Holocarboxylase synthetase (HLCS) is the human biotin--protein ligase that covalently attaches biotin to the biotin-dependent carboxylases, converting their inactive apo forms into active holoenzymes. It catalyses a two-step reaction, first activating biotin with ATP to form biotinyl-5'-AMP and then transferring biotin to a specific lysine within the biotin carboxyl carrier domain of each substrate. A single HLCS activates all of the human biotin-dependent carboxylases in both the cytosol and the mitochondria, including pyruvate carboxylase (PC), propionyl-CoA carboxylase (PCCA/PCCB), 3-methylcrotonyl-CoA carboxylase (MCCC1/MCCC2), and the acetyl-CoA carboxylases (ACACA and ACACB). Through these carboxylases it is essential for gluconeogenesis and anaplerosis, odd-chain fatty acid and propionate metabolism, leucine catabolism, and fatty acid synthesis. Loss-of-function variants cause holocarboxylase synthetase deficiency (neonatal/early-onset multiple carboxylase deficiency), an autosomal recessive, biotin-responsive disorder characterized by ketoacidosis, lactic acidosis, hyperammonemia, organic aciduria, and dermatological manifestations. HLCS has additionally been reported to enter the nucleus and biotinylate histones, a proposed chromatin/gene-regulatory role whose in vivo physiological significance remains debated.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0004077
biotin--[biotin carboxyl-carrier protein] ligase activity
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic (IBA) assertion of the core molecular function, biotin--protein ligase activity. This is the defining, disease-relevant function of HLCS and is strongly supported by direct experimental evidence.
Reason: Core molecular function. HLCS catalyses the covalent attachment of biotin to the biotin-dependent carboxylases; the IBA is consistent with abundant human experimental evidence.
Supporting Evidence:
PMID:7753853
Holocarboxylase synthetase (HCS) catalyzes the biotinylation of the four biotin-dependent carboxylases in human cells.
|
|
GO:0005737
cytoplasm
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic (IBA) assignment of cytoplasmic localization. HLCS acts in the cytosol (activating ACACA and, en route, mitochondrial apocarboxylases) as well as the mitochondrion; cytoplasmic localization is well supported.
Reason: Consistent with direct experimental localization of HLCS to the cytosol and with a single HLCS acting in both cytoplasm and mitochondria.
Supporting Evidence:
PMID:7753853
a single HCS is targeted to the mitochondria and cytoplasm
|
|
GO:0004077
biotin--[biotin carboxyl-carrier protein] ligase activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Electronic (IEA, combined-method) assertion of the core biotin--protein ligase activity, with RHEA/EC cross-references (EC 6.3.4.9/.10/.11/.15). Redundant with the experimental annotations and correct.
Reason: Correct core molecular function, consistent with UniProt catalytic-activity records and experimental data.
Supporting Evidence:
PMID:7753853
Holocarboxylase synthetase (HCS) catalyzes the biotinylation of the four biotin-dependent carboxylases in human cells.
|
|
GO:0005737
cytoplasm
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: Electronic localization to cytoplasm derived from the UniProt Subcellular Location vocabulary (SL-0086). Consistent with experimental cytosolic localization.
Reason: HLCS is a cytoplasmic (and mitochondrial) enzyme; the SubCell-derived cytoplasm term is correct.
Supporting Evidence:
PMID:16780588
the HLCS gene codes for a biotin-protein ligase and was found to localize throughout the cytosol
|
|
GO:0005739
mitochondrion
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: Electronic localization to mitochondrion from the UniProt Subcellular Location vocabulary (SL-0173). A single HLCS activates the mitochondrial apocarboxylases (PC, PCC, MCC, ACACB), so mitochondrial localization is expected and reported.
Reason: Consistent with the requirement for HLCS to biotinylate mitochondrial apocarboxylases and with UniProt's SUBCELLULAR LOCATION (Cytoplasm; Mitochondrion).
Supporting Evidence:
PMID:7753853
a single HCS is targeted to the mitochondria and cytoplasm
|
|
GO:0006768
biotin metabolic process
|
IEA
GO_REF:0000117 |
ACCEPT |
Summary: Electronic (ARBA) assignment of the broad biotin metabolic process. HLCS is a central enzyme of biotin utilization; the term is broad but correct.
Reason: HLCS is the enzyme that incorporates biotin into apocarboxylases, a core step of biotin metabolism/utilization. The parent process term is correct although general.
Supporting Evidence:
PMID:7842009
Holocarboxylase synthetase (HCS) plays an essential role in biotin utilization in eukaryotic cells
|
|
GO:0005515
protein binding
|
IPI
PMID:20085763 The N-terminal domain of human holocarboxylase synthetase fa... |
MARK AS OVER ANNOTATED |
Summary: Bare "protein binding" from an IntAct-curated pairwise interaction (partner O00763 = ACACB, an HLCS substrate). The paper concerns HLCS N-terminal domain binding its biotin-acceptor substrate, so the interaction is real, but the GO term is uninformative.
Reason: Bare protein binding conveys no specific function. The underlying biology (HLCS recognizing its carboxylase substrate) is captured better by the ligase activity and enzyme/substrate-binding annotations; per curation policy the experimental IPI is retained but marked as over-annotated rather than removed.
|
|
GO:0005515
protein binding
|
IPI
PMID:21044950 Genome-wide YFP fluorescence complementation screen identifi... |
MARK AS OVER ANNOTATED |
Summary: Bare "protein binding" from a genome-wide YFP fluorescence-complementation interaction screen (partner Q9NUX5 = POT1). High-throughput screen hit; uninformative GO term and biologically unexplained for HLCS.
Reason: Uninformative bare protein-binding term derived from a high-throughput interactome screen; no established functional relevance to HLCS. Retained per policy (experimental IPI) but marked over-annotated.
|
|
GO:0005515
protein binding
|
IPI
PMID:28514442 Architecture of the human interactome defines protein commun... |
MARK AS OVER ANNOTATED |
Summary: Bare "protein binding" from a large-scale interactome/AP-MS study (partners Q5T0L3 = SPATA46, Q86XM0 = CATSPERD). Uninformative GO term from a proteome-scale screen.
Reason: Bare protein binding from a high-throughput interactome map; not an informative molecular function. Retained per policy but marked over-annotated.
|
|
GO:0005515
protein binding
|
IPI
PMID:32296183 A reference map of the human binary protein interactome. |
MARK AS OVER ANNOTATED |
Summary: Bare "protein binding" from the HuRI binary interactome map (multiple partners incl. MED19, KRTAP5-9, SPATA46, ANKRD29). Uninformative screen-derived term.
Reason: Bare protein-binding term from a proteome-scale Y2H interactome; no specific functional insight into HLCS. Retained per policy but marked over-annotated.
|
|
GO:0005515
protein binding
|
IPI
PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... |
MARK AS OVER ANNOTATED |
Summary: Bare "protein binding" from a proteome-scale AP-MS interactome (partners SPATA46, CATSPERD). Uninformative GO term from a high-throughput dataset.
Reason: Bare protein-binding term derived from a large-scale interactome study; not functionally informative for HLCS. Retained per policy but marked over-annotated.
|
|
GO:0042802
identical protein binding
|
IEA
GO_REF:0000107 |
MARK AS OVER ANNOTATED |
Summary: Electronic "identical protein binding" (self-association/homodimerization) transferred by orthology from the rat protein (D4AA38). Human HLCS is reported to be a monomer, so self-association is not supported for the human enzyme.
Reason: Orthology-transferred (Ensembl Compara) self-binding term. UniProt records human HLCS SUBUNIT as "Monomer", so this electronic homodimerization inference is not substantiated for human HLCS.
Supporting Evidence:
PMID:7842009
Holocarboxylase synthetase (HCS) plays an essential role in biotin utilization in eukaryotic cells
|
|
GO:0070781
response to biotin
|
IEA
GO_REF:0000107 |
KEEP AS NON CORE |
Summary: Electronic "response to biotin" transferred by orthology from the rat protein. Relates to the reported (and debated) role of HLCS as a nuclear biotin sensor that adjusts biotin uptake; not the core catalytic function.
