. The more specific term is GO:0019464.
Supporting Evidence:
PMID:28244183
assess the residual activity and mutant protein stability
|
|
GO:0009055
electron transfer activity
|
TAS
PMID:2268343 One of the two genomic copies of the glycine decarboxylase c... |
MARK AS OVER ANNOTATED |
Summary: Likely over-annotation / mis-assignment. GLDC is a PLP-dependent glycine decarboxylase (EC 1.4.4.2); it does not act as an electron carrier. Within the glycine cleavage system, the redox/electron-transfer role belongs to the L protein (DLD, dihydrolipoamide dehydrogenase, FAD-dependent), not to the P protein. The cited reference (Sakakibara et al. 1990) is about a genomic deletion of the glycine decarboxylase gene in an NKH patient and provides no support for an electron transfer activity.
Reason: The molecular function of GLDC is glycine dehydrogenase (decarboxylating) activity, captured by multiple experimental and electronic annotations; electron transfer activity is not a function of the P protein and is not supported by the cited paper. Flagged as over-annotated rather than removed because it is an author-statement (TAS) annotation whose full text was not reviewed.
Supporting Evidence:
file:human/GLDC/GLDC-uniprot.txt
The P protein (GLDC) binds the alpha-amino group of glycine
|
|
GO:0004375
glycine dehydrogenase (decarboxylating) activity
|
TAS
PMID:1996985 Structural and expression analyses of normal and mutant mRNA... |
ACCEPT |
Summary: Author-stated support for the core catalytic function: expression of normal human P-protein cDNA in COS7 cells reconstituted glycine decarboxylase activity comparable to human liver, whereas the NKH mutant (Phe756del) had none.
Reason: Kure et al. demonstrated glycine decarboxylase activity for the wild-type human enzyme and its abolition by an NKH-causing deletion, supporting the catalytic MF.
Supporting Evidence:
PMID:1996985
showed no activity, indicating that the three-base deletion could cause NKH
|
|
GO:0006546
glycine catabolic process
|
TAS
PMID:1996985 Structural and expression analyses of normal and mutant mRNA... |
ACCEPT |
Summary: Author-stated support that GLDC drives glycine catabolism: loss of P-protein activity from an NKH deletion causes the glycine-accumulation phenotype, linking the enzyme to the glycine catabolic process.
Reason: Consistent with GLDC's role in glycine degradation; the loss-of-activity mutant establishes the connection to glycine catabolism. GO:0019464 is the more specific term.
Supporting Evidence:
PMID:1996985
showed no activity, indicating that the three-base deletion could cause NKH
|
Glycine dehydrogenase (decarboxylating), mitochondrial / Glycine cleavage system P protein
/ Glycine decarboxylase. HGNC:4313. EC 1.4.4.2.
Deep research: falcon out of credits (HTTP 402); no -deep-research-falcon.md. Review grounded
in GLDC-uniprot.txt, seeded GOA, and cached publications/PMID_*.md.
id: P23378
gene_symbol: GLDC
product_type: PROTEIN
status: INITIALIZED
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: >-
GLDC is the P protein (glycine decarboxylase) of the mitochondrial glycine
cleavage system (GCS), a pyridoxal-5'-phosphate (PLP)-dependent homodimeric
enzyme (EC 1.4.4.2) encoded on human chromosome 9. It catalyses the first,
committed step of glycine catabolism: it binds the alpha-amino group of glycine
through its PLP cofactor (covalently attached as a Schiff base to Lys754),
decarboxylates the glycine to release CO2, and transfers the residual
aminomethyl moiety to the lipoic-acid (lipoamide) arm of the H protein (GCSH)
rather than releasing free methylamine. Together with the T protein (AMT), the
L protein (DLD) and the H protein (GCSH), GLDC forms the glycine cleavage
system, the major route of glycine degradation, which links glycine to
one-carbon/folate metabolism and serine biosynthesis. The mature protein
localises to the mitochondrial matrix after cleavage of an N-terminal transit
peptide. Loss-of-function variants in GLDC are the most common cause (~80% of
cases) of nonketotic hyperglycinemia (glycine encephalopathy), an autosomal
recessive disorder characterised by accumulation of glycine in body fluids,
neonatal seizures and severe encephalopathy.
