Bacterial thiamine diphosphate biosynthesis

Species-neutral bacterial pathway for de novo synthesis of thiamine diphosphate (ThDP), the active thiamine cofactor. The pathway has two converging branches: a hydroxymethylpyrimidine branch in which ThiC converts an AIR-derived precursor to HMP phosphate and ThiD phosphorylates it to the diphosphate, and a thiazole branch in which Dxs, ThiO, sulfur-relay proteins, and ThiG form the thiazole phosphate moiety. ThiE couples the pyrimidine and thiazole moieties to thiamine phosphate, and ThiL phosphorylates thiamine phosphate to ThDP. The thiazole branch includes the ThiS sulfur-carrier activation/thiocarboxylation relay rather than treating sulfur delivery as a single enzyme reaction.

MODULE:thiamine_diphosphate_biosynthesisDRAFTMetabolic Pathwaymodules/thiamine_diphosphate_biosynthesis.yaml
thiamine biosynthetic processGO:0009228 thiamine diphosphate biosynthetic processGO:0009229
GO:0009228
thiamine biosynthetic process
GO biological-process term for thiamine biosynthesis; used as the parent process grounding for the module.
GO:0009229
thiamine diphosphate biosynthetic process
GO biological-process term for synthesis of active thiamine diphosphate; used as the specific process grounding for the module.
KEGG:map00730
Thiamine metabolism
KEGG thiamine-metabolism pathway context. The PSEPK map includes de novo thiamine genes plus nucleotide-metabolism and ribosome-biogenesis spillover that require curator filtering.
UniPathway:UPA00060
Thiamine diphosphate biosynthesis
UniPathway pathway context for bacterial thiamine diphosphate biosynthesis used by UniProt metadata for several PSEPK candidate genes.
file:projects/P_PUTIDA/data/psepk_gene_list.tsv
PSEPK UniProt metadata inventory
Local UniProt-derived inventory provides the Pseudomonas putida KT2440 exemplar accessions, GO terms, EC numbers, and PANTHER families used to ground representative members in this module.
file:PSEPK/thiO/thiO-ai-review.yaml
PSEPK thiO gene review
Existing review supports ThiO glycine oxidase activity and its role in supplying glyoxyl imine for thiazole/thiamine biosynthesis.
file:PSEPK/thiI/thiI-ai-review.yaml
PSEPK thiI gene review
Existing review supports ThiI tRNA sulfurtransferase activity and the family-inferred ThiS sulfur-carrier transfer role in thiazole/thiamine biosynthesis, while noting that GO lacks a precise ThiS-transfer MF term.
file:modules/thiamine_diphosphate_biosynthesis-deep-research-openscientist.md
OpenScientist module review for bacterial thiamine diphosphate biosynthesis
Generic module-level retrieval supports the de novo ThDP boundary, separates salvage/transport from the core pathway, and highlights the IscS/ThiF/ThiI/ThiS sulfur-relay order for thiazole synthesis.
file:projects/P_PUTIDA/deep-research/PSEPK__thiamine_diphosphate_biosynthesis__ppu00730-deep-research-openscientist.md
OpenScientist PSEPK ppu00730 thiamine diphosphate biosynthesis review
Species/pathway satisfiability review finds the KT2440 de novo ThDP pathway largely covered, adds PP_5105/ThiS as a missing module member, excludes KEGG overview artifacts such as adk and rsgA, and flags the ThiF-type ThiS adenylylation step as candidate_uncertain because KT2440 lacks a dedicated thiF gene.

This module is narrower than KEGG ppu00730 "Thiamine metabolism": it models de novo ThDP biosynthesis. Adenylate kinase (adk), RsgA, thiamine triphosphatase, aminopyrimidine aminohydrolases, and transport/salvage proteins are pathway neighbors or salvage context rather than required core biosynthetic steps. In P. putida KT2440, PP_5105 encodes the ThiS sulfur carrier and is a likely module member even though it is assigned to KEGG sulfur-relay map ppu04122 rather than ppu00730. The KT2440 ThiF-type ThiS adenylylation enzyme is unresolved: OpenScientist found no dedicated thiF and nominated MoeB/PP_0735 as the only plausible but unconfirmed E1-like substitute, so the module keeps a species-neutral ThiF-family step and records the PSEPK assignment as a curation gap.