Reason: The biotin-sensing/response role has some direct support in human cells but is a proposed, non-essential moonlighting activity distinct from the core biotin-protein ligase function. Kept as non-core.
Supporting Evidence:
PMID:17904341
the nuclear translocation of HCS depends on biotin
|
|
GO:0006768
biotin metabolic process
|
TAS
Reactome:R-HSA-196780 |
ACCEPT |
Summary: Reactome (TAS) placement of HLCS in "Biotin transport and metabolism". HLCS incorporates biotin into apocarboxylases, a central step of biotin metabolism/utilization. Broad but correct.
Reason: Correct broad biological process; HLCS is a core enzyme of biotin metabolism.
Supporting Evidence:
PMID:7842009
Holocarboxylase synthetase (HCS) plays an essential role in biotin utilization in eukaryotic cells
|
|
GO:0004077
biotin--[biotin carboxyl-carrier protein] ligase activity
|
TAS
Reactome:R-HSA-2993447 |
ACCEPT |
Summary: Reactome (TAS) biotin--protein ligase activity for the reaction "HLCS biotinylates 6x(PCCA:PCCB)" (biotinylation of propionyl-CoA carboxylase). Correct core molecular function on a genuine substrate.
Reason: Core molecular function; PCC is an established HLCS substrate. Duplicate of the experimental ligase-activity annotations.
Supporting Evidence:
PMID:7753853
Holocarboxylase synthetase (HCS) catalyzes the biotinylation of the four biotin-dependent carboxylases in human cells.
|
|
GO:0004077
biotin--[biotin carboxyl-carrier protein] ligase activity
|
TAS
Reactome:R-HSA-2993799 |
ACCEPT |
Summary: Reactome (TAS) biotin--protein ligase activity for "HLCS biotinylates 6xMCCC1:6xMCCC2" (biotinylation of 3-methylcrotonyl-CoA carboxylase). Correct core function on a genuine substrate.
Reason: Core molecular function; MCC is an established HLCS substrate.
Supporting Evidence:
PMID:7753853
Holocarboxylase synthetase (HCS) catalyzes the biotinylation of the four biotin-dependent carboxylases in human cells.
|
|
GO:0004077
biotin--[biotin carboxyl-carrier protein] ligase activity
|
TAS
Reactome:R-HSA-2993802 |
ACCEPT |
Summary: Reactome (TAS) biotin--protein ligase activity for "HLCS biotinylates PC:Mn2+" (biotinylation of pyruvate carboxylase). Correct core function on a genuine substrate.
Reason: Core molecular function; PC is an established HLCS substrate.
Supporting Evidence:
PMID:7753853
Holocarboxylase synthetase (HCS) catalyzes the biotinylation of the four biotin-dependent carboxylases in human cells.
|
|
GO:0004077
biotin--[biotin carboxyl-carrier protein] ligase activity
|
TAS
Reactome:R-HSA-2993814 |
ACCEPT |
Summary: Reactome (TAS) biotin--protein ligase activity for "HLCS biotinylates ACACA:Mn2+" (biotinylation of acetyl-CoA carboxylase 1). Correct core function on a genuine substrate.
Reason: Core molecular function; ACACA is an established HLCS substrate.
Supporting Evidence:
PMID:7753853
Holocarboxylase synthetase (HCS) catalyzes the biotinylation of the four biotin-dependent carboxylases in human cells.
|
|
GO:0004077
biotin--[biotin carboxyl-carrier protein] ligase activity
|
TAS
Reactome:R-HSA-3323184 |
ACCEPT |
Summary: Reactome (TAS) biotin--protein ligase activity within the disease reaction "Defective HLCS does not biotinylate ACACA:Mn2+". The annotated activity is the same core ligase function (in a defective-variant context). Correct.
Reason: Same core molecular function, annotated in a disease-variant Reactome reaction; the function itself is correct.
Supporting Evidence:
PMID:7753853
Holocarboxylase synthetase (HCS) catalyzes the biotinylation of the four biotin-dependent carboxylases in human cells.
|
|
GO:0004077
biotin--[biotin carboxyl-carrier protein] ligase activity
|
TAS
Reactome:R-HSA-4167511 |
ACCEPT |
Summary: Reactome (TAS) biotin--protein ligase activity for "HLCS biotinylates ACACB" (biotinylation of acetyl-CoA carboxylase 2). Correct core function on a genuine substrate.
Reason: Core molecular function; ACACB is an established HLCS substrate.
Supporting Evidence:
PMID:7753853
Holocarboxylase synthetase (HCS) catalyzes the biotinylation of the four biotin-dependent carboxylases in human cells.
|
|
GO:0004077
biotin--[biotin carboxyl-carrier protein] ligase activity
|
TAS
Reactome:R-HSA-9035987 |
ACCEPT |
Summary: Reactome (TAS) biotin--protein ligase activity within the disease reaction "Defective HLCS does not biotinylate 6xMCCC1:6xMCCC2". Same core ligase function in a defective-variant context. Correct.
Reason: Same core molecular function annotated in a disease-variant Reactome reaction.
Supporting Evidence:
PMID:7753853
Holocarboxylase synthetase (HCS) catalyzes the biotinylation of the four biotin-dependent carboxylases in human cells.
|
|
GO:0004077
biotin--[biotin carboxyl-carrier protein] ligase activity
|
TAS
Reactome:R-HSA-9035988 |
ACCEPT |
Summary: Reactome (TAS) biotin--protein ligase activity within the disease reaction "Defective HLCS does not biotinylate PC:Mn2+". Same core ligase function in a defective-variant context. Correct.
Reason: Same core molecular function annotated in a disease-variant Reactome reaction.
Supporting Evidence:
PMID:7753853
Holocarboxylase synthetase (HCS) catalyzes the biotinylation of the four biotin-dependent carboxylases in human cells.
|
|
GO:0004077
biotin--[biotin carboxyl-carrier protein] ligase activity
|
TAS
Reactome:R-HSA-9035990 |
ACCEPT |
Summary: Reactome (TAS) biotin--protein ligase activity within the disease reaction "Defective HLCS does not biotinylate 6x(PCCA:PCCB)". Same core ligase function in a defective-variant context. Correct.
Reason: Same core molecular function annotated in a disease-variant Reactome reaction.
Supporting Evidence:
PMID:7753853
Holocarboxylase synthetase (HCS) catalyzes the biotinylation of the four biotin-dependent carboxylases in human cells.
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-3323184 |
ACCEPT |
Summary: Reactome (TAS) cytosolic localization. Consistent with the well-documented cytosolic localization of HLCS.
Reason: HLCS acts in the cytosol; localization is directly supported experimentally.
Supporting Evidence:
PMID:16780588
the HLCS gene codes for a biotin-protein ligase and was found to localize throughout the cytosol
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-9035987 |
ACCEPT |
Summary: Reactome (TAS) cytosolic localization. Duplicate of the well-supported cytosolic localization of HLCS.
Reason: HLCS acts in the cytosol; localization is directly supported experimentally.
Supporting Evidence:
PMID:16780588
the HLCS gene codes for a biotin-protein ligase and was found to localize throughout the cytosol
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-9035988 |
ACCEPT |
Summary: Reactome (TAS) cytosolic localization. Duplicate of the well-supported cytosolic localization of HLCS.
Reason: HLCS acts in the cytosol; localization is directly supported experimentally.
Supporting Evidence:
PMID:16780588
the HLCS gene codes for a biotin-protein ligase and was found to localize throughout the cytosol
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-9035990 |
ACCEPT |
Summary: Reactome (TAS) cytosolic localization. Duplicate of the well-supported cytosolic localization of HLCS.
Reason: HLCS acts in the cytosol; localization is directly supported experimentally.
Supporting Evidence:
PMID:16780588
the HLCS gene codes for a biotin-protein ligase and was found to localize throughout the cytosol
|
|
GO:0004077
biotin--[biotin carboxyl-carrier protein] ligase activity
|
EXP
PMID:7753853 Isolation of a cDNA encoding human holocarboxylase synthetas... |
ACCEPT |
Summary: Direct experimental evidence for the core biotin--protein ligase activity. The human HCS cDNA complemented an E. coli birA (biotin ligase) mutant and promoted biotinylation of the biotin carboxyl carrier protein and of a propionyl-CoA carboxylase alpha fragment.