existing_annotations:
- term:
id: GO:0004375
label: glycine dehydrogenase (decarboxylating) activity
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: enables
review:
summary: >-
Core molecular function. The phylogenetic (IBA) annotation to glycine
dehydrogenase (decarboxylating) activity is the correct, informative MF for
the GCS P protein and is corroborated by experimental and TAS evidence in
this same gene.
action: ACCEPT
reason: >-
GLDC is the P protein of the glycine cleavage system and catalyses the
PLP-dependent decarboxylation of glycine (EC 1.4.4.2). This IBA is
concordant with the EXP, IDA and TAS annotations to the same term.
supported_by:
- reference_id: file:human/GLDC/GLDC-uniprot.txt
supporting_text: "The P protein (GLDC) binds the alpha-amino group of glycine"
- term:
id: GO:0019464
label: glycine decarboxylation via glycine cleavage system
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: >-
Core biological process. This is the most specific process term for GLDC:
glycine decarboxylation carried out as the P-protein step of the glycine
cleavage system.
action: ACCEPT
reason: >-
Matches the experimentally established role of GLDC as the P protein of the
GCS and is the preferred, most-informative process term for this gene.
supported_by:
- reference_id: file:human/GLDC/GLDC-uniprot.txt
supporting_text: "remaining methylamine moiety is then transferred to the lipoamide"
- term:
id: GO:0005739
label: mitochondrion
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: is_active_in
review:
summary: >-
Correct subcellular localisation. GLDC acts in the mitochondrion (matrix).
This IBA is consistent with IDA, HTP and TAS localisation evidence.
action: ACCEPT
reason: >-
GLDC carries an N-terminal mitochondrial transit peptide and the GCS
operates in the mitochondrial matrix; mitochondrion is the correct compartment,
though the matrix (GO:0005759) is more precise.
supported_by:
- reference_id: file:human/GLDC/GLDC-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Mitochondrion"
- term:
id: GO:0004375
label: glycine dehydrogenase (decarboxylating) activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: enables
review:
summary: >-
Electronic assignment of the core catalytic MF via EC 1.4.4.2 / RHEA:24304
and InterPro. Correct and concordant with experimental evidence.
action: ACCEPT
reason: >-
The EC/RHEA and InterPro mappings correctly capture the glycine
dehydrogenase (decarboxylating) activity of the P protein.
supported_by:
- reference_id: file:human/GLDC/GLDC-uniprot.txt
supporting_text: "EC=1.4.4.2"
- term:
id: GO:0005739
label: mitochondrion
evidence_type: IEA
original_reference_id: GO_REF:0000044
qualifier: located_in
review:
summary: >-
Electronic localisation from the UniProt Subcellular Location vocabulary
(SL-0173, Mitochondrion). Correct.
action: ACCEPT
reason: >-
Consistent with the curated UniProt subcellular location and with IDA/HTP/TAS
evidence.
supported_by:
- reference_id: file:human/GLDC/GLDC-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Mitochondrion"
- term:
id: GO:0006520
label: amino acid metabolic process
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: involved_in
review:
summary: >-
Very general parent process. GLDC does participate in amino acid metabolism,
but this is far broader than its actual role in glycine cleavage.
action: ACCEPT
reason: >-
Correct as a broad InterPro-based grouping term; the informative process is
the more specific GO:0019464 (glycine decarboxylation via glycine cleavage
system). Broad IEA parents may be retained.
supported_by:
- reference_id: file:human/GLDC/GLDC-uniprot.txt
supporting_text: "The glycine cleavage system catalyzes the degradation of"
- term:
id: GO:0006544
label: glycine metabolic process
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: involved_in
review:
summary: >-
Broad but correct grouping term. GLDC is central to glycine metabolism;
GO:0019464 is the more specific catabolic term.
action: ACCEPT
reason: >-
Accurate InterPro-based parent term consistent with the enzyme acting on
glycine.
supported_by:
- reference_id: file:human/GLDC/GLDC-uniprot.txt
supporting_text: "The glycine cleavage system catalyzes the degradation of"
- term:
id: GO:0006546
label: glycine catabolic process
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: involved_in
review:
summary: >-
Correct process: GLDC catalyses the first step of glycine degradation. This
is the direct parent of the more specific GO:0019464.
