DTYMK is thymidylate kinase (dTMP kinase; EC 2.7.4.9), a small cytosolic P-loop nucleotide kinase that catalyses the ATP- and Mg2+-dependent phosphorylation of thymidine monophosphate (dTMP) to thymidine diphosphate (dTDP) (dTMP + ATP -> dTDP + ADP). This is the common penultimate step in the synthesis of the DNA building block dTTP: the de novo route (dUMP -> dTMP via thymidylate synthase) and the salvage route (thymidine -> dTMP via thymidine kinase) both converge on dTMP kinase, making it the bottleneck for dTTP biosynthesis; dTDP is subsequently phosphorylated to dTTP by nucleoside diphosphate kinase. Because dTTP cannot be generated by any bypass, the enzyme is essential for DNA replication and genome integrity; its expression and activity peak in S phase. The active enzyme is a homodimer and has been crystallised extensively in complex with dTMP/ATP analogues. It also activates thymidine-analogue prodrugs (e.g. zidovudine/AZT monophosphate). Biallelic loss-of-function variants cause a severe childhood-onset neurodegenerative disorder with progressive microcephaly.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0004798
dTMP kinase activity
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetically inferred dTMP kinase activity, the defining molecular function of the thymidylate kinase family. This is correct and central for DTYMK and is independently supported by direct human experimental evidence.
Reason: dTMP kinase activity is the core, experimentally validated molecular function of the human enzyme, catalysing dTMP + ATP -> dTDP + ADP. The IBA call is consistent with abundant human EXP/IDA evidence.
Supporting Evidence:
file:human/DTYMK/DTYMK-uniprot.txt
Catalyzes the phosphorylation of thymidine monophosphate
PMID:34918187
catalyzes the penultimate step in dTTP biosynthesis
|
|
GO:0005737
cytoplasm
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetically inferred cytoplasmic localization. DTYMK is a small soluble kinase with no targeting signal and is described as cytosolic; cytoplasm is a correct, appropriately general compartment.
Reason: Consistent with the cytosolic localization of the enzyme reported by Reactome and with GOA cytosol (GO:0005829) annotations.
Supporting Evidence:
Reactome:R-HSA-73635
Cytosolic deoxythymidylate kinase (DTYMK) catalyzes the reversible reaction
|
|
GO:0006233
dTDP biosynthetic process
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetically inferred involvement in dTDP biosynthesis. This is the direct product-forming reaction of DTYMK (dTMP -> dTDP) and is a core process for the gene.
Reason: The immediate reaction product of DTYMK is dTDP; this is the enzyme's direct biosynthetic contribution and is experimentally supported.
Supporting Evidence:
file:human/DTYMK/DTYMK-uniprot.txt
the immediate precursor for the
PMID:34918187
The thymidine de novo and salvage pathways converge at the point of the phosphorylation of dTMP to dTDP by dTMPK
|
|
GO:0005739
mitochondrion
|
IBA
GO_REF:0000033 |
MARK AS OVER ANNOTATED |
Summary: Phylogenetically inferred mitochondrial localization. The human enzyme is established as cytosolic, and this IBA call is propagated from a subset of orthologs; it is weakly supported and not the functionally relevant compartment for human DTYMK.
Reason: DTYMK is a small soluble protein with no mitochondrial targeting sequence and is described as cytosolic deoxythymidylate kinase (Reactome). The mitochondrial IBA is over-propagated from the PANTHER family; the established and functionally relevant compartment is the cytosol/cytoplasm.
Propagation Review
Root cause:
PROPAGATION BAD
Failure modes:
COMPARTMENT OR COMPLEX MISMATCH
Supporting Evidence:
Reactome:R-HSA-73635
Cytosolic deoxythymidylate kinase (DTYMK) catalyzes the reversible reaction
|
|
GO:0006227
dUDP biosynthetic process
|
IBA
GO_REF:0000033 |
KEEP AS NON CORE |
Summary: Phylogenetically inferred involvement in dUDP biosynthesis, reflecting the enzyme's ability to also phosphorylate dUMP to dUDP. This is a secondary/promiscuous activity, not the biological purpose of DTYMK, which is dTTP synthesis.
Reason: Reactome records dUMP as an alternative substrate (dUMP or TMP + ATP -> dUDP or TDP), so dUDP formation is biochemically plausible, but the physiological role of DTYMK is the synthesis of thymidine nucleotides (dTDP/dTTP). Retain as a non-core, secondary activity rather than a core function.
Supporting Evidence:
Reactome:R-HSA-73635
dUMP or TMP + ATP <=> dUDP or TDP + ADP [DTYMK]
|
|
GO:0006235
dTTP biosynthetic process
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetically inferred involvement in dTTP biosynthesis. DTYMK performs the penultimate, common step of dTTP synthesis (dTMP -> dTDP), and is the essential bottleneck for making dTTP; this is a core biological process for the gene.
Reason: Both de novo and salvage routes converge on DTYMK, which is indispensable for dTTP biosynthesis and DNA replication; loss of function completely blocks dTTP synthesis.
