Pentose phosphate pathway

A reusable central-carbon module for the pentose phosphate pathway, covering the oxidative conversion of glucose 6-phosphate to ribulose 5-phosphate and the non-oxidative interconversion of pentose phosphates with fructose 6-phosphate and glyceraldehyde 3-phosphate. The oxidative branch generates NADPH through glucose-6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase, with 6-phosphogluconolactonase hydrolyzing the intermediate lactone. The non-oxidative branch uses ribose-5-phosphate isomerase, ribulose-phosphate 3-epimerase, transketolase, and transaldolase to balance ribose 5-phosphate, xylulose 5-phosphate, sedoheptulose 7-phosphate, erythrose 4-phosphate, fructose 6-phosphate, and glyceraldehyde 3-phosphate. Pseudomonas putida KT2440 proteins are used as concrete exemplars, but the boundary is the conserved PPP chemistry rather than a KT2440-specific KEGG map.

MODULE:pentose_phosphate_pathwayDRAFTCONCRETEMetabolic Pathwaymodules/pentose_phosphate_pathway.yaml
pentose-phosphate shuntGO:0006098
GO:0006098
pentose-phosphate shunt
GO:0006098 grounds the overall pathway as the pentose-phosphate shunt, spanning oxidative and non-oxidative pentose-phosphate chemistry.
GO:0009051
pentose-phosphate shunt, oxidative branch
GO:0009051 grounds the oxidative branch from glucose 6-phosphate to ribulose 5-phosphate with NADPH production.
GO:0009052
pentose-phosphate shunt, non-oxidative branch
GO:0009052 grounds the non-oxidative branch that rearranges pentose phosphates with glycolytic sugar phosphates.
KEGG:ppu00030
Pseudomonas putida KT2440 pentose phosphate pathway
The PSEPK KEGG ppu00030 membership bucket contains core PPP genes plus ED, gluconate, glycolysis, and nucleotide-biosynthesis spillovers; this module records only the core oxidative and non-oxidative PPP steps.
file:projects/P_PUTIDA/data/psepk_pathway_membership.tsv
PSEPK pathway membership table
The local membership table supplies the ppu00030 candidate list that was partitioned into core PPP steps and adjacent pathway spillovers.
file:projects/P_PUTIDA/deep-research/PSEPK__pentose_phosphate_pathway__ppu00030-deep-research-openscientist.md
OpenScientist PSEPK ppu00030 pathway satisfiability review
OpenScientist concluded that canonical PPP steps are satisfiable in KT2440 and that the main curation issue is the broad KEGG ppu00030 boundary, which mixes PPP with ED, peripheral glucose/gluconate oxidation, PRPP synthesis, and other spillovers.
file:modules/pentose_phosphate_pathway-deep-research-openscientist.md
OpenScientist module-level review for the pentose phosphate pathway
OpenScientist describes the PPP as two coupled biochemical modules: an irreversible oxidative branch and a reversible non-oxidative branch, while treating Entner-Doudoroff routing and downstream NADPH consumers as adjacent biology outside the module boundary.
file:genes/PSEPK/zwfA/zwfA-ai-review.yaml
PSEPK zwfA review
zwfA is a KT2440 glucose-6-phosphate dehydrogenase paralog and a primary exemplar for the oxidative branch first step.
file:genes/PSEPK/zwfB/zwfB-ai-review.yaml
PSEPK zwfB review
zwfB is a KT2440 glucose-6-phosphate dehydrogenase paralog and a primary exemplar for the oxidative branch first step.
file:genes/PSEPK/zwf/zwf-ai-review.yaml
PSEPK zwf/zwfC review
The curated zwf review supports G6PDH chemistry for PP_5351 but treats it as a minor or condition-specific paralog relative to zwfA and zwfB.
file:genes/PSEPK/pgl/pgl-ai-review.yaml
PSEPK pgl review
pgl is curated as 6-phosphogluconolactonase, the hydrolysis step after glucose-6-phosphate dehydrogenase.
file:genes/PSEPK/gntZ/gntZ-ai-review.yaml
PSEPK gntZ review
gntZ is the KT2440 6-phosphogluconate dehydrogenase exemplar for the oxidative branch decarboxylation step.
file:genes/PSEPK/rpe/rpe-ai-review.yaml
PSEPK rpe review
rpe is the KT2440 ribulose-phosphate 3-epimerase exemplar for xylulose 5-phosphate supply in the non-oxidative branch.
file:genes/PSEPK/rpiA/rpiA-ai-review.yaml
PSEPK rpiA review
rpiA is the KT2440 ribose-5-phosphate isomerase exemplar for ribose 5-phosphate supply in the non-oxidative branch.
file:genes/PSEPK/tktA/tktA-ai-review.yaml
PSEPK tktA review
tktA is the KT2440 transketolase exemplar for both two-carbon transfer steps in the non-oxidative branch.
file:genes/PSEPK/tal/tal-ai-review.yaml
PSEPK tal review
tal is the KT2440 transaldolase exemplar for the three-carbon transfer step in the non-oxidative branch.

