MTHFD1L

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005829 cytosol	IBA GO_REF:0000033	MARK AS OVER ANNOTATED	Summary: Phylogenetic (IBA) cytosol annotation propagated across the C1-THF synthase family, which includes the cytosolic paralog MTHFD1. The experimentally characterized human MTHFD1L protein is exclusively mitochondrial (IDA in PMID:12937168), so a cytosolic location is not supported for this gene. Reason: Human MTHFD1L localizes exclusively to mitochondria; the cytosol call is an IBA artifact of grouping with the cytosolic paralog MTHFD1. Not removed because the underlying family-level tree is legitimate, but it does not reflect this gene's location. Propagation Review Root cause: PROPAGATION BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: UniProtKB:P11586 · MTHFD1 (human cytosolic C1-THF synthase) SUPPORTS SOURCE BUT NOT TARGET Cytosolic localization is correct for the paralog MTHFD1 but does not transfer to the mitochondrial MTHFD1L. PANTHER:PTN000002250 · C1-THF synthase family node (cytosolic members) SUPPORTS SOURCE BUT NOT TARGET Family node mixes cytosolic and mitochondrial isozymes.
GO:0004329 formate-tetrahydrofolate ligase activity	IBA GO_REF:0000033	ACCEPT	Summary: Formate--tetrahydrofolate ligase (10-formyl-THF synthetase) is the defining and experimentally confirmed molecular function of MTHFD1L. The IBA correctly captures the core catalytic activity. Reason: Direct enzyme assays (PMID:12937168, PMID:16171773) confirm this as the sole catalytic activity; the phylogenetic inference is fully consistent.
GO:0005739 mitochondrion	IBA GO_REF:0000033	ACCEPT	Summary: Mitochondrial localization is directly demonstrated for the human protein and consistent with the phylogenetic inference. Reason: Supported by IDA (PMID:12937168) showing the V5-tagged protein exclusively in mitochondrial fractions; the more specific matrix term is used in core_functions.
GO:0009257 10-formyltetrahydrofolate biosynthetic process	IBA GO_REF:0000033	ACCEPT	Summary: The ligase reaction, run left-to-right, synthesizes 10-formyl-THF from THF + formate + ATP. This IBA is consistent with the experimental IDA on the same term. Reason: Consistent with the reversible EC 6.3.4.3 reaction and with the IDA annotation from PMID:12937168.
GO:0004329 formate-tetrahydrofolate ligase activity	IEA GO_REF:0000120	ACCEPT	Summary: Electronic (InterPro/RHEA/EC 6.3.4.3) assertion of the core catalytic activity, redundant with and consistent with the experimental EXP/IDA annotations. Reason: Correctly maps EC 6.3.4.3 / IPR000559 to the enzyme's confirmed activity.
GO:0004488 methylenetetrahydrofolate dehydrogenase (NADP+) activity	IEA GO_REF:0000002	REMOVE	Summary: InterPro predicts a methylene-THF dehydrogenase activity from the retained N-terminal dehydrogenase/cyclohydrolase domain. However, this activity was specifically assayed for and NOT detected: MTHFD1L is monofunctional, possessing only 10-formyl-THF synthetase activity. The dehydrogenase domain is present but catalytically inactive. Reason: Directly contradicted by enzyme assays. PMID:16171773 revealed only the presence of 10-formyl-THF synthetase activity; PMID:12937168 detected no dehydrogenase activity with either NADP+ or NAD+. Clearly-wrong IEA (domain-based over-prediction of an ancestral activity lost in this paralog).
GO:0005524 ATP binding	IEA GO_REF:0000002	ACCEPT	Summary: ATP binding is required by the ATP-dependent ligase mechanism and is supported experimentally (ATP Km determined; P-loop/ATP-binding site annotated). Reason: Consistent with EC 6.3.4.3 and with the experimental IDA on ATP binding (PMID:16171773).
GO:0005739 mitochondrion	IEA GO_REF:0000120	ACCEPT	Summary: Electronic mitochondrial localization, consistent with experimental IDA. Reason: Corroborated by IDA (PMID:12937168) and HTP/HPA evidence.
GO:0005759 mitochondrial matrix	IEA GO_REF:0000117	ACCEPT	Summary: Mitochondrial matrix is the correct, specific compartment for this soluble one-carbon metabolism enzyme, consistent with the Reactome TAS matrix annotations. Reason: Matrix localization is appropriate for a soluble folate-interconverting enzyme and agrees with Reactome (R-HSA-5696839, R-HSA-6801456). Used as the core location.
GO:0015942 formate metabolic process	IEA GO_REF:0000117	ACCEPT	Summary: MTHFD1L is central to mitochondrial formate metabolism, generating the formate exported to the cytosol. Supported experimentally (IDA from PMID:16171773). Reason: Core biological process; also supported by an experimental IDA.