Supporting Evidence:
PMID:34918187
This makes dTMPK the bottleneck for dTTP biosynthesis
file:human/DTYMK/DTYMK-uniprot.txt
Pyrimidine metabolism; dTTP biosynthesis.
|
|
GO:0005634
nucleus
|
IBA
GO_REF:0000033 |
MARK AS OVER ANNOTATED |
Summary: Phylogenetically inferred nuclear localization, propagated from a subset of orthologs. The human enzyme is characterised as cytosolic, and nuclear localization is weakly supported.
Reason: DTYMK has no nuclear-localization signal and is described as cytosolic (Reactome). Although dNTP synthesis serves nuclear DNA replication, the enzyme itself acts in the cytosol; the nuclear IBA is an over-propagation.
Propagation Review
Root cause:
PROPAGATION BAD
Failure modes:
COMPARTMENT OR COMPLEX MISMATCH
Supporting Evidence:
Reactome:R-HSA-73635
Cytosolic deoxythymidylate kinase (DTYMK) catalyzes the reversible reaction
|
|
GO:0004798
dTMP kinase activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Electronic annotation of dTMP kinase activity from combined IEA methods (ARBA, InterPro, RHEA/EC mapping). This correctly captures the defining molecular function.
Reason: Matches the experimentally validated function and the RHEA:13517 / EC:2.7.4.9 reaction; a correct, well-supported electronic call.
Supporting Evidence:
file:human/DTYMK/DTYMK-uniprot.txt
Reaction=dTMP + ATP = dTDP + ADP
|
|
GO:0005524
ATP binding
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: InterPro-based electronic annotation of ATP binding. DTYMK is a P-loop ATP-dependent kinase; ATP binding is directly confirmed by crystal structures.
Reason: ATP is the phosphoryl donor and is bound at a defined P-loop site (structurally characterised, PMID:12614151); the electronic call is correct and supported by experimental evidence.
Supporting Evidence:
file:human/DTYMK/DTYMK-uniprot.txt
Reaction=dTMP + ATP = dTDP + ADP
|
|
GO:0006233
dTDP biosynthetic process
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Electronic annotation of involvement in dTDP biosynthesis, matching the direct product-forming reaction of DTYMK.
Reason: dTDP is the immediate reaction product; the call is consistent with experimental and IBA evidence.
Supporting Evidence:
file:human/DTYMK/DTYMK-uniprot.txt
the immediate precursor for the
|
|
GO:0006235
dTTP biosynthetic process
|
IEA
GO_REF:0000041 |
ACCEPT |
Summary: Electronic annotation (UniPathway mapping) of involvement in dTTP biosynthesis, matching the UniProt pathway assignment "Pyrimidine metabolism; dTTP biosynthesis".
Reason: DTYMK performs the penultimate step of dTTP biosynthesis; the UniPathway-derived call is correct.
Supporting Evidence:
file:human/DTYMK/DTYMK-uniprot.txt
Pyrimidine metabolism; dTTP biosynthesis.
|
|
GO:0004798
dTMP kinase activity
|
EXP
PMID:2017365 Molecular cloning and expression of the human deoxythymidyla... |
ACCEPT |
Summary: Human dTMP kinase cDNA cloned by functional complementation of a yeast dTMP kinase temperature-sensitive mutant; expression in yeast produces dTMP kinase activity, experimentally establishing the molecular function.
Reason: Direct experimental demonstration that the human gene product has dTMP kinase activity (phosphorylates dTMP to dTDP with ATP and Mg2+).
Supporting Evidence:
PMID:2017365
the cloned human cDNA, when expressed in yeast, produces dTMP kinase
activity.
PMID:2017365
(Deoxy)thymidylate (dTMP) kinase is an enzyme which phosphorylates dTMP to dTDP
in the presence of ATP and magnesium.
|
|
GO:0004798
dTMP kinase activity
|
EXP
PMID:34918187 DTYMK is essential for genome integrity and neuronal surviva... |
ACCEPT |
Summary: dTMPK enzyme activity measured directly in patient fibroblasts (severely reduced in individuals with biallelic DTYMK variants), and the enzyme is defined as catalysing the phosphorylation of dTMP to dTDP, confirming dTMP kinase activity for the human protein.
Reason: Provides human experimental (activity assay) evidence for dTMP kinase activity and links loss of this activity to disease; the affected step is the phosphorylation of dTMP to dTDP.
Supporting Evidence:
PMID:34918187
The thymidine de novo and salvage pathways converge at the point of the phosphorylation of dTMP to dTDP by dTMPK
PMID:34918187
dTMPK enzyme activity of the individual is significantly lower than those of the parents
|
|
GO:0005739
mitochondrion
|
HTP
PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... |
MARK AS OVER ANNOTATED |
Summary: High-throughput mitochondrial proteomics (MitoCoP) call. DTYMK is an established cytosolic enzyme; a proteomics dataset hit likely reflects co-purification or dual/low-level reporting rather than a bona fide mitochondrial function.
Reason: DTYMK has no mitochondrial targeting presequence and its characterised, functional compartment is the cytosol (Reactome). A single HTP proteomics localization does not establish the mitochondrion as a functional site for this soluble kinase; treat as an over-annotation relative to the core cytosolic localization.