11Nodes
10Parts
0Variant Sets
0Variants
11Annotons
10Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✓ present

  • thiamine_diphosphate_biosynthesis-deep-research-openscientist.md (openscientist)

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Reaction chaining (advisory)

✓ every PRECEDES step chains, or its break is acknowledged via chaining_status.

  • thiC_step → thiD_step [NOT_CHECKED]
  • thiE_coupling_step → thiL_activation_step [NOT_CHECKED]

Gene-review completeness (3/12 grounded genes reviewed)

3 complete review(s) · 3 with deep research · 9 missing review · 0 reviewed but lacking deep research

Gene Review Complete Deep research
dxs Q88QG7 ✓ ✓ ✓
thiF (Escherichia coli K-12) P30138 ✗ — —
ThiS sulfur carrier protein (Pseudomonas putida KT2440) Q88CS5 ✗ — —
thiG (Pseudomonas putida KT2440) Q88CS6 ✗ — —
thiC (Pseudomonas putida KT2440) Q88DA5 ✗ — —
thiE (Pseudomonas putida KT2440) Q88DP1 ✗ — —
thiD (Pseudomonas putida KT2440) Q88DP2 ✗ — —
iscS-II (Pseudomonas putida KT2440) Q88K56 ✗ — —
iscS (Pseudomonas putida KT2440) Q88PK8 ✗ — —
thiL (Pseudomonas putida KT2440) Q88QH4 ✗ — —
thiI Q88CY4 ✓ ✓ ✓
thiO Q88Q83 ✓ ✓ ✓

Details

Context
cytosolGO:0005829
Thiamine diphosphate biosynthesisMetabolic Pathwaythiamine_diphosphate_biosynthesis
thiamine biosynthetic processGO:0009228 thiamine diphosphate biosynthetic processGO:0009229
Context
cytosolGO:0005829

Connections

thiC_step -> thiD_step Precedes
dxs_step -> thiG_step Provides Input For
thiO_step -> thiG_step Provides Input For
thiS_sulfur_carrier_role -> thiG_step Provides Input For
thiD_step -> thiE_coupling_step Provides Input For
thiG_step -> thiE_coupling_step Provides Input For
Part 1: hydroxymethylpyrimidine branch
Hydroxymethylpyrimidine diphosphate branchMetabolic Pathwayhmp_branch

Produces the activated pyrimidine moiety, HMP diphosphate, for coupling to thiazole phosphate.

Part 1: HMP phosphate formation
AIR-derived precursor to HMP phosphateReactionthiC_step

Annotons

ThiC: phosphomethylpyrimidine synthase
phosphomethylpyrimidine_synthase_activity
Participant: Family: ThiC phosphomethylpyrimidine synthase family
Family:
ThiC phosphomethylpyrimidine synthase familyPANTHER:PTHR30557
Representative Members: thiC (Pseudomonas putida KT2440)UniProtKB:Q88DA5

Function

phosphomethylpyrimidine synthase activityGO:0070284
Substrates: 5-aminoimidazole ribonucleotide-derived precursor
Products: 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate
Cofactors: iron-sulfur cluster

Forms the phosphorylated HMP pyrimidine moiety.

Part 2: HMP phosphate activation
HMP phosphate to HMP diphosphateReactionthiD_step

Annotons

ThiD: phosphomethylpyrimidine kinase
phosphomethylpyrimidine_kinase_activity
Participant: Family: ThiD hydroxymethylpyrimidine/phosphomethylpyrimidine kinase family
Family:
ThiD hydroxymethylpyrimidine/phosphomethylpyrimidine kinase familyPANTHER:PTHR20858
Representative Members: thiD (Pseudomonas putida KT2440)UniProtKB:Q88DP2

Function

phosphomethylpyrimidine kinase activityGO:0008972
Substrates: 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate ATP
Products: 4-amino-5-hydroxymethyl-2-methylpyrimidine diphosphate ADP

Activates HMP phosphate to the diphosphate used by ThiE.