GO:0046394 carboxylic acid biosynthetic process	IEA GO_REF:0000117	MARK AS OVER ANNOTATED	Summary: Generic parent term (formate is a carboxylic acid). Over-general relative to the specific formate/one-carbon roles already captured by more informative terms. Reason: Too high-level to be informative; the specific formate metabolic process and tetrahydrofolate interconversion terms convey the relevant biology.
GO:0046653 tetrahydrofolate metabolic process	IEA GO_REF:0000117	KEEP AS NON CORE	Summary: Correct high-level folate-cofactor process. The more specific tetrahydrofolate interconversion term better captures the enzyme's role. Reason: Accurate but general; retained as supporting context, with GO:0035999 as the core-level process.
GO:0001843 neural tube closure	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Neural tube closure is a downstream developmental phenotype: loss of the mouse ortholog (Q3V3R1) causes neural tube defects. This is a physiological consequence of impaired one-carbon metabolism, not the core molecular function, and is transferred from mouse. Reason: Real but indirect developmental role, inferred from the mouse ortholog; keep as non-core context for the metabolic function.
GO:0048702 embryonic neurocranium morphogenesis	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Craniofacial morphogenesis phenotype transferred from the mouse ortholog; a downstream developmental consequence of the metabolic defect rather than a core function. Reason: Indirect developmental phenotype inferred from mouse; non-core.
GO:0048703 embryonic viscerocranium morphogenesis	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Craniofacial morphogenesis phenotype transferred from the mouse ortholog; a downstream developmental consequence, not the core molecular function. Reason: Indirect developmental phenotype inferred from mouse; non-core.
GO:0035999 tetrahydrofolate interconversion	IEA GO_REF:0000041	ACCEPT	Summary: Tetrahydrofolate interconversion (movement of one-carbon units among THF species) is the core pathway to which MTHFD1L contributes, matching the UniPathway assignment (UPA00193). Reason: Accurately captures the enzyme's role in folate one-carbon interconversion; selected as a core biological process.
GO:0005739 mitochondrion	IDA GO_REF:0000052	ACCEPT	Summary: Immunofluorescence-based (HPA) mitochondrial localization, consistent with the primary experimental IDA and the enzyme's biology. Reason: Corroborates mitochondrial localization; core location is the matrix.
GO:0004329 formate-tetrahydrofolate ligase activity	EXP PMID:16171773 Enzymatic characterization of human mitochondrial C1-tetrahy...	ACCEPT	Summary: Direct enzymatic characterization of purified recombinant human MTHFD1L established formate--THF ligase (10-formyl-THF synthetase) as its sole catalytic activity, with full steady-state kinetics. This is the strongest evidence for the core molecular function. Reason: Definitive experimental support for GO:0004329; PMID:16171773 reports that enzyme assays revealed only 10-formyl-THF synthetase activity.
GO:0005739 mitochondrion	HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an...	ACCEPT	Summary: High-throughput quantitative mitochondrial proteome study identifying MTHFD1L among high-confidence mitochondrial proteins, corroborating its localization. Reason: Consistent with the primary IDA; mitochondrial localization is well established.
GO:0009257 10-formyltetrahydrofolate biosynthetic process	IDA PMID:12937168 Human mitochondrial C1-tetrahydrofolate synthase: gene struc...	ACCEPT	Summary: Expression of the human cDNA in yeast produced elevated 10-formyl-THF synthetase activity, demonstrating the enzyme's participation in 10-formyl-THF formation (the left-to-right ligase direction). Reason: Supports the biosynthetic-direction process annotation; the human cDNA overexpressed 10-formyl-THF synthetase activity approximately 9-fold in yeast (PMID:12937168).
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-5696839	ACCEPT	Summary: Reactome places the MTHFD1L ligation reaction (formate + THF -> 10-formyl-THF) in the mitochondrial matrix, the correct compartment for this soluble enzyme. Reason: Accurate specific compartment; adopted as the core location.
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-6801456	ACCEPT	Summary: Reactome places the reverse MTHFD1L reaction (10-formyl-THF -> formate + THF), which releases formate for export, in the mitochondrial matrix. Reason: Correct compartment; this reaction direction underlies the enzyme's main physiological role of exporting one-carbon units as formate.