Supporting Evidence:
PMID:34800366
high-confidence proteome of >1,100 proteins
Reactome:R-HSA-73635
Cytosolic deoxythymidylate kinase (DTYMK) catalyzes the reversible reaction
|
|
GO:0004798
dTMP kinase activity
|
IDA
PMID:12614151 Structures of human thymidylate kinase in complex with prodr... |
ACCEPT |
Summary: Structural and steady-state kinetic characterisation of human thymidylate kinase (TMPK) converting thymidine monophosphate analogues to the corresponding diphosphates, directly demonstrating dTMP kinase activity.
Reason: Crystal structures with substrate/product analogues plus steady-state kinetics directly establish the dTMP kinase catalytic activity of the human enzyme.
Supporting Evidence:
PMID:12614151
the enzyme thymidylate kinase (TMPK) of clinically important
thymidine monophosphate analogues to the corresponding diphosphates
|
|
GO:0005524
ATP binding
|
IDA
PMID:12614151 Structures of human thymidylate kinase in complex with prodr... |
ACCEPT |
Summary: Crystal structures solved with ADP or the ATP analogue AppNHp bound at the phosphoryl-donor site, providing direct experimental evidence of ATP binding.
Reason: Structures with the ATP analogue at the phosphoryl-donor site directly demonstrate ATP binding by human thymidylate kinase.
Supporting Evidence:
PMID:12614151
with either ADP or the ATP analogue AppNHp
at the phosphoryl donor site
|
|
GO:0006233
dTDP biosynthetic process
|
IDA
PMID:12614151 Structures of human thymidylate kinase in complex with prodr... |
ACCEPT |
Summary: Direct assay of the conversion of thymidine monophosphates to the corresponding diphosphates by human thymidylate kinase, supporting involvement in dTDP biosynthesis.
Reason: The reaction assayed produces the diphosphate (dTDP) from the monophosphate (dTMP), the direct biosynthetic contribution of DTYMK.
Supporting Evidence:
PMID:12614151
thymidine monophosphate analogues to the corresponding diphosphates
|
|
GO:0046105
thymidine biosynthetic process
|
IDA
PMID:12614151 Structures of human thymidylate kinase in complex with prodr... |
MARK AS OVER ANNOTATED |
Summary: Annotation to thymidine biosynthetic process. This mislabels the biology: DTYMK acts on the nucleotide dTMP (producing dTDP), not on the nucleoside thymidine, and the process it serves is dTDP/dTTP biosynthesis, not thymidine biosynthesis.
Reason: The paper characterises phosphorylation of thymidine monophosphate to the diphosphate; it does not establish biosynthesis of thymidine (the nucleoside). The more accurate process terms are dTDP biosynthetic process (GO:0006233) and dTTP biosynthetic process (GO:0006235), both already annotated. Treat this term as an over-annotation relative to the correctly captured dTDP/dTTP processes.
Supporting Evidence:
PMID:12614151
thymidine monophosphate analogues to the corresponding diphosphates
|
|
GO:0046105
thymidine biosynthetic process
|
TAS
PMID:8024690 Human dTMP kinase: gene expression and enzymatic activity co... |
MARK AS OVER ANNOTATED |
Summary: Author-statement annotation to thymidine biosynthetic process. As with the IDA above, the described activity is phosphorylation of dTMP to the diphosphate en route to dTTP, not biosynthesis of the nucleoside thymidine.
Reason: DTYMK catalyses dTMP -> dTDP and is essential for dTTP synthesis, not for making thymidine; the correct process terms (dTDP/dTTP biosynthetic process) are already annotated. Over-annotation via a mismatched process term.
Supporting Evidence:
PMID:8024690
dTMP kinase (E.C.2.7.4.9.) catalyzes the phosphorylation of dTMP to the
corresponding diphosphate.
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-73635 |
ACCEPT |
Summary: Reactome traceable-author-statement localizing DTYMK to the cytosol, consistent with the enzyme being a small soluble cytosolic kinase. This is the core, functionally relevant compartment.
Reason: Reactome explicitly describes cytosolic deoxythymidylate kinase; matches the established localization of the human enzyme.
Supporting Evidence:
Reactome:R-HSA-73635
Cytosolic deoxythymidylate kinase (DTYMK) catalyzes the reversible reaction
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-75126 |
ACCEPT |
Summary: Reactome traceable-author-statement (reverse reaction module) localizing DTYMK to the cytosol; duplicate of the cytosol call and equally correct.
Reason: Consistent with the cytosolic localization of the human enzyme described by Reactome.
Supporting Evidence:
Reactome:R-HSA-75126
Cytosolic deoxythymidylate kinase (DTYMK) catalyzes the reversible reaction
|
|
GO:0004798
dTMP kinase activity
|
IDA
PMID:8845311 Molecular characterization of the murine thymidylate kinase ... |
ACCEPT |
Summary: Characterisation of the (murine) thymidylate kinase gene, defining TMK as catalysing the essential conversion of dTMP to dTDP; supports the conserved dTMP kinase activity of the orthologous mammalian enzyme.