ThiD-family enzymes may also support HMP salvage via hydroxymethylpyrimidine kinase activity; this annoton represents the de novo HMP-P to HMP-PP step.

Part 2: thiazole branch
Thiazole phosphate branchMetabolic Pathwaythiazole_branch

Produces the thiazole phosphate moiety from DXP, glycine-derived imine chemistry, and sulfur carried through IscS/ThiI/ThiS.

Part 1: DXP precursor supply
DXP formationReactiondxs_step

Annotons

Dxs: 1-deoxy-D-xylulose-5-phosphate synthase
dxp_synthase_activity
Participant: Family: Dxs 1-deoxy-D-xylulose-5-phosphate synthase family
Family:
Dxs 1-deoxy-D-xylulose-5-phosphate synthase familyPANTHER:PTHR43322
Representative Members: dxs (Pseudomonas putida KT2440)UniProtKB:Q88QG7

Function

1-deoxy-D-xylulose-5-phosphate synthase activityGO:0008661
Substrates: pyruvate D-glyceraldehyde 3-phosphate
Products: 1-deoxy-D-xylulose 5-phosphate carbon dioxide

Supplies DXP, the carbon precursor for the thiazole moiety.

DXP is also used in non-mevalonate isoprenoid biosynthesis; the Dxs step is substrate supply for this module rather than a thiamine-specific commitment step.

Part 2: iminoglycine supply
Glycine oxidation to iminoglycineReactionthiO_step

Annotons

ThiO: glycine oxidase
glycine_oxidase_activity
Participant: Family: ThiO glycine oxidase family
Family:
ThiO glycine oxidase familyPANTHER:PTHR13847
Representative Members: thiO (Pseudomonas putida KT2440)UniProtKB:Q88Q83

Function

glycine oxidase activityGO:0043799
Substrates: glycine oxygen
Products: iminoglycine (2-iminoacetate; dehydroglycine) hydrogen peroxide
Cofactors: FAD

Supplies iminoglycine, the glycine-derived imine intermediate for thiazole formation.

Part 3: sulfur mobilization and ThiS thiocarboxylation
ThiS sulfur-carrier thiocarboxylationMetabolic Pathwaythis_sulfur_relay

Annotons

IscS: cysteine desulfurase sulfur donor
cysteine_desulfurase_activity
Participant: Family: IscS cysteine desulfurase family
Family:
IscS cysteine desulfurase familyPANTHER:PTHR11601
Representative Members: iscS (Pseudomonas putida KT2440)UniProtKB:Q88PK8 iscS-II (Pseudomonas putida KT2440)UniProtKB:Q88K56

Function

cysteine desulfurase activityGO:0031071
Substrates: L-cysteine
Products: enzyme-bound persulfide sulfur L-alanine

Mobilizes sulfur as persulfide for ThiI-mediated ThiS thiocarboxylation.

P. putida KT2440 encodes iscS and iscS-II candidates; the exact thiamine-branch contributor should be checked in full gene reviews.

ThiF: ThiS sulfur-carrier activation
thiF_this_adenylylation_activity
Participant: Family: ThiF sulfur carrier protein ThiS adenylyltransferase subfamily
Family:
ThiF sulfur carrier protein ThiS adenylyltransferase subfamilyPANTHER:PTHR10953:SF240
Representative Members: thiF (Escherichia coli K-12)UniProtKB:P30138

Function

ThiS ubiquitin-like sulfur-carrier activating enzyme activityGO:0008641
Substrates: ThiS C-terminal glycine ATP
Products: adenylylated ThiS diphosphate

Activates the ThiS C-terminus by ATP-dependent adenylylation before sulfur transfer and thiocarboxylate formation.