action: ACCEPT
reason: >-
Glycine catabolic process accurately describes the pathway GLDC initiates;
concordant with IDA and TAS annotations to the same term.
supported_by:
- reference_id: file:human/GLDC/GLDC-uniprot.txt
supporting_text: "The glycine cleavage system catalyzes the degradation of"
- term:
id: GO:0016829
label: lyase activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: >-
Wrong-branch electronic mapping. GLDC is classified EC 1.4.4.2, an
oxidoreductase acting on the CH-NH2 group of donors (glycine dehydrogenase
(decarboxylating)); it is not a lyase. The lyase term derives from the broad
PLP-fold InterPro signature IPR001597 (aromatic-amino-acid beta-eliminating
lyase / threonine aldolase), which over-generalises to a lyase MF that does
not apply to this enzyme.
action: REMOVE
reason: >-
This is a demonstrably incorrect electronic (IEA/InterPro) MF inference: the
enzyme's molecular function is glycine dehydrogenase (decarboxylating)
activity (GO:0004375, an oxidoreductase, EC 1.4.4.2), captured accurately by
other annotations. Lyase activity is the wrong ontology branch for this
protein and is safe to remove per the IEA-mis-mapping criterion.
supported_by:
- reference_id: file:human/GLDC/GLDC-uniprot.txt
supporting_text: "EC=1.4.4.2"
- term:
id: GO:0005960
label: glycine cleavage complex
evidence_type: NAS
original_reference_id: PMID:28244183
qualifier: part_of
review:
summary: >-
Correct complex membership. GLDC is the P protein subunit of the
four-protein glycine cleavage system (P/GLDC, T/AMT, L/DLD, H/GCSH).
action: ACCEPT
reason: >-
Well-established: GLDC is a bona fide subunit of the glycine cleavage
complex. Curated by ComplexPortal.
supported_by:
- reference_id: file:human/GLDC/GLDC-uniprot.txt
supporting_text: "P (GLDC), T (GCST), L (DLD) and H (GCSH)"
- term:
id: GO:0019464
label: glycine decarboxylation via glycine cleavage system
evidence_type: NAS
original_reference_id: PMID:24467211
qualifier: involved_in
review:
summary: >-
Core process, independently supported by the mechanistic study of Go et al.
(2014), which shows GLDC decarboxylates glycine and hands the aminomethyl
group to the H protein within the GCS.
action: ACCEPT
reason: >-
The cited mechanistic paper directly characterises GLDC-catalysed glycine
decarboxylation as the P-protein step of the glycine cleavage system.
supported_by:
- reference_id: PMID:24467211
supporting_text: "aminomethyl moiety is instead transferred to an accessory H-protein"
- term:
id: GO:0005739
label: mitochondrion
evidence_type: IDA
original_reference_id: GO_REF:0000052
qualifier: located_in
review:
summary: >-
Immunofluorescence (HPA) localisation to mitochondrion. Consistent with all
other localisation evidence.
action: ACCEPT
reason: >-
Direct immunofluorescence evidence supports mitochondrial localisation,
concordant with the transit peptide and matrix localisation.
supported_by:
- reference_id: file:human/GLDC/GLDC-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Mitochondrion"
- term:
id: GO:0004375
label: glycine dehydrogenase (decarboxylating) activity
evidence_type: EXP
original_reference_id: PMID:1993704
qualifier: enables
review:
summary: >-
Experimental support for the core catalytic function. Kume et al. cloned the
human glycine decarboxylase cDNA and characterised the PLP-binding
active-site region essential for enzyme activity.
action: ACCEPT
reason: >-
Direct experimental characterisation of human glycine decarboxylase,
including the PLP-binding lysine and glycine-rich phosphate-binding region
that organise the active site.
supported_by:
- reference_id: PMID:1993704
supporting_text: "The pyridoxal phosphate binding site lysine and a glycine-rich region"
- term:
id: GO:0005739
label: mitochondrion
evidence_type: HTP
original_reference_id: PMID:34800366
qualifier: located_in
review:
summary: >-
High-throughput mitochondrial proteomics localises GLDC to mitochondria,
concordant with all other localisation evidence.
