Thymidylate (dTMP -> dTTP) synthesis; thymidylate synthase / dUTPase / dTMP kinase

Thymidylate synthesis is the route that makes the DNA-specific precursor dTTP, distinguishing DNA (thymine) from RNA (uracil) precursors. dUTP diphosphatase (DUT) hydrolyses dUTP to dUMP + diphosphate, which both keeps the cellular dUTP:dTTP ratio low (preventing mutagenic uracil misincorporation into DNA) and supplies dUMP as substrate. Thymidylate synthase (TYMS) then reductively methylates dUMP to dTMP, using 5,10-methylenetetrahydrofolate as the one-carbon donor (oxidised to dihydrofolate, regenerated by DHFR) — the sole de novo source of dTMP. Thymidylate kinase (DTYMK) phosphorylates dTMP to dTDP, the essential step common to both the de novo and salvage routes; nucleoside diphosphate kinase then makes dTTP. This pathway is a central target of chemotherapy — TYMS is inhibited by the 5-fluorouracil metabolite FdUMP and by antifolates (raltitrexed, pemetrexed), and the folate cofactor supply is targeted by methotrexate — because rapidly dividing cells depend on de novo dTTP for DNA replication. Perturbing the balance (e.g. DUT loss, TYMS inhibition) causes dUTP accumulation, uracil misincorporation and DNA damage.

MODULE:thymidylate_synthesisDRAFTMetabolic Pathwaymodules/thymidylate_synthesis.yaml
dTMP biosynthetic processGO:0006231
GO:0006231
dTMP biosynthetic process
The module is grounded in the GO dTMP biosynthetic process (GO:0006231) and its continuation to dTTP: dUTP -> dUMP -> dTMP -> dTDP.
Reactome:R-HSA-73605
conversion of dUMP to dTMP
Reactions follow the human Reactome pyrimidine reactions R-HSA-73666 (DUT), R-HSA-73605 (TYMS) and R-HSA-73635 (DTYMK).
file:human/DUT/DUT-ai-review.yaml
DUT gene review (human)
The dUTP -> dUMP step (UniProtKB:P33316, GO:0004170) matches the completed human DUT review.
file:human/TYMS/TYMS-ai-review.yaml
TYMS gene review (human)
The dUMP -> dTMP step (UniProtKB:P04818, GO:0004799) matches the completed human TYMS review.
file:human/DHFR/DHFR-ai-review.yaml
DHFR gene review (human)
The dihydrofolate -> tetrahydrofolate regeneration step (UniProtKB:P00374, GO:0004146) matches the completed human DHFR review.
file:human/DTYMK/DTYMK-ai-review.yaml
DTYMK gene review (human)
The dTMP -> dTDP step (UniProtKB:P23919, GO:0004798) matches the completed human DTYMK review.
5Nodes
4Parts
0Variant Sets
0Variants
4Annotons
3Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:thymidylate_synthesis deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