Reason: Establishes thymidylate kinase activity (dTMP -> dTDP) for the mammalian enzyme; the function is directly and abundantly supported for the human protein by other evidence.
Supporting Evidence:
PMID:8845311
Thymidylate kinase (TMK) catalyzes an essential reaction of converting dTMP to
dTDP, leading to formation of the DNA precursor dTTP.
|
|
GO:0004798
dTMP kinase activity
|
TAS
PMID:8024690 Human dTMP kinase: gene expression and enzymatic activity co... |
ACCEPT |
Summary: Traceable-author-statement annotation of dTMP kinase activity for the human enzyme, defined as catalysing the phosphorylation of dTMP to the corresponding diphosphate.
Reason: Directly states the dTMP kinase catalytic activity of human dTMP kinase; concordant with the EXP/IDA evidence.
Supporting Evidence:
PMID:8024690
dTMP kinase (E.C.2.7.4.9.) catalyzes the phosphorylation of dTMP to the
corresponding diphosphate.
|
UniProtKB:P23919 (KTHY_HUMAN), HGNC:3061, gene symbol DTYMK (synonyms CDC8, TMPK, TYMK).
EC 2.7.4.9. 212 aa, cytosolic. Belongs to the thymidylate kinase family (P-loop NTPase fold).
DTYMK is thymidylate kinase (dTMP kinase). It catalyses the ATP-dependent, Mg2+-dependent
phosphorylation of dTMP to dTDP:
This is the penultimate, common step of dTTP synthesis. dTMP is produced by BOTH the
de novo route (dUMP -> dTMP by thymidylate synthase) and the salvage route (thymidine ->
dTMP by thymidine kinase); both converge on dTMPK, which is therefore the bottleneck for
dTTP biosynthesis. dTDP is then phosphorylated to dTTP by nucleoside diphosphate kinase.
[PMID:34918187 "The thymidine de novo and salvage pathways converge at the point of the
phosphorylation of dTMP to dTDP by dTMPK"; "This makes dTMPK the bottleneck for dTTP
biosynthesis"]
Homodimer (Lee & Cheng 1977, PMID:18469; cited in UniProt SUBUNIT "Homodimer.").
Cofactor Mg2+. KM for dTMP ~5 uM (PMID:12614151).
Extensively crystallised (PDB 1E2Dā1NN5, 2XX3) in complex with dTMP/analogues and ATP/ADP
analogues; P-loop (res 13-21 / binding 16-21), DR(Y/H) motif (96-98), LID domain (133-157).
Drug-activation relevance: phosphorylates AZT-MP (zidovudine monophosphate), so it is on
the activation pathway for thymidine-analogue prodrugs (PMID:12614151).
Core: MF GO:0004798 dTMP kinase activity; directly involved in GO:0006233 dTDP biosynthetic
process and GO:0006235 dTTP biosynthetic process; located in cytosol GO:0005829.
id: P23919
gene_symbol: DTYMK
product_type: PROTEIN
status: INITIALIZED
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: >-
DTYMK is thymidylate kinase (dTMP kinase; EC 2.7.4.9), a small cytosolic P-loop
nucleotide kinase that catalyses the ATP- and Mg2+-dependent phosphorylation of
thymidine monophosphate (dTMP) to thymidine diphosphate (dTDP) (dTMP + ATP -> dTDP +
ADP). This is the common penultimate step in the synthesis of the DNA building block
dTTP: the de novo route (dUMP -> dTMP via thymidylate synthase) and the salvage route
(thymidine -> dTMP via thymidine kinase) both converge on dTMP kinase, making it the
bottleneck for dTTP biosynthesis; dTDP is subsequently phosphorylated to dTTP by
nucleoside diphosphate kinase. Because dTTP cannot be generated by any bypass, the
enzyme is essential for DNA replication and genome integrity; its expression and
activity peak in S phase. The active enzyme is a homodimer and has been crystallised
extensively in complex with dTMP/ATP analogues. It also activates thymidine-analogue
prodrugs (e.g. zidovudine/AZT monophosphate). Biallelic loss-of-function variants cause
a severe childhood-onset neurodegenerative disorder with progressive microcephaly.
alternative_products:
- name: '1'
id: P23919-1
- name: '2'
id: P23919-2
sequence_note: VSP_054164
existing_annotations:
- term:
id: GO:0004798
label: dTMP kinase activity
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: enables
review:
summary: >-
Phylogenetically inferred dTMP kinase activity, the defining molecular function of
the thymidylate kinase family. This is correct and central for DTYMK and is
independently supported by direct human experimental evidence.
action: ACCEPT
reason: >-
dTMP kinase activity is the core, experimentally validated molecular function of the
human enzyme, catalysing dTMP + ATP -> dTDP + ADP. The IBA call is consistent with
abundant human EXP/IDA evidence.
supported_by:
- reference_id: file:human/DTYMK/DTYMK-uniprot.txt
supporting_text: "Catalyzes the phosphorylation of thymidine monophosphate"
- reference_id: PMID:34918187
supporting_text: "catalyzes the penultimate step in dTTP biosynthesis"
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: is_active_in
review:
summary: >-
Phylogenetically inferred cytoplasmic localization. DTYMK is a small soluble kinase
with no targeting signal and is described as cytosolic; cytoplasm is a correct,
appropriately general compartment.