action: ACCEPT
reason: >-
GLDC was identified in a high-confidence quantitative human mitochondrial
proteome; this HTP evidence agrees with the transit peptide, IDA
immunofluorescence and matrix TAS annotations.
supported_by:
- reference_id: file:human/GLDC/GLDC-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Mitochondrion"
- term:
id: GO:0005759
label: mitochondrial matrix
evidence_type: TAS
original_reference_id: Reactome:R-HSA-5693967
qualifier: located_in
review:
summary: >-
Most precise localisation: the glycine decarboxylation reaction occurs in
the mitochondrial matrix. Retained as the informative compartment.
action: ACCEPT
reason: >-
The GCS operates in the mitochondrial matrix; Reactome places the
GLDC-catalysed decarboxylation there. This is the preferred, more specific
cellular-component term.
supported_by:
- reference_id: file:human/GLDC/GLDC-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Mitochondrion"
- term:
id: GO:0036255
label: response to methylamine
evidence_type: ISS
original_reference_id: GO_REF:0000024
qualifier: involved_in
review:
summary: >-
Peripheral regulatory response inferred by similarity from rat (P15505).
Reflects that GCS P-protein activity is inhibited in the presence of
methylamine, not a distinct biological role of GLDC.
action: KEEP_AS_NON_CORE
reason: >-
Derived from an activity-regulation observation (methylamine inhibits the
enzyme). It is a plausible ISS-transferred response but does not represent a
core function of GLDC; retained as non-core.
supported_by:
- reference_id: file:human/GLDC/GLDC-uniprot.txt
supporting_text: "Inhibited in presence"
- term:
id: GO:0042803
label: protein homodimerization activity
evidence_type: ISS
original_reference_id: GO_REF:0000024
qualifier: enables
review:
summary: >-
Supported: the functional P protein is a homodimer. Retained as a supporting
(non-core) molecular function underpinning the catalytic unit.
action: KEEP_AS_NON_CORE
reason: >-
UniProt records GLDC as a homodimer (by similarity to rat P15505), and the
PLP-dependent active site is formed in the dimer. Real but ancillary to the
catalytic MF.
supported_by:
- reference_id: file:human/GLDC/GLDC-uniprot.txt
supporting_text: "Homodimer (By similarity)"
- term:
id: GO:0070280
label: pyridoxal binding
evidence_type: ISS
original_reference_id: GO_REF:0000024
qualifier: enables
review:
summary: >-
The cofactor is pyridoxal 5'-phosphate (PLP), covalently bound as a Schiff
base at Lys754, not free pyridoxal. The more accurate MF is pyridoxal
phosphate binding (GO:0030170), which UniProt itself also carries.
action: MODIFY
reason: >-
GLDC binds pyridoxal 5'-phosphate (the phosphorylated, active cofactor),
attached as N6-(pyridoxal phosphate)lysine at Lys754; the specific,
accurate term is GO:0030170 pyridoxal phosphate binding rather than the more
general pyridoxal binding.
proposed_replacement_terms:
- id: GO:0030170
label: pyridoxal phosphate binding
supported_by:
- reference_id: file:human/GLDC/GLDC-uniprot.txt
supporting_text: "Name=pyridoxal 5'-phosphate"
- reference_id: file:human/GLDC/GLDC-uniprot.txt
supporting_text: "N6-(pyridoxal phosphate)lysine"
- term:
id: GO:1903442
label: response to lipoic acid
evidence_type: ISS
original_reference_id: GO_REF:0000024
qualifier: involved_in
review:
summary: >-
Peripheral regulatory response inferred by similarity from rat (P15505),
reflecting that P-protein activity is stimulated by lipoic acid (the
lipoamide arm of the H protein is the physiological acceptor).
action: KEEP_AS_NON_CORE
reason: >-
Derived from an activity-regulation observation (lipoic acid stimulates the
enzyme). Consistent with the mechanism but not a core function; retained as
non-core.
supported_by:
- reference_id: file:human/GLDC/GLDC-uniprot.txt
supporting_text: "Stimulated by lipoic acid"
- term:
id: GO:0004375
label: glycine dehydrogenase (decarboxylating) activity
evidence_type: IDA
original_reference_id: PMID:28244183
qualifier: enables
review:
summary: >-
Direct experimental support for the core catalytic MF: enzymatic assays of
GCS P-protein activity for wild-type and NKH missense variants expressed in
COS7 cells.