P. putida KT2440 lacks a dedicated thiF gene. MoeB/PP_0735 is an E1-like PTHR10953 paralog and the only plausible local substitute identified by OpenScientist, but it remains a candidate_uncertain member until full gene review or experiment resolves whether it activates ThiS in vivo.

ThiI: sulfur transfer to ThiS
thiI_this_sulfurtransfer_role
Participant: Family: ThiI tRNA/ThiS sulfurtransferase family
Family:
ThiI tRNA/ThiS sulfurtransferase familyPANTHER:PTHR43209
Representative Members: thiI (Pseudomonas putida KT2440)UniProtKB:Q88CY4

Processes

thiazole biosynthetic processGO:0052837

Transfers sulfur to the ThiS sulfur carrier to form ThiS thiocarboxylate for thiazole biosynthesis.

file:PSEPK/thiI/thiI-ai-review.yaml
Existing PSEPK review accepts the family-inferred ThiI role in thiazole biosynthesis and notes the missing precise ThiS-transfer MF term.

GO currently lacks the precise ThiS sulfur-carrier protein sulfurtransferase MF proposed in the PSEPK thiI review, so this role is represented by the specific thiazole process and curator notes rather than a broad sulfurtransferase MF.

ThiS: sulfur carrier protein
thiS_sulfur_carrier_role
Participant: Gene Product: ThiS sulfur carrier protein (Pseudomonas putida KT2440)
Gene Product:
ThiS sulfur carrier protein (Pseudomonas putida KT2440)UniProtKB:Q88CS5

Function

sulfur carrier activityGO:0097163
Targets: thiazole synthase reaction
Cargo: sulfur

Processes

thiazole biosynthetic processGO:0052837

Carries activated sulfur for ThiG-mediated thiazole phosphate formation.

PP_5105 is assigned to KEGG sulfur-relay map ppu04122 in the local partition but is a likely missing ppu00730 member for the thiazole branch.

Part 4: thiazole phosphate formation
Thiazole phosphate synthesisReactionthiG_step

Annotons

ThiG: thiazole synthase
thiazole_synthase_activity
Participant: Family: ThiG thiazole synthase family
Family:
ThiG thiazole synthase familyPANTHER:PTHR34266
Representative Members: thiG (Pseudomonas putida KT2440)UniProtKB:Q88CS6

Function

thiazole synthase activityGO:1990107
Substrates: 1-deoxy-D-xylulose 5-phosphate glyoxyl imine ThiS-thiocarboxylate
Products: 4-methyl-5-(2-phosphooxyethyl)thiazole

Forms the activated thiazole phosphate moiety.

Part 3: pyrimidine-thiazole coupling
HMP diphosphate plus thiazole phosphate to thiamine phosphateReactionthiE_coupling_step

Annotons

ThiE: thiamine-phosphate diphosphorylase
thiamine_phosphate_diphosphorylase_activity
Participant: Family: ThiE thiamine-phosphate synthase family
Family:
ThiE thiamine-phosphate synthase familyPANTHER:PTHR20857
Representative Members: thiE (Pseudomonas putida KT2440)UniProtKB:Q88DP1

Function

thiamine-phosphate diphosphorylase activityGO:0004789
Substrates: HMP diphosphate thiazole phosphate
Products: thiamine phosphate diphosphate

Couples the pyrimidine and thiazole moieties to form thiamine phosphate.

Part 4: thiamine diphosphate activation
Thiamine phosphate to thiamine diphosphateReactionthiL_activation_step

Annotons

ThiL: thiamine-phosphate kinase
thiamine_phosphate_kinase_activity
Participant: Family: ThiL thiamine-phosphate kinase family
Family:
ThiL thiamine-phosphate kinase familyPANTHER:PTHR30270
Representative Members: thiL (Pseudomonas putida KT2440)UniProtKB:Q88QH4

Function

thiamine-phosphate kinase activityGO:0009030
Substrates: thiamine phosphate ATP
Products: thiamine diphosphate ADP
Cofactors: magnesium ion

Produces the active cofactor thiamine diphosphate.