action: ACCEPT
reason: >-
Consistent with the cytosolic localization of the enzyme reported by Reactome and
with GOA cytosol (GO:0005829) annotations.
supported_by:
- reference_id: Reactome:R-HSA-73635
supporting_text: "Cytosolic deoxythymidylate kinase (DTYMK) catalyzes the reversible reaction"
- term:
id: GO:0006233
label: dTDP biosynthetic process
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: >-
Phylogenetically inferred involvement in dTDP biosynthesis. This is the direct
product-forming reaction of DTYMK (dTMP -> dTDP) and is a core process for the gene.
action: ACCEPT
reason: >-
The immediate reaction product of DTYMK is dTDP; this is the enzyme's direct
biosynthetic contribution and is experimentally supported.
supported_by:
- reference_id: file:human/DTYMK/DTYMK-uniprot.txt
supporting_text: "the immediate precursor for the"
- reference_id: PMID:34918187
supporting_text: "The thymidine de novo and salvage pathways converge at the point of the phosphorylation of dTMP to dTDP by dTMPK"
- term:
id: GO:0005739
label: mitochondrion
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: is_active_in
review:
summary: >-
Phylogenetically inferred mitochondrial localization. The human enzyme is
established as cytosolic, and this IBA call is propagated from a subset of orthologs;
it is weakly supported and not the functionally relevant compartment for human DTYMK.
action: MARK_AS_OVER_ANNOTATED
reason: >-
DTYMK is a small soluble protein with no mitochondrial targeting sequence and is
described as cytosolic deoxythymidylate kinase (Reactome). The mitochondrial IBA is
over-propagated from the PANTHER family; the established and functionally relevant
compartment is the cytosol/cytoplasm.
propagation_review:
root_cause: PROPAGATION_BAD
failure_modes:
- COMPARTMENT_OR_COMPLEX_MISMATCH
supported_by:
- reference_id: Reactome:R-HSA-73635
supporting_text: "Cytosolic deoxythymidylate kinase (DTYMK) catalyzes the reversible reaction"
- term:
id: GO:0006227
label: dUDP biosynthetic process
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: >-
Phylogenetically inferred involvement in dUDP biosynthesis, reflecting the enzyme's
ability to also phosphorylate dUMP to dUDP. This is a secondary/promiscuous activity,
not the biological purpose of DTYMK, which is dTTP synthesis.
action: KEEP_AS_NON_CORE
reason: >-
Reactome records dUMP as an alternative substrate (dUMP or TMP + ATP -> dUDP or TDP),
so dUDP formation is biochemically plausible, but the physiological role of DTYMK is
the synthesis of thymidine nucleotides (dTDP/dTTP). Retain as a non-core, secondary
activity rather than a core function.
supported_by:
- reference_id: Reactome:R-HSA-73635
supporting_text: "dUMP or TMP + ATP <=> dUDP or TDP + ADP [DTYMK]"
- term:
id: GO:0006235
label: dTTP biosynthetic process
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: >-
Phylogenetically inferred involvement in dTTP biosynthesis. DTYMK performs the
penultimate, common step of dTTP synthesis (dTMP -> dTDP), and is the essential
bottleneck for making dTTP; this is a core biological process for the gene.
action: ACCEPT
reason: >-
Both de novo and salvage routes converge on DTYMK, which is indispensable for dTTP
biosynthesis and DNA replication; loss of function completely blocks dTTP synthesis.
supported_by:
- reference_id: PMID:34918187
supporting_text: "This makes dTMPK the bottleneck for dTTP biosynthesis"
- reference_id: file:human/DTYMK/DTYMK-uniprot.txt
supporting_text: "Pyrimidine metabolism; dTTP biosynthesis."
- term:
id: GO:0005634
label: nucleus
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: is_active_in
review:
summary: >-
Phylogenetically inferred nuclear localization, propagated from a subset of orthologs.
The human enzyme is characterised as cytosolic, and nuclear localization is weakly
supported.
action: MARK_AS_OVER_ANNOTATED
reason: >-
DTYMK has no nuclear-localization signal and is described as cytosolic (Reactome).
Although dNTP synthesis serves nuclear DNA replication, the enzyme itself acts in the
cytosol; the nuclear IBA is an over-propagation.
propagation_review:
root_cause: PROPAGATION_BAD
failure_modes:
- COMPARTMENT_OR_COMPLEX_MISMATCH
supported_by:
- reference_id: Reactome:R-HSA-73635
supporting_text: "Cytosolic deoxythymidylate kinase (DTYMK) catalyzes the reversible reaction"
- term:
id: GO:0004798
label: dTMP kinase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: enables
review:
summary: >-
Electronic annotation of dTMP kinase activity from combined IEA methods (ARBA,
InterPro, RHEA/EC mapping). This correctly captures the defining molecular function.
action: ACCEPT
reason: >-
Matches the experimentally validated function and the RHEA:13517 / EC:2.7.4.9
reaction; a correct, well-supported electronic call.