Reason: Gold-standard experimental evidence for the defining molecular function of HLCS.
Supporting Evidence:
PMID:7753853
complementation of an Escherichia coli birA
PMID:7753853
Holocarboxylase synthetase (HCS) catalyzes the biotinylation of the four biotin-dependent carboxylases in human cells.
|
|
GO:0004077
biotin--[biotin carboxyl-carrier protein] ligase activity
|
IDA
PMID:14613969 Reduced histone biotinylation in multiple carboxylase defici... |
ACCEPT |
Summary: Direct-assay evidence that HLCS possesses biotin--protein ligase activity. This study, focused on the nuclear/histone role, also confirmed that HLCS retains biotinylating activity.
Reason: Direct experimental support for the core ligase activity.
Supporting Evidence:
PMID:14613969
The attachment of biotin to apocarboxylases is catalyzed by holocarboxylase
PMID:14613969
Nuclear HCS retains its biotinylating activity
|
|
GO:0043687
post-translational protein modification
|
IDA
PMID:14613969 Reduced histone biotinylation in multiple carboxylase defici... |
ACCEPT |
Summary: HLCS mediates a post-translational modification (covalent attachment of biotin to lysine residues of acceptor proteins). This is the process-level view of its ligase activity; the biotinylation-specific process terms (e.g. GO:0009305 protein biotinylation) are obsolete, so this is the best available BP term.
Reason: Correct process-level annotation of HLCS-catalysed protein biotinylation. Biotinylation is a bona fide post-translational modification and the annotation is directly supported.
Supporting Evidence:
PMID:14613969
The attachment of biotin to apocarboxylases is catalyzed by holocarboxylase
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-2993447 |
ACCEPT |
Summary: Reactome (TAS) cytosolic localization associated with the PCC-biotinylation reaction. Consistent with cytosolic HLCS.
Reason: HLCS acts in the cytosol; localization is directly supported experimentally.
Supporting Evidence:
PMID:16780588
the HLCS gene codes for a biotin-protein ligase and was found to localize throughout the cytosol
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-2993799 |
ACCEPT |
Summary: Reactome (TAS) cytosolic localization associated with the MCC-biotinylation reaction. Consistent with cytosolic HLCS.
Reason: HLCS acts in the cytosol; localization is directly supported experimentally.
Supporting Evidence:
PMID:16780588
the HLCS gene codes for a biotin-protein ligase and was found to localize throughout the cytosol
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-2993802 |
ACCEPT |
Summary: Reactome (TAS) cytosolic localization associated with the PC-biotinylation reaction. Consistent with cytosolic HLCS.
Reason: HLCS acts in the cytosol; localization is directly supported experimentally.
Supporting Evidence:
PMID:16780588
the HLCS gene codes for a biotin-protein ligase and was found to localize throughout the cytosol
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-2993814 |
ACCEPT |
Summary: Reactome (TAS) cytosolic localization associated with the ACACA-biotinylation reaction. Consistent with cytosolic HLCS.
Reason: HLCS acts in the cytosol; localization is directly supported experimentally.
Supporting Evidence:
PMID:16780588
the HLCS gene codes for a biotin-protein ligase and was found to localize throughout the cytosol
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-4167511 |
ACCEPT |
Summary: Reactome (TAS) cytosolic localization associated with the ACACB-biotinylation reaction. Consistent with cytosolic HLCS.
Reason: HLCS acts in the cytosol; localization is directly supported experimentally.
Supporting Evidence:
PMID:16780588
the HLCS gene codes for a biotin-protein ligase and was found to localize throughout the cytosol
|
|
GO:0070781
response to biotin
|
IDA
PMID:17904341 Holocarboxylase synthetase regulates expression of biotin tr... |
KEEP AS NON CORE |
Summary: Direct-assay evidence that HLCS responds to biotin availability - its nuclear translocation increases with biotin supplementation, and it participates in a proposed biotin-sensing/homeostasis loop that regulates the SMVT biotin transporter via histone biotinylation. This is a proposed regulatory/moonlighting role, not the core catalytic function, and its in vivo significance is debated.
Reason: Experimentally observed biotin-responsive behavior, but it reflects a proposed nuclear/regulatory moonlighting role rather than the essential biotin-protein ligase function. Retained as non-core.
Supporting Evidence:
PMID:17904341
the nuclear translocation of HCS depends on biotin
PMID:17904341
HCS senses biotin
|
|
GO:0000785
chromatin
|
IDA
PMID:14613969 Reduced histone biotinylation in multiple carboxylase defici... |
KEEP AS NON CORE |
Summary: Direct-assay (subnuclear fractionation/immunofluorescence) evidence that a fraction of HLCS associates with chromatin, linked to the proposed histone-biotinylation role. This nuclear/chromatin function is a moonlighting activity whose in vivo physiological relevance is contested.
Reason: A real experimental observation from a specific study, but chromatin association reflects a debated nuclear moonlighting role rather than the core cytosolic/mitochondrial carboxylase-activation function. Retained as non-core.
Supporting Evidence:
PMID:14613969
localizes to the nucleus rather than the cytoplasm
PMID:14613969
biotinylate purified histones in vitro
|
|
GO:0004077
biotin--[biotin carboxyl-carrier protein] ligase activity
|
IMP
PMID:18429047 Reduced half-life of holocarboxylase synthetase from patient... |
ACCEPT |
Summary: Mutation-based evidence that HLCS is the biotin--protein ligase. Patient cells homozygous for p.L216R lacked detectable HLCS enzyme activity, and recombinant p.L216R showed severely compromised ligase activity that could not be rescued by additional biotin, with a doubled protein turnover rate.
Reason: Loss-of-function/variant analysis directly supports the core ligase activity.
Supporting Evidence:
PMID:18429047
the turn-over rate for the mutant protein was double that of wildtype HLCS
|
|
GO:0004077
biotin--[biotin carboxyl-carrier protein] ligase activity
|
IDA
PMID:7842009 Isolation and characterization of mutations in the human hol... |
ACCEPT |
Summary: Direct-assay evidence for the core biotin--protein ligase activity from the original human HCS cDNA cloning/characterization, which established HLCS as essential for biotin utilization and homologous to E. coli BirA (biotin-[acetyl-CoA-carboxylase] ligase).
Reason: Foundational direct experimental evidence for the defining molecular function.
Supporting Evidence:
PMID:7842009
Holocarboxylase synthetase (HCS) plays an essential role in biotin utilization in eukaryotic cells
|
|
GO:0004077
biotin--[biotin carboxyl-carrier protein] ligase activity
|
IDA
PMID:9630604 Identification of holocarboxylase synthetase (HCS) proteins ... |
ACCEPT |
Summary: Direct-assay evidence for the ligase activity. Anti-HCS antibodies to the Ile128-Pro398 region inhibited HCS enzymatic activity, mapping the catalytically essential region; three cytosolic HCS proteins (86/82/76 kDa) were identified in placenta.
Reason: Direct experimental support for the core molecular function.
Supporting Evidence:
PMID:9630604
we have identified, in human placenta, three cytosolic HCS
PMID:9630604
essential for the catalytic activity of
|
|
GO:0005652
nuclear lamina
|
IDA
PMID:14613969 Reduced histone biotinylation in multiple carboxylase defici... |
KEEP AS NON CORE |
Summary: Direct-assay (subnuclear fractionation) evidence that a fraction of HLCS associates with the nuclear lamina, part of the proposed nuclear/histone-biotinylation role. This moonlighting localization is debated and is not the core function.
Reason: Real experimental observation but reflects a contested nuclear moonlighting role, not the core cytosolic/mitochondrial carboxylase-activation function. Retained as non-core.