4 gene-function check(s) reflected in core functions · 0 conflict(s) · 1 evidence or coverage gap(s) (8 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
dut_activity DUT (human)
UniProtKB:P33316
Family Representative 		dUTP diphosphatase activity
GO:0004170 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
tyms_activity TYMS (human)
UniProtKB:P04818
Family Representative 		thymidylate synthase activity
GO:0004799 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
dtymk_activity DTYMK (human)
UniProtKB:P23919
Family Representative 		dTMP kinase activity
GO:0004798 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
dhfr_activity DHFR (human)
UniProtKB:P00374
Family Representative 		dihydrofolate reductase activity
GO:0004146 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
dut_activity dUTP diphosphatase family (DUT)
PANTHER:PTHR11241
Family 		dUTP diphosphatase activity
GO:0004170 		Family Scope Restricted
GO:0004170 is SUBFAMILY_ONLY; this family grounding does not establish the allowed subfamily scope. The activity both the dNTP and the thymidylate-synthesis modules assert for this family. It is safe for SF0 (all characterized cellular dUTPases, including yeast DUT1) and SF11 (human DUT). It is not to be assumed for SF12, which PANTHER labels inactive. SF8 and the other subfamilies were not examined.
tyms_activity Thymidylate synthase family (TYMS)
PANTHER:PTHR11548
Family 		thymidylate synthase activity
GO:0004799 		Family Supported
Family review supports GO:0004799 FAMILY_WIDE. This is the defining activity, shared by bacterial ThyA, fungal CDC21, the TS domain of S. pombe hal3, animal TYMS and the TS domains of the plant and protist DHFR-TS proteins. Both modules that use this family (dntp_de_novo_synthesis and thymidylate_synthesis) assert exactly this term. Two phage members of SF1, the SPO1 and M6 dUMP hydroxymethylases, are exceptions.
dtymk_activity Thymidylate kinase family (DTYMK)
PANTHER:PTHR10344
Family 		dTMP kinase activity
GO:0004798 		Family Supported
Family review supports GO:0004798 FAMILY_WIDE. This is the defining activity of the bacterial, viral and eukaryotic thymidylate kinases. Both modules that use the family (dntp_de_novo_synthesis with CDC8, DTYMK and E. coli tmk; thymidylate_synthesis with DTYMK) assert it, and all their representative members are true TMPKs. Vertebrate CMPK2 (SF4) is an exception: PAINT pruned it with an IRD, and its characterized substrates are dUMP, dCMP, CMP and UMP.
dhfr_activity Dihydrofolate reductase family (DHFR)
PANTHER:PTHR48069
Family 		dihydrofolate reductase activity
GO:0004146 		Family Supported
Family review supports GO:0004146 FAMILY_WIDE. Asserted by tetrahydrofolate_biosynthesis; accepted by every reviewed member.

Gene-review completeness (4/4 grounded genes reviewed)

4 complete review(s) · 1 with deep research · 0 missing review · 3 reviewed but lacking deep research

Gene Review Complete Deep research
DHFR P00374 ✓ ✓ ✓
DTYMK P23919 ✓ ✓ ✗
DUT P33316 ✓ ✓ ✗
TYMS P04818 ✓ ✓ ✗

Details

Context
cytosolGO:0005829
Thymidylate (dTMP -> dTTP) synthesisMetabolic Pathwaythymidylate_synthesis
dTMP biosynthetic processGO:0006231
Context
cytosolGO:0005829

Thymidylate (dTMP -> dTTP) synthesis grounded to the human enzymes DUT (UniProtKB:P33316, GO:0004170, EC 3.6.1.23), thymidylate synthase TYMS (P04818, GO:0004799, EC 2.1.1.45), thymidylate kinase DTYMK (P23919, GO:0004798, EC 2.7.4.9) and the cofactor-regenerating dihydrofolate reductase DHFR (P00374, GO:0004146, EC 1.5.1.3). GO molecular-function terms were taken from the human GOA records; Reactome reaction ids and titles were verified against the local reactome cache. Each step uses a PANTHER family selector (generic over orthologs) with the human enzyme as representative. The pathway converts dUTP -> dUMP -> dTMP -> dTDP, with dTDP then phosphorylated to dTTP by nucleoside diphosphate kinase (NME family, not modelled here). It is tightly coupled to folate one-carbon metabolism (TYMS consumes 5,10-methylene-THF and releases DHF, regenerated by DHFR) and is the pre-eminent antiproliferative drug target: 5-fluorouracil (via FdUMP) and antifolates (raltitrexed, pemetrexed) inhibit TYMS, and methotrexate depletes the folate cofactor. dUMP also arises by salvage/deamination routes, and dTMP by thymidine salvage (TK1/TK2), which feed the same DTYMK step. Loss of the dUTPase gate (DUT) or TYMS inhibition raises dUTP and causes uracil misincorporation / DNA damage. Disease relevance is largely pharmacologic/pharmacogenetic; DTYMK has been linked to a severe neurodevelopmental disorder.