supported_by:
- reference_id: file:human/DTYMK/DTYMK-uniprot.txt
supporting_text: "Reaction=dTMP + ATP = dTDP + ADP"
- term:
id: GO:0005524
label: ATP binding
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: >-
InterPro-based electronic annotation of ATP binding. DTYMK is a P-loop ATP-dependent
kinase; ATP binding is directly confirmed by crystal structures.
action: ACCEPT
reason: >-
ATP is the phosphoryl donor and is bound at a defined P-loop site (structurally
characterised, PMID:12614151); the electronic call is correct and supported by
experimental evidence.
supported_by:
- reference_id: file:human/DTYMK/DTYMK-uniprot.txt
supporting_text: "Reaction=dTMP + ATP = dTDP + ADP"
- term:
id: GO:0006233
label: dTDP biosynthetic process
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: involved_in
review:
summary: >-
Electronic annotation of involvement in dTDP biosynthesis, matching the direct
product-forming reaction of DTYMK.
action: ACCEPT
reason: >-
dTDP is the immediate reaction product; the call is consistent with experimental and
IBA evidence.
supported_by:
- reference_id: file:human/DTYMK/DTYMK-uniprot.txt
supporting_text: "the immediate precursor for the"
- term:
id: GO:0006235
label: dTTP biosynthetic process
evidence_type: IEA
original_reference_id: GO_REF:0000041
qualifier: involved_in
review:
summary: >-
Electronic annotation (UniPathway mapping) of involvement in dTTP biosynthesis,
matching the UniProt pathway assignment "Pyrimidine metabolism; dTTP biosynthesis".
action: ACCEPT
reason: >-
DTYMK performs the penultimate step of dTTP biosynthesis; the UniPathway-derived call
is correct.
supported_by:
- reference_id: file:human/DTYMK/DTYMK-uniprot.txt
supporting_text: "Pyrimidine metabolism; dTTP biosynthesis."
- term:
id: GO:0004798
label: dTMP kinase activity
evidence_type: EXP
original_reference_id: PMID:2017365
qualifier: enables
review:
summary: >-
Human dTMP kinase cDNA cloned by functional complementation of a yeast dTMP kinase
temperature-sensitive mutant; expression in yeast produces dTMP kinase activity,
experimentally establishing the molecular function.
action: ACCEPT
reason: >-
Direct experimental demonstration that the human gene product has dTMP kinase
activity (phosphorylates dTMP to dTDP with ATP and Mg2+).
supported_by:
- reference_id: PMID:2017365
supporting_text: "the cloned human cDNA, when expressed in yeast, produces dTMP kinase\n activity."
- reference_id: PMID:2017365
supporting_text: "(Deoxy)thymidylate (dTMP) kinase is an enzyme which phosphorylates dTMP to dTDP \nin the presence of ATP and magnesium."
- term:
id: GO:0004798
label: dTMP kinase activity
evidence_type: EXP
original_reference_id: PMID:34918187
qualifier: enables
review:
summary: >-
dTMPK enzyme activity measured directly in patient fibroblasts (severely reduced in
individuals with biallelic DTYMK variants), and the enzyme is defined as catalysing
the phosphorylation of dTMP to dTDP, confirming dTMP kinase activity for the human
protein.
action: ACCEPT
reason: >-
Provides human experimental (activity assay) evidence for dTMP kinase activity and
links loss of this activity to disease; the affected step is the phosphorylation of
dTMP to dTDP.
supported_by:
- reference_id: PMID:34918187
supporting_text: "The thymidine de novo and salvage pathways converge at the point of the phosphorylation of dTMP to dTDP by dTMPK"
- reference_id: PMID:34918187
supporting_text: "dTMPK enzyme activity of the individual is significantly lower than those of the parents"
- term:
id: GO:0005739
label: mitochondrion
evidence_type: HTP
original_reference_id: PMID:34800366
qualifier: located_in
review:
summary: >-
High-throughput mitochondrial proteomics (MitoCoP) call. DTYMK is an established
cytosolic enzyme; a proteomics dataset hit likely reflects co-purification or
dual/low-level reporting rather than a bona fide mitochondrial function.
action: MARK_AS_OVER_ANNOTATED
reason: >-
DTYMK has no mitochondrial targeting presequence and its characterised, functional
compartment is the cytosol (Reactome). A single HTP proteomics localization does not
establish the mitochondrion as a functional site for this soluble kinase; treat as an
over-annotation relative to the core cytosolic localization.
supported_by:
- reference_id: PMID:34800366
supporting_text: "high-confidence proteome of >1,100 proteins"
- reference_id: Reactome:R-HSA-73635
supporting_text: "Cytosolic deoxythymidylate kinase (DTYMK) catalyzes the reversible reaction"
- term:
id: GO:0004798
label: dTMP kinase activity
evidence_type: IDA
original_reference_id: PMID:12614151
qualifier: enables
review:
summary: >-
Structural and steady-state kinetic characterisation of human thymidylate kinase
(TMPK) converting thymidine monophosphate analogues to the corresponding
diphosphates, directly demonstrating dTMP kinase activity.