Supporting Evidence:
PMID:14613969
localizes to the nucleus rather than the cytoplasm
|
|
GO:0005829
cytosol
|
IDA
PMID:9630604 Identification of holocarboxylase synthetase (HCS) proteins ... |
ACCEPT |
Summary: Direct-assay evidence for cytosolic localization; HLCS proteins were identified as cytosolic in human placenta, and cell-free-synthesized HCS was not translocated into mitochondria, consistent with a cytosolic pool.
Reason: Direct experimental support for cytosolic localization, a core compartment for HLCS.
Supporting Evidence:
PMID:9630604
we have identified, in human placenta, three cytosolic HCS
|
|
GO:0009374
biotin binding
|
IDA
PMID:14613969 Reduced histone biotinylation in multiple carboxylase defici... |
ACCEPT |
Summary: Direct-assay evidence that HLCS binds biotin, the substrate it activates (as biotinyl-5'-AMP) prior to transfer to apocarboxylases. A supporting molecular function underpinning the core ligase activity.
Reason: Biotin binding is an integral part of the HLCS catalytic mechanism and is directly supported; retained as a supporting molecular function.
Supporting Evidence:
PMID:14613969
Nuclear HCS retains its biotinylating activity
|
|
GO:0016363
nuclear matrix
|
IDA
PMID:14613969 Reduced histone biotinylation in multiple carboxylase defici... |
KEEP AS NON CORE |
Summary: Direct-assay (subnuclear fractionation) evidence associating a fraction of HLCS with the nuclear matrix, part of the proposed nuclear/histone role. Debated moonlighting localization, not the core function.
Reason: Real experimental observation but reflects the contested nuclear moonlighting role rather than the core function. Retained as non-core.
Supporting Evidence:
PMID:14613969
localizes to the nucleus rather than the cytoplasm
|
|
GO:0019899
enzyme binding
|
IPI
PMID:19157941 N- and C-terminal domains in human holocarboxylase synthetas... |
ACCEPT |
Summary: Physical-interaction evidence (Y2H) with a propionyl-CoA carboxylase-derived polypeptide (p67; partner P05165 = PCCA). This captures HLCS binding to its carboxylase (apoenzyme) substrate via the N- and C-terminal domains, i.e. substrate recognition preceding biotinylation.
Reason: More informative than bare protein binding - the partner PCCA is a genuine HLCS substrate (an enzyme), and the interaction reflects substrate recognition central to HLCS catalysis. Retained.
Supporting Evidence:
PMID:19157941
essential for biotinylation of carboxylases by HCS
PMID:19157941
N- and C-termini play roles in substrate recognition
|
|
GO:0005829
cytosol
|
HDA
PMID:16780588 Cell array-based intracellular localization screening reveal... |
ACCEPT |
Summary: High-throughput direct-assay (transfected-cell array localization screen of chromosome 21 proteins) placing HLCS in the cytosol. Consistent with the broader experimental and Reactome cytosolic annotations.
Reason: Consistent cytosolic localization, corroborating multiple other lines of evidence.
Supporting Evidence:
PMID:16780588
the HLCS gene codes for a biotin-protein ligase and was found to localize throughout the cytosol
|
UniProtKB: P50747 (BPL1_HUMAN). HGNC:4976. Chromosome 21q22.13. 726 aa.
RecName: Biotin--protein ligase; AltName: Biotin apo-protein ligase; Holocarboxylase synthetase (HCS).
HLCS is the human biotin--protein ligase (holocarboxylase synthetase): it covalently
attaches biotin to the biotin-dependent carboxylases, activating the apo-enzymes. It
catalyses a two-step reaction — biotin + ATP -> biotinyl-5'-AMP, then transfer of biotin
to a specific lysine on the biotin carboxyl carrier domain of each apocarboxylase.
Substrate carboxylases activated (UniProt CATALYTIC ACTIVITY, EC 6.3.4.9/.10/.11/.15;
PMID:7753853, PMID:10590022):
- Pyruvate carboxylase (PC) — gluconeogenesis/anaplerosis (mitochondrial)
- Propionyl-CoA carboxylase (PCC; PCCA/PCCB) — odd-chain FA / propionate (mitochondrial)
- 3-Methylcrotonyl-CoA carboxylase (MCC; MCCC1/MCCC2) — leucine catabolism (mitochondrial)
- Acetyl-CoA carboxylases ACC1/ACC2 (ACACA cytosolic; ACACB mitochondrial outer membrane)
A single HLCS biotinylates carboxylases in both cytosol and mitochondria
(PMID:7753853 "a single HCS is targeted to the mitochondria and cytoplasm"). GOA carries
both cytoplasm (IBA) and mitochondrion (IEA-SubCell) plus cytosol (many IDA/TAS). All are
consistent with the dual-compartment biology.
Kinetics: KM = 224 nM for biotin (PMID:10590022, via UniProt). Monomer (PMID:7842009).
Holocarboxylase synthetase deficiency (HLCS deficiency; MIM 253270): neonatal/early-onset
multiple carboxylase deficiency, autosomal recessive. Loss of HLCS -> all 4/5 carboxylases
remain in inactive apo form -> ketoacidosis, lactic acidosis, hyperammonemia, organic aciduria,
dermatitis/alopecia, seizures. Biotin-responsive (10-20 mg/day). Extensive allelic series
of missense variants clustering in the biotin-binding region; some KM mutants, some non-KM
(e.g. R508W very common, biotin-responsive; L216R reduces protein half-life, PMID:18429047).
(Confirmed against ~/repos/dismech/kb/disorders/Holocarboxylase_Synthetase_Deficiency.yaml.)
A body of work (Zempleni, Gravel labs) reports HLCS in the nucleus, associated with chromatin
/ nuclear lamina / nuclear matrix, biotinylating histones (esp. K12-biotinyl H4) and thereby
implicated in gene silencing and biotin-uptake homeostasis at the SMVT locus (PMID:14613969,
PMID:17904341). The physiological significance and even the existence of appreciable histone
biotinylation in vivo has been disputed in the broader literature (stoichiometry very low;
some argue it is a chemical/acetyl-CoA-carboxylase artifact). Treat chromatin/nuclear-lamina/
nuclear-matrix localizations and the "response to biotin" / histone-remodeling roles as
non-core (KEEP_AS_NON_CORE) — real experimental observations from a specific lab, but not
the established, disease-defining core function, and their in vivo relevance is contested.
id: P50747
gene_symbol: HLCS
product_type: PROTEIN
status: INITIALIZED
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: Holocarboxylase synthetase (HLCS) is the human biotin--protein ligase
that covalently attaches biotin to the biotin-dependent carboxylases, converting
their inactive apo forms into active holoenzymes. It catalyses a two-step reaction,
first activating biotin with ATP to form biotinyl-5'-AMP and then transferring biotin
to a specific lysine within the biotin carboxyl carrier domain of each substrate.
A single HLCS activates all of the human biotin-dependent carboxylases in both the
cytosol and the mitochondria, including pyruvate carboxylase (PC), propionyl-CoA
carboxylase (PCCA/PCCB), 3-methylcrotonyl-CoA carboxylase (MCCC1/MCCC2), and the
acetyl-CoA carboxylases (ACACA and ACACB). Through these carboxylases it is essential
for gluconeogenesis and anaplerosis, odd-chain fatty acid and propionate metabolism,
leucine catabolism, and fatty acid synthesis. Loss-of-function variants cause holocarboxylase
synthetase deficiency (neonatal/early-onset multiple carboxylase deficiency), an
autosomal recessive, biotin-responsive disorder characterized by ketoacidosis, lactic
acidosis, hyperammonemia, organic aciduria, and dermatological manifestations. HLCS
has additionally been reported to enter the nucleus and biotinylate histones, a proposed
chromatin/gene-regulatory role whose in vivo physiological significance remains debated.
alternative_products:
- name: '1'
id: P50747-1
- name: '2'
id: P50747-2
sequence_note: VSP_061442
existing_annotations:
- term:
id: GO:0004077
label: biotin--[biotin carboxyl-carrier protein] ligase activity
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: enables
review:
summary: Phylogenetic (IBA) assertion of the core molecular function, biotin--protein
ligase activity. This is the defining, disease-relevant function of HLCS and
is strongly supported by direct experimental evidence.
action: ACCEPT
reason: Core molecular function. HLCS catalyses the covalent attachment of biotin
to the biotin-dependent carboxylases; the IBA is consistent with abundant human
experimental evidence.
supported_by:
- reference_id: PMID:7753853
supporting_text: Holocarboxylase synthetase (HCS) catalyzes the biotinylation
of the four biotin-dependent carboxylases in human cells.