action: ACCEPT
reason: >-
Bravo-Alonso et al. measured residual GCS P-protein (glycine decarboxylase)
activity for GLDC constructs, directly assaying this molecular function.
supported_by:
- reference_id: PMID:28244183
supporting_text: "assess the residual activity and mutant protein stability"
- term:
id: GO:0005739
label: mitochondrion
evidence_type: IDA
original_reference_id: PMID:28244183
qualifier: located_in
review:
summary: >-
Direct evidence of mitochondrial localisation; the same study also reported
NKH variants with altered (partially cytosolic) localisation, confirming the
wild-type mitochondrial targeting.
action: ACCEPT
reason: >-
Localisation of GLDC to mitochondria was directly assessed; consistent with
the transit peptide and all other localisation evidence.
supported_by:
- reference_id: file:human/GLDC/GLDC-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Mitochondrion"
- term:
id: GO:0006546
label: glycine catabolic process
evidence_type: IDA
original_reference_id: PMID:28244183
qualifier: involved_in
review:
summary: >-
Direct evidence linking GLDC to glycine catabolism: NKH variants cause loss
or reduction of glycine catabolic process, as characterised functionally in
this study.
action: ACCEPT
reason: >-
The functional assessment demonstrates that pathogenic GLDC variants impair
the glycine catabolic process, confirming GLDC's role in it. The more
specific term is GO:0019464.
supported_by:
- reference_id: PMID:28244183
supporting_text: "assess the residual activity and mutant protein stability"
- term:
id: GO:0009055
label: electron transfer activity
evidence_type: TAS
original_reference_id: PMID:2268343
qualifier: enables
review:
summary: >-
Likely over-annotation / mis-assignment. GLDC is a PLP-dependent glycine
decarboxylase (EC 1.4.4.2); it does not act as an electron carrier. Within
the glycine cleavage system, the redox/electron-transfer role belongs to the
L protein (DLD, dihydrolipoamide dehydrogenase, FAD-dependent), not to the P
protein. The cited reference (Sakakibara et al. 1990) is about a genomic
deletion of the glycine decarboxylase gene in an NKH patient and provides no
support for an electron transfer activity.
action: MARK_AS_OVER_ANNOTATED
reason: >-
The molecular function of GLDC is glycine dehydrogenase (decarboxylating)
activity, captured by multiple experimental and electronic annotations;
electron transfer activity is not a function of the P protein and is not
supported by the cited paper. Flagged as over-annotated rather than removed
because it is an author-statement (TAS) annotation whose full text was not
reviewed.
supported_by:
- reference_id: file:human/GLDC/GLDC-uniprot.txt
supporting_text: "The P protein (GLDC) binds the alpha-amino group of glycine"
- term:
id: GO:0004375
label: glycine dehydrogenase (decarboxylating) activity
evidence_type: TAS
original_reference_id: PMID:1996985
qualifier: enables
review:
summary: >-
Author-stated support for the core catalytic function: expression of normal
human P-protein cDNA in COS7 cells reconstituted glycine decarboxylase
activity comparable to human liver, whereas the NKH mutant (Phe756del) had
none.
action: ACCEPT
reason: >-
Kure et al. demonstrated glycine decarboxylase activity for the wild-type
human enzyme and its abolition by an NKH-causing deletion, supporting the
catalytic MF.
supported_by:
- reference_id: PMID:1996985
supporting_text: "showed no activity, indicating that the three-base deletion could cause NKH"
- term:
id: GO:0006546
label: glycine catabolic process
evidence_type: TAS
original_reference_id: PMID:1996985
qualifier: involved_in
review:
summary: >-
Author-stated support that GLDC drives glycine catabolism: loss of P-protein
activity from an NKH deletion causes the glycine-accumulation phenotype,
linking the enzyme to the glycine catabolic process.
action: ACCEPT
reason: >-
Consistent with GLDC's role in glycine degradation; the loss-of-activity
mutant establishes the connection to glycine catabolism. GO:0019464 is the
more specific term.