Connections

dut_step -> tyms_step Provides Input For
The dUMP from DUT is the thymidylate-synthase substrate.
tyms_step -> dtymk_step Provides Input For
The dTMP from TYMS is phosphorylated by DTYMK.
tyms_step -> dhfr_step Provides Input For
The dihydrofolate released by TYMS is reduced by DHFR to tetrahydrofolate, which is re-methylenated (SHMT, outside this module) to regenerate the TYMS one-carbon donor.
Part 1: dUTP hydrolysis (supplies dUMP; blocks uracil misincorporation)
dUTP + H2O to dUMP + diphosphateReactiondut_step

Annotons

DUT: dUTP diphosphatase (dUTPase)
dut_activity
Participant: Family: dUTP diphosphatase family (DUT)
Family:
dUTP diphosphatase family (DUT)PANTHER:PTHR11241
Representative Members: DUT (human)UniProtKB:P33316

Function

dUTP diphosphatase activityGO:0004170
Substrates: dUTP water
Products: dUMP diphosphate

Locations

cytosolGO:0005829

Hydrolyses dUTP to dUMP + PPi (nuclear and mitochondrial isoforms), preventing mutagenic uracil misincorporation into DNA and feeding dUMP to thymidylate synthase.

Part 2: reductive methylation of dUMP to dTMP (de novo)
dUMP + 5,10-methylene-THF to dTMP + dihydrofolateReactiontyms_step

Annotons

TYMS: thymidylate synthase
tyms_activity
Participant: Family: Thymidylate synthase family (TYMS)
Family:
Thymidylate synthase family (TYMS)PANTHER:PTHR11548
Representative Members: TYMS (human)UniProtKB:P04818

Function

thymidylate synthase activityGO:0004799
Substrates: dUMP 5,10-methylenetetrahydrofolate
Products: dTMP dihydrofolate (DHF)

Locations

cytosolGO:0005829

Homodimer catalysing the sole de novo source of dTMP; couples to folate one-carbon metabolism (produces DHF, regenerated by DHFR). Central 5-FU/ antifolate chemotherapy target; autoregulates its own translation.

Part 3: phosphorylation of dTMP to dTDP
dTMP + ATP to dTDP + ADPReactiondtymk_step

Annotons

DTYMK: thymidylate kinase (dTMP kinase)
dtymk_activity
Participant: Family: Thymidylate kinase family (DTYMK)
Family:
Thymidylate kinase family (DTYMK)PANTHER:PTHR10344
Representative Members: DTYMK (human)UniProtKB:P23919

Function

dTMP kinase activityGO:0004798
Substrates: dTMP ATP
Products: dTDP ADP

Locations

cytosolGO:0005829

Phosphorylates dTMP to dTDP — the rate-limiting step common to both the de novo (TYMS) and salvage (thymidine kinase) routes to dTTP; essential for DNA replication. dTDP is then converted to dTTP by nucleoside diphosphate kinase.

Part 4: folate cofactor regeneration (dihydrofolate to tetrahydrofolate)
dihydrofolate + NADPH to tetrahydrofolate + NADP+Reactiondhfr_step

Annotons

DHFR: dihydrofolate reductase
dhfr_activity
Participant: Family: Dihydrofolate reductase family (DHFR)
Family:
Dihydrofolate reductase family (DHFR)PANTHER:PTHR48069
Representative Members: DHFR (human)UniProtKB:P00374

Function

dihydrofolate reductase activityGO:0004146
Substrates: 7,8-dihydrofolate (DHF, released by TYMS) NADPH
Products: 5,6,7,8-tetrahydrofolate (THF) NADP+

Locations

cytosolGO:0005829

Regenerates tetrahydrofolate from the dihydrofolate released by thymidylate synthase; THF is then re-loaded to 5,10-methylene-THF by serine hydroxymethyltransferase (SHMT1/2, folate one-carbon module), closing the thymidylate cycle. Methotrexate inhibits this step, depleting the TYMS cofactor.