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: is_active_in
review:
summary: Phylogenetic (IBA) assignment of cytoplasmic localization. HLCS acts
in the cytosol (activating ACACA and, en route, mitochondrial apocarboxylases)
as well as the mitochondrion; cytoplasmic localization is well supported.
action: ACCEPT
reason: Consistent with direct experimental localization of HLCS to the cytosol
and with a single HLCS acting in both cytoplasm and mitochondria.
supported_by:
- reference_id: PMID:7753853
supporting_text: a single HCS is targeted to the mitochondria and cytoplasm
- term:
id: GO:0004077
label: biotin--[biotin carboxyl-carrier protein] ligase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: enables
review:
summary: Electronic (IEA, combined-method) assertion of the core biotin--protein
ligase activity, with RHEA/EC cross-references (EC 6.3.4.9/.10/.11/.15). Redundant
with the experimental annotations and correct.
action: ACCEPT
reason: Correct core molecular function, consistent with UniProt catalytic-activity
records and experimental data.
supported_by:
- reference_id: PMID:7753853
supporting_text: Holocarboxylase synthetase (HCS) catalyzes the biotinylation
of the four biotin-dependent carboxylases in human cells.
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IEA
original_reference_id: GO_REF:0000044
qualifier: located_in
review:
summary: Electronic localization to cytoplasm derived from the UniProt Subcellular
Location vocabulary (SL-0086). Consistent with experimental cytosolic localization.
action: ACCEPT
reason: HLCS is a cytoplasmic (and mitochondrial) enzyme; the SubCell-derived
cytoplasm term is correct.
supported_by:
- reference_id: PMID:16780588
supporting_text: the HLCS gene codes for a biotin-protein ligase and was found
to localize throughout the cytosol
- term:
id: GO:0005739
label: mitochondrion
evidence_type: IEA
original_reference_id: GO_REF:0000044
qualifier: located_in
review:
summary: Electronic localization to mitochondrion from the UniProt Subcellular
Location vocabulary (SL-0173). A single HLCS activates the mitochondrial apocarboxylases
(PC, PCC, MCC, ACACB), so mitochondrial localization is expected and reported.
action: ACCEPT
reason: Consistent with the requirement for HLCS to biotinylate mitochondrial
apocarboxylases and with UniProt's SUBCELLULAR LOCATION (Cytoplasm; Mitochondrion).
supported_by:
- reference_id: PMID:7753853
supporting_text: a single HCS is targeted to the mitochondria and cytoplasm
- term:
id: GO:0006768
label: biotin metabolic process
evidence_type: IEA
original_reference_id: GO_REF:0000117
qualifier: involved_in
review:
summary: Electronic (ARBA) assignment of the broad biotin metabolic process. HLCS
is a central enzyme of biotin utilization; the term is broad but correct.
action: ACCEPT
reason: HLCS is the enzyme that incorporates biotin into apocarboxylases, a core
step of biotin metabolism/utilization. The parent process term is correct although
general.
supported_by:
- reference_id: PMID:7842009
supporting_text: Holocarboxylase synthetase (HCS) plays an essential role in
biotin utilization in eukaryotic cells
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:20085763
qualifier: enables
review:
summary: Bare "protein binding" from an IntAct-curated pairwise interaction (partner
O00763 = ACACB, an HLCS substrate). The paper concerns HLCS N-terminal domain
binding its biotin-acceptor substrate, so the interaction is real, but the GO
term is uninformative.
action: MARK_AS_OVER_ANNOTATED
reason: Bare protein binding conveys no specific function. The underlying biology
(HLCS recognizing its carboxylase substrate) is captured better by the ligase
activity and enzyme/substrate-binding annotations; per curation policy the experimental
IPI is retained but marked as over-annotated rather than removed.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:21044950
qualifier: enables
review:
summary: Bare "protein binding" from a genome-wide YFP fluorescence-complementation
interaction screen (partner Q9NUX5 = POT1). High-throughput screen hit; uninformative
GO term and biologically unexplained for HLCS.
action: MARK_AS_OVER_ANNOTATED
reason: Uninformative bare protein-binding term derived from a high-throughput
interactome screen; no established functional relevance to HLCS. Retained per
policy (experimental IPI) but marked over-annotated.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:28514442
qualifier: enables
review:
summary: Bare "protein binding" from a large-scale interactome/AP-MS study (partners
Q5T0L3 = SPATA46, Q86XM0 = CATSPERD). Uninformative GO term from a proteome-scale
screen.
action: MARK_AS_OVER_ANNOTATED
reason: Bare protein binding from a high-throughput interactome map; not an informative
molecular function. Retained per policy but marked over-annotated.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:32296183
qualifier: enables
review:
summary: Bare "protein binding" from the HuRI binary interactome map (multiple
partners incl. MED19, KRTAP5-9, SPATA46, ANKRD29). Uninformative screen-derived
term.
action: MARK_AS_OVER_ANNOTATED
reason: Bare protein-binding term from a proteome-scale Y2H interactome; no specific
functional insight into HLCS. Retained per policy but marked over-annotated.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:33961781
qualifier: enables
review:
summary: Bare "protein binding" from a proteome-scale AP-MS interactome (partners
SPATA46, CATSPERD). Uninformative GO term from a high-throughput dataset.
action: MARK_AS_OVER_ANNOTATED
reason: Bare protein-binding term derived from a large-scale interactome study;
not functionally informative for HLCS. Retained per policy but marked over-annotated.
- term:
id: GO:0042802
label: identical protein binding
evidence_type: IEA
original_reference_id: GO_REF:0000107
qualifier: enables
review:
summary: Electronic "identical protein binding" (self-association/homodimerization)
transferred by orthology from the rat protein (D4AA38). Human HLCS is reported
to be a monomer, so self-association is not supported for the human enzyme.
action: MARK_AS_OVER_ANNOTATED
reason: Orthology-transferred (Ensembl Compara) self-binding term. UniProt records
human HLCS SUBUNIT as "Monomer", so this electronic homodimerization inference
is not substantiated for human HLCS.
supported_by:
- reference_id: PMID:7842009
supporting_text: Holocarboxylase synthetase (HCS) plays an essential role in
biotin utilization in eukaryotic cells
- term:
id: GO:0070781
label: response to biotin
evidence_type: IEA
original_reference_id: GO_REF:0000107
qualifier: involved_in
review:
summary: Electronic "response to biotin" transferred by orthology from the rat
protein. Relates to the reported (and debated) role of HLCS as a nuclear biotin
sensor that adjusts biotin uptake; not the core catalytic function.
action: KEEP_AS_NON_CORE
reason: The biotin-sensing/response role has some direct support in human cells
but is a proposed, non-essential moonlighting activity distinct from the core
biotin-protein ligase function. Kept as non-core.
supported_by:
- reference_id: PMID:17904341
supporting_text: the nuclear translocation of HCS depends on biotin
- term:
id: GO:0006768
label: biotin metabolic process
evidence_type: TAS
original_reference_id: Reactome:R-HSA-196780
qualifier: involved_in
review:
summary: Reactome (TAS) placement of HLCS in "Biotin transport and metabolism".
HLCS incorporates biotin into apocarboxylases, a central step of biotin metabolism/utilization.
Broad but correct.
action: ACCEPT
reason: Correct broad biological process; HLCS is a core enzyme of biotin metabolism.
supported_by:
- reference_id: PMID:7842009
supporting_text: Holocarboxylase synthetase (HCS) plays an essential role in
biotin utilization in eukaryotic cells
- term:
id: GO:0004077
label: biotin--[biotin carboxyl-carrier protein] ligase activity
evidence_type: TAS
original_reference_id: Reactome:R-HSA-2993447
qualifier: enables
review:
summary: Reactome (TAS) biotin--protein ligase activity for the reaction "HLCS
biotinylates 6x(PCCA:PCCB)" (biotinylation of propionyl-CoA carboxylase). Correct
core molecular function on a genuine substrate.
action: ACCEPT
reason: Core molecular function; PCC is an established HLCS substrate. Duplicate
of the experimental ligase-activity annotations.
supported_by:
- reference_id: PMID:7753853
supporting_text: Holocarboxylase synthetase (HCS) catalyzes the biotinylation
of the four biotin-dependent carboxylases in human cells.