supported_by:
- reference_id: PMID:1996985
supporting_text: "showed no activity, indicating that the three-base deletion could cause NKH"
core_functions:
- description: >-
Pyridoxal-5'-phosphate-dependent decarboxylation of glycine as the P protein
of the mitochondrial glycine cleavage system: releases CO2 from glycine and
transfers the residual aminomethyl group to the lipoamide arm of the H protein
(GCSH).
molecular_function:
id: GO:0004375
label: glycine dehydrogenase (decarboxylating) activity
directly_involved_in:
- id: GO:0019464
label: glycine decarboxylation via glycine cleavage system
locations:
- id: GO:0005759
label: mitochondrial matrix
supported_by:
- reference_id: file:human/GLDC/GLDC-uniprot.txt
supporting_text: "The P protein (GLDC) binds the alpha-amino group of glycine"
- reference_id: PMID:24467211
supporting_text: "aminomethyl moiety is instead transferred to an accessory H-protein"
- description: >-
Binds the pyridoxal 5'-phosphate cofactor (covalently attached as a Schiff
base at Lys754) required for glycine decarboxylation.
molecular_function:
id: GO:0030170
label: pyridoxal phosphate binding
locations:
- id: GO:0005759
label: mitochondrial matrix
supported_by:
- reference_id: file:human/GLDC/GLDC-uniprot.txt
supporting_text: "N6-(pyridoxal phosphate)lysine"
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO
terms
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: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: file:human/GLDC/GLDC-uniprot.txt
title: UniProtKB entry P23378 (GCSP_HUMAN), Glycine dehydrogenase (decarboxylating),
mitochondrial
findings: []
- id: PMID:1993704
title: The glycine cleavage system. Molecular cloning of the chicken and human glycine
decarboxylase cDNAs and some characteristics involved in the deduced protein structures.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Abstract-only cache; PubMed-verified. Cloned human glycine decarboxylase cDNA
and characterised the PLP-binding active-site region. Supports the catalytic
MF and PLP cofactor role.
- id: PMID:1996985
title: 'Structural and expression analyses of normal and mutant mRNA encoding glycine
decarboxylase: three-base deletion in mRNA causes nonketotic hyperglycinemia.'
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Abstract-only cache; PubMed-verified. WT human P-protein cDNA reconstituted
glycine decarboxylase activity in COS7; NKH Phe756del abolished it. Supports
catalytic MF and glycine catabolic process.
- id: PMID:2268343
title: One of the two genomic copies of the glycine decarboxylase cDNA has been
deleted at a 5' region in a patient with nonketotic hyperglycinemia.
findings: []
reference_review:
relevance: LOW
correctness: MISCITED
review_notes: >-
Abstract-only cache; PubMed-verified. The paper describes a genomic deletion
of the glycine decarboxylase gene in an NKH patient and does NOT support the
electron transfer activity (GO:0009055) it is cited for; that MF annotation is
an over-annotation/mis-assignment for the P protein.
- id: PMID:24467211
title: Glycine decarboxylase is an unusual amino acid decarboxylase involved in
tumorigenesis.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Abstract-only cache; PubMed-verified. Mechanistic study showing GLDC is an
unusual PLP-dependent alpha-amino acid decarboxylase that removes CO2 without
releasing free methylamine and transfers the aminomethyl group to the H
protein. Directly supports the GCS decarboxylation function.
- id: PMID:28244183
title: 'Nonketotic hyperglycinemia: Functional assessment of missense variants in
GLDC to understand phenotypes of the disease.'
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Abstract-only cache; PubMed-verified. Enzymatic assays of GCS P-protein
activity and structural modelling for 19 GLDC missense variants; supports the
catalytic MF, glycine catabolic process, mitochondrial localisation and
complex membership.
- id: PMID:34800366
title: Quantitative high-confidence human mitochondrial proteome and its dynamics
in cellular context.
findings: []
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: >-
Abstract-only cache (GLDC data in supplementary tables not present in the
cache). High-throughput mitochondrial proteomics; supports mitochondrial
localisation of GLDC.
- id: Reactome:R-HSA-5693967
title: PXLP-K754-GLDC dimer decarboxylates Gly
findings: []