GO:0001843 neural tube closure	ISS GO_REF:0000024	KEEP AS NON CORE	Summary: Sequence-similarity transfer from the mouse ortholog (Q3V3R1), whose loss causes neural tube defects. Downstream developmental phenotype rather than the core molecular function. Reason: Indirect developmental role inferred from mouse; non-core context.
GO:0048702 embryonic neurocranium morphogenesis	ISS GO_REF:0000024	KEEP AS NON CORE	Summary: ISS transfer from the mouse ortholog of a craniofacial morphogenesis role; a downstream developmental consequence of the metabolic function. Reason: Indirect developmental phenotype inferred from mouse; non-core.
GO:0048703 embryonic viscerocranium morphogenesis	ISS GO_REF:0000024	KEEP AS NON CORE	Summary: ISS transfer from the mouse ortholog of a craniofacial morphogenesis role; a downstream developmental consequence of the metabolic function. Reason: Indirect developmental phenotype inferred from mouse; non-core.
GO:0016020 membrane	HDA PMID:19946888 Defining the membrane proteome of NK cells.	MARK AS OVER ANNOTATED	Summary: Detected in a high-throughput NK-cell membrane proteome study. MTHFD1L is a soluble mitochondrial matrix enzyme with no transmembrane segments; the membrane assignment is a co-fractionation/proteomics artifact and does not reflect the true localization. Reason: Membrane call is inconsistent with the enzyme's soluble matrix biology and no TM regions in UniProt; retained (not removed) per policy for experimental HDA, but flagged as an over-annotation.
GO:0004329 formate-tetrahydrofolate ligase activity	IDA PMID:12937168 Human mitochondrial C1-tetrahydrofolate synthase: gene struc...	ACCEPT	Summary: 10-formyl-THF synthetase (formate--THF ligase) activity demonstrated by expressing the human cDNA in an ade3 yeast strain, giving ~9-fold elevated synthetase activity. Core molecular function. Reason: Supports GO:0004329; the human cDNA overexpressed 10-formyl-THF synthetase activity approximately 9-fold in yeast (PMID:12937168).
GO:0005524 ATP binding	IDA PMID:16171773 Enzymatic characterization of human mitochondrial C1-tetrahy...	ACCEPT	Summary: ATP is a required co-substrate of the ligase; steady-state kinetics for the purified enzyme included ATP Km determinations, supporting ATP binding. Reason: Core function accompanying the ligase activity; PMID:16171773 reports ATP Km values for the purified enzyme.
GO:0005739 mitochondrion	IDA PMID:12937168 Human mitochondrial C1-tetrahydrofolate synthase: gene struc...	ACCEPT	Summary: Primary experimental evidence for mitochondrial localization: a V5-tagged full-length construct was detected exclusively in mitochondrial fractions of CHO cells. Reason: Strongest localization evidence; PMID:12937168 confirms the mitochondrial localization of the protein.
GO:0006760 folic acid-containing compound metabolic process	IDA PMID:12937168 Human mitochondrial C1-tetrahydrofolate synthase: gene struc...	KEEP AS NON CORE	Summary: Broad but correct: MTHFD1L metabolizes folate (tetrahydrofolate) coenzymes. More specific one-carbon/THF-interconversion terms capture the core role. Reason: Accurate high-level folate-metabolism term; retained as context, with GO:0035999 as the core process.
GO:0015942 formate metabolic process	IDA PMID:16171773 Enzymatic characterization of human mitochondrial C1-tetrahy...	ACCEPT	Summary: Experimentally supported role in formate metabolism: the enzyme interconverts formate and 10-formyl-THF, and physiologically generates the formate exported from mitochondria. Reason: Supported by the enzymatic characterization (PMID:16171773) of the formate--THF ligase reaction; core biological process.
GO:0042803 protein homodimerization activity	IDA PMID:16171773 Enzymatic characterization of human mitochondrial C1-tetrahy...	KEEP AS NON CORE	Summary: Gel filtration and crosslinking showed MTHFD1L is a homodimer in solution, the functional oligomeric state of the enzyme. Reason: A real structural property but not the enzyme's catalytic core function; PMID:16171773 shows it exists as a homodimer in solution.

Gene Description

Existing Annotations Review

Core Functions

Formate--tetrahydrofolate ligase (10-formyl-THF synthetase): reversible, ATP-dependent interconversion of tetrahydrofolate + formate + ATP with 10-formyltetrahydrofolate + ADP + phosphate, using polyglutamylated tetrahydrofolate as the physiological substrate.

Binds ATP as the co-substrate driving the ligase reaction that activates formate onto tetrahydrofolate.

References

📚 Additional Documentation

Notes

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