- term:
id: GO:0004077
label: biotin--[biotin carboxyl-carrier protein] ligase activity
evidence_type: TAS
original_reference_id: Reactome:R-HSA-2993799
qualifier: enables
review:
summary: Reactome (TAS) biotin--protein ligase activity for "HLCS biotinylates
6xMCCC1:6xMCCC2" (biotinylation of 3-methylcrotonyl-CoA carboxylase). Correct
core function on a genuine substrate.
action: ACCEPT
reason: Core molecular function; MCC is an established HLCS substrate.
supported_by:
- reference_id: PMID:7753853
supporting_text: Holocarboxylase synthetase (HCS) catalyzes the biotinylation
of the four biotin-dependent carboxylases in human cells.
- term:
id: GO:0004077
label: biotin--[biotin carboxyl-carrier protein] ligase activity
evidence_type: TAS
original_reference_id: Reactome:R-HSA-2993802
qualifier: enables
review:
summary: Reactome (TAS) biotin--protein ligase activity for "HLCS biotinylates
PC:Mn2+" (biotinylation of pyruvate carboxylase). Correct core function on a
genuine substrate.
action: ACCEPT
reason: Core molecular function; PC is an established HLCS substrate.
supported_by:
- reference_id: PMID:7753853
supporting_text: Holocarboxylase synthetase (HCS) catalyzes the biotinylation
of the four biotin-dependent carboxylases in human cells.
- term:
id: GO:0004077
label: biotin--[biotin carboxyl-carrier protein] ligase activity
evidence_type: TAS
original_reference_id: Reactome:R-HSA-2993814
qualifier: enables
review:
summary: Reactome (TAS) biotin--protein ligase activity for "HLCS biotinylates
ACACA:Mn2+" (biotinylation of acetyl-CoA carboxylase 1). Correct core function
on a genuine substrate.
action: ACCEPT
reason: Core molecular function; ACACA is an established HLCS substrate.
supported_by:
- reference_id: PMID:7753853
supporting_text: Holocarboxylase synthetase (HCS) catalyzes the biotinylation
of the four biotin-dependent carboxylases in human cells.
- term:
id: GO:0004077
label: biotin--[biotin carboxyl-carrier protein] ligase activity
evidence_type: TAS
original_reference_id: Reactome:R-HSA-3323184
qualifier: enables
review:
summary: Reactome (TAS) biotin--protein ligase activity within the disease reaction
"Defective HLCS does not biotinylate ACACA:Mn2+". The annotated activity is the
same core ligase function (in a defective-variant context). Correct.
action: ACCEPT
reason: Same core molecular function, annotated in a disease-variant Reactome reaction;
the function itself is correct.
supported_by:
- reference_id: PMID:7753853
supporting_text: Holocarboxylase synthetase (HCS) catalyzes the biotinylation
of the four biotin-dependent carboxylases in human cells.
- term:
id: GO:0004077
label: biotin--[biotin carboxyl-carrier protein] ligase activity
evidence_type: TAS
original_reference_id: Reactome:R-HSA-4167511
qualifier: enables
review:
summary: Reactome (TAS) biotin--protein ligase activity for "HLCS biotinylates
ACACB" (biotinylation of acetyl-CoA carboxylase 2). Correct core function on
a genuine substrate.
action: ACCEPT
reason: Core molecular function; ACACB is an established HLCS substrate.
supported_by:
- reference_id: PMID:7753853
supporting_text: Holocarboxylase synthetase (HCS) catalyzes the biotinylation
of the four biotin-dependent carboxylases in human cells.
- term:
id: GO:0004077
label: biotin--[biotin carboxyl-carrier protein] ligase activity
evidence_type: TAS
original_reference_id: Reactome:R-HSA-9035987
qualifier: enables
review:
summary: Reactome (TAS) biotin--protein ligase activity within the disease reaction
"Defective HLCS does not biotinylate 6xMCCC1:6xMCCC2". Same core ligase function
in a defective-variant context. Correct.
action: ACCEPT
reason: Same core molecular function annotated in a disease-variant Reactome reaction.
supported_by:
- reference_id: PMID:7753853
supporting_text: Holocarboxylase synthetase (HCS) catalyzes the biotinylation
of the four biotin-dependent carboxylases in human cells.
- term:
id: GO:0004077
label: biotin--[biotin carboxyl-carrier protein] ligase activity
evidence_type: TAS
original_reference_id: Reactome:R-HSA-9035988
qualifier: enables
review:
summary: Reactome (TAS) biotin--protein ligase activity within the disease reaction
"Defective HLCS does not biotinylate PC:Mn2+". Same core ligase function in a
defective-variant context. Correct.
action: ACCEPT
reason: Same core molecular function annotated in a disease-variant Reactome reaction.
supported_by:
- reference_id: PMID:7753853
supporting_text: Holocarboxylase synthetase (HCS) catalyzes the biotinylation
of the four biotin-dependent carboxylases in human cells.
- term:
id: GO:0004077
label: biotin--[biotin carboxyl-carrier protein] ligase activity
evidence_type: TAS
original_reference_id: Reactome:R-HSA-9035990
qualifier: enables
review:
summary: Reactome (TAS) biotin--protein ligase activity within the disease reaction
"Defective HLCS does not biotinylate 6x(PCCA:PCCB)". Same core ligase function
in a defective-variant context. Correct.
action: ACCEPT
reason: Same core molecular function annotated in a disease-variant Reactome reaction.
supported_by:
- reference_id: PMID:7753853
supporting_text: Holocarboxylase synthetase (HCS) catalyzes the biotinylation
of the four biotin-dependent carboxylases in human cells.
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-3323184
qualifier: located_in
review:
summary: Reactome (TAS) cytosolic localization. Consistent with the well-documented
cytosolic localization of HLCS.
action: ACCEPT
reason: HLCS acts in the cytosol; localization is directly supported experimentally.
supported_by:
- reference_id: PMID:16780588
supporting_text: the HLCS gene codes for a biotin-protein ligase and was found
to localize throughout the cytosol
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-9035987
qualifier: located_in
review:
summary: Reactome (TAS) cytosolic localization. Duplicate of the well-supported
cytosolic localization of HLCS.
action: ACCEPT
reason: HLCS acts in the cytosol; localization is directly supported experimentally.
supported_by:
- reference_id: PMID:16780588
supporting_text: the HLCS gene codes for a biotin-protein ligase and was found
to localize throughout the cytosol
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-9035988
qualifier: located_in
review:
summary: Reactome (TAS) cytosolic localization. Duplicate of the well-supported
cytosolic localization of HLCS.
action: ACCEPT
reason: HLCS acts in the cytosol; localization is directly supported experimentally.
supported_by:
- reference_id: PMID:16780588
supporting_text: the HLCS gene codes for a biotin-protein ligase and was found
to localize throughout the cytosol
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-9035990
qualifier: located_in
review:
summary: Reactome (TAS) cytosolic localization. Duplicate of the well-supported
cytosolic localization of HLCS.
action: ACCEPT
reason: HLCS acts in the cytosol; localization is directly supported experimentally.
supported_by:
- reference_id: PMID:16780588
supporting_text: the HLCS gene codes for a biotin-protein ligase and was found
to localize throughout the cytosol
- term:
id: GO:0004077
label: biotin--[biotin carboxyl-carrier protein] ligase activity
evidence_type: EXP
original_reference_id: PMID:7753853
qualifier: enables
review:
summary: Direct experimental evidence for the core biotin--protein ligase activity.