action: ACCEPT
reason: >-
Crystal structures with substrate/product analogues plus steady-state kinetics
directly establish the dTMP kinase catalytic activity of the human enzyme.
supported_by:
- reference_id: PMID:12614151
supporting_text: "the enzyme thymidylate kinase (TMPK) of clinically important \nthymidine monophosphate analogues to the corresponding diphosphates"
- term:
id: GO:0005524
label: ATP binding
evidence_type: IDA
original_reference_id: PMID:12614151
qualifier: enables
review:
summary: >-
Crystal structures solved with ADP or the ATP analogue AppNHp bound at the
phosphoryl-donor site, providing direct experimental evidence of ATP binding.
action: ACCEPT
reason: >-
Structures with the ATP analogue at the phosphoryl-donor site directly demonstrate
ATP binding by human thymidylate kinase.
supported_by:
- reference_id: PMID:12614151
supporting_text: "with either ADP or the ATP analogue AppNHp \nat the phosphoryl donor site"
- term:
id: GO:0006233
label: dTDP biosynthetic process
evidence_type: IDA
original_reference_id: PMID:12614151
qualifier: involved_in
review:
summary: >-
Direct assay of the conversion of thymidine monophosphates to the corresponding
diphosphates by human thymidylate kinase, supporting involvement in dTDP biosynthesis.
action: ACCEPT
reason: >-
The reaction assayed produces the diphosphate (dTDP) from the monophosphate (dTMP),
the direct biosynthetic contribution of DTYMK.
supported_by:
- reference_id: PMID:12614151
supporting_text: "thymidine monophosphate analogues to the corresponding diphosphates"
- term:
id: GO:0046105
label: thymidine biosynthetic process
evidence_type: IDA
original_reference_id: PMID:12614151
qualifier: involved_in
review:
summary: >-
Annotation to thymidine biosynthetic process. This mislabels the biology: DTYMK acts
on the nucleotide dTMP (producing dTDP), not on the nucleoside thymidine, and the
process it serves is dTDP/dTTP biosynthesis, not thymidine biosynthesis.
action: MARK_AS_OVER_ANNOTATED
reason: >-
The paper characterises phosphorylation of thymidine monophosphate to the
diphosphate; it does not establish biosynthesis of thymidine (the nucleoside). The
more accurate process terms are dTDP biosynthetic process (GO:0006233) and dTTP
biosynthetic process (GO:0006235), both already annotated. Treat this term as an
over-annotation relative to the correctly captured dTDP/dTTP processes.
supported_by:
- reference_id: PMID:12614151
supporting_text: "thymidine monophosphate analogues to the corresponding diphosphates"
- term:
id: GO:0046105
label: thymidine biosynthetic process
evidence_type: TAS
original_reference_id: PMID:8024690
qualifier: involved_in
review:
summary: >-
Author-statement annotation to thymidine biosynthetic process. As with the IDA above,
the described activity is phosphorylation of dTMP to the diphosphate en route to dTTP,
not biosynthesis of the nucleoside thymidine.
action: MARK_AS_OVER_ANNOTATED
reason: >-
DTYMK catalyses dTMP -> dTDP and is essential for dTTP synthesis, not for making
thymidine; the correct process terms (dTDP/dTTP biosynthetic process) are already
annotated. Over-annotation via a mismatched process term.
supported_by:
- reference_id: PMID:8024690
supporting_text: "dTMP kinase (E.C.2.7.4.9.) catalyzes the phosphorylation of dTMP to the \ncorresponding diphosphate."
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-73635
qualifier: located_in
review:
summary: >-
Reactome traceable-author-statement localizing DTYMK to the cytosol, consistent with
the enzyme being a small soluble cytosolic kinase. This is the core, functionally
relevant compartment.
action: ACCEPT
reason: >-
Reactome explicitly describes cytosolic deoxythymidylate kinase; matches the
established localization of the human enzyme.
supported_by:
- reference_id: Reactome:R-HSA-73635
supporting_text: "Cytosolic deoxythymidylate kinase (DTYMK) catalyzes the reversible reaction"
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-75126
qualifier: located_in
review:
summary: >-
Reactome traceable-author-statement (reverse reaction module) localizing DTYMK to the
cytosol; duplicate of the cytosol call and equally correct.
action: ACCEPT
reason: >-
Consistent with the cytosolic localization of the human enzyme described by Reactome.
supported_by:
- reference_id: Reactome:R-HSA-75126
supporting_text: "Cytosolic deoxythymidylate kinase (DTYMK) catalyzes the reversible reaction"
- term:
id: GO:0004798
label: dTMP kinase activity
evidence_type: IDA
original_reference_id: PMID:8845311
qualifier: enables
review:
summary: >-
Characterisation of the (murine) thymidylate kinase gene, defining TMK as catalysing
the essential conversion of dTMP to dTDP; supports the conserved dTMP kinase activity
of the orthologous mammalian enzyme.
action: ACCEPT
reason: >-
Establishes thymidylate kinase activity (dTMP -> dTDP) for the mammalian enzyme; the
function is directly and abundantly supported for the human protein by other evidence.
supported_by:
- reference_id: PMID:8845311
supporting_text: "Thymidylate kinase (TMK) catalyzes an essential reaction of converting dTMP to \ndTDP, leading to formation of the DNA precursor dTTP."