The human HCS cDNA complemented an E. coli birA (biotin ligase) mutant and promoted
biotinylation of the biotin carboxyl carrier protein and of a propionyl-CoA
carboxylase alpha fragment.
action: ACCEPT
reason: Gold-standard experimental evidence for the defining molecular function
of HLCS.
supported_by:
- reference_id: PMID:7753853
supporting_text: complementation of an Escherichia coli birA
- reference_id: PMID:7753853
supporting_text: Holocarboxylase synthetase (HCS) catalyzes the biotinylation
of the four biotin-dependent carboxylases in human cells.
- term:
id: GO:0004077
label: biotin--[biotin carboxyl-carrier protein] ligase activity
evidence_type: IDA
original_reference_id: PMID:14613969
qualifier: enables
review:
summary: Direct-assay evidence that HLCS possesses biotin--protein ligase activity.
This study, focused on the nuclear/histone role, also confirmed that HLCS retains
biotinylating activity.
action: ACCEPT
reason: Direct experimental support for the core ligase activity.
supported_by:
- reference_id: PMID:14613969
supporting_text: The attachment of biotin to apocarboxylases is catalyzed by
holocarboxylase
- reference_id: PMID:14613969
supporting_text: Nuclear HCS retains its biotinylating activity
- term:
id: GO:0043687
label: post-translational protein modification
evidence_type: IDA
original_reference_id: PMID:14613969
qualifier: involved_in
review:
summary: HLCS mediates a post-translational modification (covalent attachment
of biotin to lysine residues of acceptor proteins). This is the process-level
view of its ligase activity; the biotinylation-specific process terms (e.g.
GO:0009305 protein biotinylation) are obsolete, so this is the best available
BP term.
action: ACCEPT
reason: Correct process-level annotation of HLCS-catalysed protein biotinylation.
Biotinylation is a bona fide post-translational modification and the annotation
is directly supported.
supported_by:
- reference_id: PMID:14613969
supporting_text: The attachment of biotin to apocarboxylases is catalyzed by
holocarboxylase
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-2993447
qualifier: located_in
review:
summary: Reactome (TAS) cytosolic localization associated with the PCC-biotinylation
reaction. Consistent with cytosolic HLCS.
action: ACCEPT
reason: HLCS acts in the cytosol; localization is directly supported experimentally.
supported_by:
- reference_id: PMID:16780588
supporting_text: the HLCS gene codes for a biotin-protein ligase and was found
to localize throughout the cytosol
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-2993799
qualifier: located_in
review:
summary: Reactome (TAS) cytosolic localization associated with the MCC-biotinylation
reaction. Consistent with cytosolic HLCS.
action: ACCEPT
reason: HLCS acts in the cytosol; localization is directly supported experimentally.
supported_by:
- reference_id: PMID:16780588
supporting_text: the HLCS gene codes for a biotin-protein ligase and was found
to localize throughout the cytosol
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-2993802
qualifier: located_in
review:
summary: Reactome (TAS) cytosolic localization associated with the PC-biotinylation
reaction. Consistent with cytosolic HLCS.
action: ACCEPT
reason: HLCS acts in the cytosol; localization is directly supported experimentally.
supported_by:
- reference_id: PMID:16780588
supporting_text: the HLCS gene codes for a biotin-protein ligase and was found
to localize throughout the cytosol
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-2993814
qualifier: located_in
review:
summary: Reactome (TAS) cytosolic localization associated with the ACACA-biotinylation
reaction. Consistent with cytosolic HLCS.
action: ACCEPT
reason: HLCS acts in the cytosol; localization is directly supported experimentally.
supported_by:
- reference_id: PMID:16780588
supporting_text: the HLCS gene codes for a biotin-protein ligase and was found
to localize throughout the cytosol
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-4167511
qualifier: located_in
review:
summary: Reactome (TAS) cytosolic localization associated with the ACACB-biotinylation
reaction. Consistent with cytosolic HLCS.
action: ACCEPT
reason: HLCS acts in the cytosol; localization is directly supported experimentally.
supported_by:
- reference_id: PMID:16780588
supporting_text: the HLCS gene codes for a biotin-protein ligase and was found
to localize throughout the cytosol
- term:
id: GO:0070781
label: response to biotin
evidence_type: IDA
original_reference_id: PMID:17904341
qualifier: involved_in
review:
summary: Direct-assay evidence that HLCS responds to biotin availability - its
nuclear translocation increases with biotin supplementation, and it participates
in a proposed biotin-sensing/homeostasis loop that regulates the SMVT biotin
transporter via histone biotinylation. This is a proposed regulatory/moonlighting
role, not the core catalytic function, and its in vivo significance is debated.
action: KEEP_AS_NON_CORE
reason: Experimentally observed biotin-responsive behavior, but it reflects a
proposed nuclear/regulatory moonlighting role rather than the essential biotin-protein
ligase function. Retained as non-core.
supported_by:
- reference_id: PMID:17904341
supporting_text: the nuclear translocation of HCS depends on biotin
- reference_id: PMID:17904341
supporting_text: HCS senses biotin
- term:
id: GO:0000785
label: chromatin
evidence_type: IDA
original_reference_id: PMID:14613969
qualifier: located_in
review:
summary: Direct-assay (subnuclear fractionation/immunofluorescence) evidence that
a fraction of HLCS associates with chromatin, linked to the proposed histone-biotinylation
role. This nuclear/chromatin function is a moonlighting activity whose in vivo
physiological relevance is contested.
action: KEEP_AS_NON_CORE
reason: A real experimental observation from a specific study, but chromatin association
reflects a debated nuclear moonlighting role rather than the core cytosolic/mitochondrial
carboxylase-activation function. Retained as non-core.
supported_by:
- reference_id: PMID:14613969
supporting_text: localizes to the nucleus rather than the cytoplasm
- reference_id: PMID:14613969
supporting_text: biotinylate purified histones in vitro
- term:
id: GO:0004077
label: biotin--[biotin carboxyl-carrier protein] ligase activity
evidence_type: IMP
original_reference_id: PMID:18429047
qualifier: enables
review:
summary: Mutation-based evidence that HLCS is the biotin--protein ligase. Patient
cells homozygous for p.L216R lacked detectable HLCS enzyme activity, and recombinant
p.L216R showed severely compromised ligase activity that could not be rescued
by additional biotin, with a doubled protein turnover rate.
action: ACCEPT
reason: Loss-of-function/variant analysis directly supports the core ligase activity.
supported_by:
- reference_id: PMID:18429047
supporting_text: the turn-over rate for the mutant protein was double that of
wildtype HLCS
- term:
id: GO:0004077
label: biotin--[biotin carboxyl-carrier protein] ligase activity
evidence_type: IDA
original_reference_id: PMID:7842009
qualifier: enables
review:
summary: Direct-assay evidence for the core biotin--protein ligase activity from
the original human HCS cDNA cloning/characterization, which established HLCS
as essential for biotin utilization and homologous to E. coli BirA (biotin-[acetyl-CoA-carboxylase]
ligase).
action: ACCEPT
reason: Foundational direct experimental evidence for the defining molecular function.
supported_by:
- reference_id: PMID:7842009
supporting_text: Holocarboxylase synthetase (HCS) plays an essential role in
biotin utilization in eukaryotic cells
- term:
id: GO:0004077
label: biotin--[biotin carboxyl-carrier protein] ligase activity
evidence_type: IDA
original_reference_id: PMID:9630604
qualifier: enables
review:
summary: Direct-assay evidence for the ligase activity. Anti-HCS antibodies to
the Ile128-Pro398 region inhibited HCS enzymatic activity, mapping the catalytically
essential region; three cytosolic HCS proteins (86/82/76 kDa) were identified
in placenta.
action: ACCEPT
reason: Direct experimental support for the core molecular function.
supported_by:
- reference_id: PMID:9630604
supporting_text: we have identified, in human placenta, three cytosolic HCS
- reference_id: PMID:9630604
supporting_text: essential for the catalytic activity of
- term:
id: GO:0005652
label: nuclear lamina
evidence_type: IDA
original_reference_id: PMID:14613969
qualifier: located_in
review:
summary: Direct-assay (subnuclear fractionation) evidence that a fraction of HLCS
associates with the nuclear lamina, part of the proposed nuclear/histone-biotinylation
role. This moonlighting localization is debated and is not the core function.
action: KEEP_AS_NON_CORE
reason: Real experimental observation but reflects a contested nuclear moonlighting
role, not the core cytosolic/mitochondrial carboxylase-activation function.