- term:
id: GO:0004798
label: dTMP kinase activity
evidence_type: TAS
original_reference_id: PMID:8024690
qualifier: enables
review:
summary: >-
Traceable-author-statement annotation of dTMP kinase activity for the human enzyme,
defined as catalysing the phosphorylation of dTMP to the corresponding diphosphate.
action: ACCEPT
reason: >-
Directly states the dTMP kinase catalytic activity of human dTMP kinase; concordant
with the EXP/IDA evidence.
supported_by:
- reference_id: PMID:8024690
supporting_text: "dTMP kinase (E.C.2.7.4.9.) catalyzes the phosphorylation of dTMP to the \ncorresponding diphosphate."
core_functions:
- description: >-
Thymidylate (dTMP) kinase activity: ATP- and Mg2+-dependent phosphorylation of dTMP to
dTDP, the common penultimate step of dTTP synthesis shared by the de novo and salvage
routes; essential for supplying dTTP for DNA replication.
molecular_function:
id: GO:0004798
label: dTMP kinase activity
directly_involved_in:
- id: GO:0006235
label: dTTP biosynthetic process
supported_by:
- reference_id: file:human/DTYMK/DTYMK-uniprot.txt
supporting_text: "Catalyzes the phosphorylation of thymidine monophosphate"
- reference_id: PMID:34918187
supporting_text: "This makes dTMPK the bottleneck for dTTP biosynthesis"
- description: >-
Formation of dTDP as the direct reaction product of dTMP phosphorylation, the immediate
biosynthetic output of DTYMK en route to dTTP.
molecular_function:
id: GO:0004798
label: dTMP kinase activity
directly_involved_in:
- id: GO:0006233
label: dTDP biosynthetic process
locations:
- id: GO:0005829
label: cytosol
supported_by:
- reference_id: PMID:34918187
supporting_text: "The thymidine de novo and salvage pathways converge at the point of the phosphorylation of dTMP to dTDP by dTMPK"
- reference_id: Reactome:R-HSA-73635
supporting_text: "Cytosolic deoxythymidylate kinase (DTYMK) catalyzes the reversible reaction"
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO
terms
findings: []
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings: []
- id: GO_REF:0000041
title: Gene Ontology annotation based on UniPathway vocabulary mapping
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: PMID:12614151
title: 'Structures of human thymidylate kinase in complex with prodrugs: implications
for the structure-based design of novel compounds.'
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Structural/kinetic characterisation of human TMPK; directly supports dTMP kinase
activity, ATP binding, and dTDP formation. Abstract quotes verified verbatim.
- id: PMID:2017365
title: Molecular cloning and expression of the human deoxythymidylate kinase gene
in yeast.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Cloned human dTMP kinase; complementation of yeast cdc8-type mutant and dTMP kinase
activity on expression establish the molecular function. Quotes verified verbatim.
- id: PMID:34800366
title: Quantitative high-confidence human mitochondrial proteome and its dynamics
in cellular context.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: >-
MitoCoP high-throughput mitochondrial proteomics dataset; source of the HTP
mitochondrion call. DTYMK is not discussed in the prose; the enzyme is established as
cytosolic, so this localization is treated as an over-annotation.
- id: PMID:34918187
title: DTYMK is essential for genome integrity and neuronal survival.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Establishes DTYMK as the penultimate step of dTTP biosynthesis at the convergence of
de novo and salvage pathways, with patient-fibroblast activity assays and disease
linkage (CONPM). Full text available; quotes verified verbatim.
- id: PMID:8024690
title: 'Human dTMP kinase: gene expression and enzymatic activity coinciding with
cell cycle progression and cell growth.'
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Human dTMP kinase catalysing dTMP phosphorylation; S-phase-regulated expression and
activity. Supports MF and cell-cycle context. Quotes verified verbatim.
- id: PMID:8845311
title: Molecular characterization of the murine thymidylate kinase gene.
findings: []
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: >-
Murine ortholog; defines TMK as converting dTMP to dTDP toward dTTP and shows
G0-to-S cell-cycle regulation. Supports the conserved mammalian function. Quotes
verified verbatim.
- id: Reactome:R-HSA-73635
title: dUMP or TMP + ATP <=> dUDP or TDP + ADP [DTYMK]
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Reactome reaction defining cytosolic DTYMK acting on dTMP (and, as an alternative
substrate, dUMP). Supports cytosol localization and the dUDP secondary activity.
- id: Reactome:R-HSA-75126
title: dUDP or TDP + ADP <=> dUMP or TMP + ATP [DTYMK]
findings: []
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: >-
Reverse-direction Reactome reaction for cytosolic DTYMK; supports cytosol
localization.
- id: file:human/DTYMK/DTYMK-uniprot.txt
title: UniProtKB entry P23919 (KTHY_HUMAN), thymidylate kinase
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
UniProt curated record; FUNCTION, CATALYTIC ACTIVITY (RHEA:13517), PATHWAY, and
SUBUNIT fields support the core function and localization. Quotes verified verbatim.