Retained as non-core.
supported_by:
- reference_id: PMID:14613969
supporting_text: localizes to the nucleus rather than the cytoplasm
- term:
id: GO:0005829
label: cytosol
evidence_type: IDA
original_reference_id: PMID:9630604
qualifier: located_in
review:
summary: Direct-assay evidence for cytosolic localization; HLCS proteins were
identified as cytosolic in human placenta, and cell-free-synthesized HCS was
not translocated into mitochondria, consistent with a cytosolic pool.
action: ACCEPT
reason: Direct experimental support for cytosolic localization, a core compartment
for HLCS.
supported_by:
- reference_id: PMID:9630604
supporting_text: we have identified, in human placenta, three cytosolic HCS
- term:
id: GO:0009374
label: biotin binding
evidence_type: IDA
original_reference_id: PMID:14613969
qualifier: enables
review:
summary: Direct-assay evidence that HLCS binds biotin, the substrate it activates
(as biotinyl-5'-AMP) prior to transfer to apocarboxylases. A supporting molecular
function underpinning the core ligase activity.
action: ACCEPT
reason: Biotin binding is an integral part of the HLCS catalytic mechanism and
is directly supported; retained as a supporting molecular function.
supported_by:
- reference_id: PMID:14613969
supporting_text: Nuclear HCS retains its biotinylating activity
- term:
id: GO:0016363
label: nuclear matrix
evidence_type: IDA
original_reference_id: PMID:14613969
qualifier: located_in
review:
summary: Direct-assay (subnuclear fractionation) evidence associating a fraction
of HLCS with the nuclear matrix, part of the proposed nuclear/histone role.
Debated moonlighting localization, not the core function.
action: KEEP_AS_NON_CORE
reason: Real experimental observation but reflects the contested nuclear moonlighting
role rather than the core function. Retained as non-core.
supported_by:
- reference_id: PMID:14613969
supporting_text: localizes to the nucleus rather than the cytoplasm
- term:
id: GO:0019899
label: enzyme binding
evidence_type: IPI
original_reference_id: PMID:19157941
qualifier: enables
review:
summary: Physical-interaction evidence (Y2H) with a propionyl-CoA carboxylase-derived
polypeptide (p67; partner P05165 = PCCA). This captures HLCS binding to its
carboxylase (apoenzyme) substrate via the N- and C-terminal domains, i.e. substrate
recognition preceding biotinylation.
action: ACCEPT
reason: More informative than bare protein binding - the partner PCCA is a genuine
HLCS substrate (an enzyme), and the interaction reflects substrate recognition
central to HLCS catalysis. Retained.
supported_by:
- reference_id: PMID:19157941
supporting_text: essential for biotinylation of carboxylases by HCS
- reference_id: PMID:19157941
supporting_text: N- and C-termini play roles in substrate recognition
- term:
id: GO:0005829
label: cytosol
evidence_type: HDA
original_reference_id: PMID:16780588
qualifier: located_in
review:
summary: High-throughput direct-assay (transfected-cell array localization screen
of chromosome 21 proteins) placing HLCS in the cytosol. Consistent with the
broader experimental and Reactome cytosolic annotations.
action: ACCEPT
reason: Consistent cytosolic localization, corroborating multiple other lines
of evidence.
supported_by:
- reference_id: PMID:16780588
supporting_text: the HLCS gene codes for a biotin-protein ligase and was found
to localize throughout the cytosol
core_functions:
- description: Biotin--protein ligase (holocarboxylase synthetase) that covalently
attaches biotin to the biotin carboxyl carrier lysine of the biotin-dependent
apocarboxylases (pyruvate carboxylase, propionyl-CoA carboxylase, 3-methylcrotonyl-CoA
carboxylase, and the acetyl-CoA carboxylases ACACA/ACACB), activating them. A
single HLCS acts in both the cytosol and the mitochondrion. Catalysis proceeds
via ATP-dependent formation of biotinyl-5'-AMP followed by transfer of biotin
to the acceptor lysine; biotin binding and ATP binding are integral to this activity.
molecular_function:
id: GO:0004077
label: biotin--[biotin carboxyl-carrier protein] ligase activity
supported_by:
- reference_id: PMID:7753853
supporting_text: Holocarboxylase synthetase (HCS) catalyzes the biotinylation
of the four biotin-dependent carboxylases in human cells.
- reference_id: PMID:7753853
supporting_text: a single HCS is targeted to the mitochondria and cytoplasm
directly_involved_in:
- id: GO:0043687
label: post-translational protein modification
- id: GO:0006768
label: biotin metabolic process
locations:
- id: GO:0005829
label: cytosol
- id: GO:0005739
label: mitochondrion
references:
- 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:0000107
title: Automatic transfer of experimentally verified manual GO annotation data to
orthologs using Ensembl Compara
findings: []
- id: GO_REF:0000117
title: Electronic Gene Ontology annotations created by ARBA machine learning models
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: PMID:14613969
title: 'Reduced histone biotinylation in multiple carboxylase deficiency patients:
a nuclear role for holocarboxylase synthetase.'
findings: []
- id: PMID:16780588
title: Cell array-based intracellular localization screening reveals novel functional
features of human chromosome 21 proteins.
findings: []
- id: PMID:17904341
title: Holocarboxylase synthetase regulates expression of biotin transporters by
chromatin remodeling events at the SMVT locus.
findings: []
- id: PMID:18429047
title: Reduced half-life of holocarboxylase synthetase from patients with severe
multiple carboxylase deficiency.
findings: []
- id: PMID:19157941
title: N- and C-terminal domains in human holocarboxylase synthetase participate
in substrate recognition.
findings: []
- id: PMID:20085763
title: The N-terminal domain of human holocarboxylase synthetase facilitates biotinylation
via direct interaction with the substrate protein.
findings: []
- id: PMID:21044950
title: Genome-wide YFP fluorescence complementation screen identifies new regulators
for telomere signaling in human cells.
findings: []
- id: PMID:28514442
title: Architecture of the human interactome defines protein communities and disease
networks.
findings: []
- id: PMID:32296183
title: A reference map of the human binary protein interactome.
findings: []
- id: PMID:33961781
title: Dual proteome-scale networks reveal cell-specific remodeling of the human
interactome.
findings: []
- id: PMID:7753853
title: Isolation of a cDNA encoding human holocarboxylase synthetase by functional
complementation of a biotin auxotroph of Escherichia coli.
findings: []
- id: PMID:7842009
title: Isolation and characterization of mutations in the human holocarboxylase
synthetase cDNA.
findings: []
- id: PMID:9630604
title: Identification of holocarboxylase synthetase (HCS) proteins in human placenta.
findings: []
- id: Reactome:R-HSA-196780
title: Biotin transport and metabolism
findings: []
- id: Reactome:R-HSA-2993447
title: HLCS biotinylates 6x(PCCA:PCCB)
findings: []
- id: Reactome:R-HSA-2993799
title: HLCS biotinylates 6xMCCC1:6xMCCC2
findings: []
- id: Reactome:R-HSA-2993802
title: HLCS biotinylates PC:Mn2+
findings: []
- id: Reactome:R-HSA-2993814
title: HLCS biotinylates ACACA:Mn2+
findings: []
- id: Reactome:R-HSA-3323184
title: Defective HLCS does not biotinylate ACACA:Mn2+
findings: []
- id: Reactome:R-HSA-4167511
title: HLCS biotinylates ACACB
findings: []
- id: Reactome:R-HSA-9035987
title: Defective HLCS does not biotinylate 6xMCCC1:6xMCCC2
findings: []
- id: Reactome:R-HSA-9035988
title: Defective HLCS does not biotinylate PC:Mn2+
findings: []
- id: Reactome:R-HSA-9035990
title: Defective HLCS does not biotinylate 6x(PCCA:PCCB)
findings: []