Boundary decision for PSEPK ppu00030: keep the core PPP reactions in this module and treat glucose/gluconate oxidation, Entner-Doudoroff dehydratase and aldolase, lower glycolysis, phosphoglucomutase, and PRPP synthesis as adjacent modules or exits. The pgl product 6-phosphogluconate can feed either the ED route or the oxidative PPP decarboxylation step; that branch point is recorded here without pulling ED enzymes into the PPP module. The KT2440 G6PDH family has paralogs; zwfA and zwfB are represented as the main local exemplars, while PP_5351/zwfC is retained as a condition-specific paralog caveat from the existing curated review.

11Nodes
10Parts
0Variant Sets
0Variants
8Annotons
9Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✓ present

  • pentose_phosphate_pathway-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.

Gene-review completeness (9/11 grounded genes reviewed)

9 complete review(s) · 9 with deep research · 2 missing review · 0 reviewed but lacking deep research

Gene Review Complete Deep research
gntZ Q88FP6 ✓ ✓ ✓
E. coli gnd PAINT seed exemplar P00350 ✗ — —
E. coli zwf PAINT seed exemplar P0AC53 ✗ — —
pgl Q88P30 ✓ ✓ ✓
rpe Q88QS3 ✓ ✓ ✓
rpiA Q88CN0 ✓ ✓ ✓
tal Q88KX1 ✓ ✓ ✓
tktA Q88D62 ✓ ✓ ✓
zwf Q88C32 ✓ ✓ ✓
zwfA Q88P31 ✓ ✓ ✓
zwfB Q88FP7 ✓ ✓ ✓

Details

Context
cytosolGO:0005829
Pentose phosphate pathwayMetabolic Pathwaypentose_phosphate_pathway
pentose-phosphate shuntGO:0006098
Context
cytosolGO:0005829
Part 1: oxidative branch from glucose 6-phosphate to ribulose 5-phosphate
Pentose phosphate oxidative branchMetabolic Pathwayoxidative_branch
pentose-phosphate shunt, oxidative branchGO:0009051

Connections

6-phospho-D-glucono-1,5-lactone produced by G6PDH is the Pgl substrate.
6-phospho-D-gluconate produced by Pgl is the substrate for the decarboxylating dehydrogenase step.
Part 1: glucose 6-phosphate oxidation
Glucose-6-phosphate dehydrogenaseReactionglucose_6_phosphate_dehydrogenase_step

Annotons

Glucose-6-phosphate dehydrogenase
glucose_6_phosphate_dehydrogenase_activity
Participant: Family: glucose-6-phosphate dehydrogenase family
Family:
glucose-6-phosphate dehydrogenase familyPANTHER:PTHR23429
Representative Members: PSEPK zwfA exemplarUniProtKB:Q88P31 PSEPK zwfB exemplarUniProtKB:Q88FP7 PSEPK zwfC minor paralog exemplarUniProtKB:Q88C32 E. coli zwf PAINT seed exemplarUniProtKB:P0AC53

Function

glucose-6-phosphate dehydrogenase activityGO:0004345
Substrates: D-glucose 6-phosphate NADP+
Products: 6-phospho-D-glucono-1,5-lactone NADPH H+

Processes

pentose-phosphate shunt, oxidative branchGO:0009051

First oxidative PPP step, producing the reactive lactone intermediate and the first NADPH. KT2440 encodes multiple G6PDH paralogs, so the module uses family grounding plus representative paralogs rather than treating one locus as universally defining the step.

Part 2: lactone hydrolysis
6-phosphogluconolactonaseReactionphosphogluconolactonase_step

Annotons

6-phosphogluconolactonase
phosphogluconolactonase_activity
Participant: Family: 6-phosphogluconolactonase family
Family:
6-phosphogluconolactonase familyPANTHER:PTHR11054
Representative Members: PSEPK pgl exemplarUniProtKB:Q88P30

Function

6-phosphogluconolactonase activityGO:0017057
Substrates: 6-phospho-D-glucono-1,5-lactone water
Products: 6-phospho-D-gluconate

Processes

pentose-phosphate shunt, oxidative branchGO:0009051

Hydrolyzes the 6-phosphogluconolactone generated by G6PDH to 6-phosphogluconate, a branch-point metabolite that can enter the ED pathway or continue through oxidative PPP.

Part 3: oxidative decarboxylation to ribulose 5-phosphate
6-phosphogluconate dehydrogenaseReactionphosphogluconate_dehydrogenase_step

Annotons

6-phosphogluconate dehydrogenase
phosphogluconate_dehydrogenase_activity
Participant: Family: 6-phosphogluconate dehydrogenase family
Family:
6-phosphogluconate dehydrogenase familyPANTHER:PTHR11811
Representative Members: PSEPK gntZ exemplarUniProtKB:Q88FP6 E. coli gnd PAINT seed exemplarUniProtKB:P00350

Function

phosphogluconate dehydrogenase (decarboxylating) activityGO:0004616
Substrates: 6-phospho-D-gluconate NADP+
Products: D-ribulose 5-phosphate carbon dioxide NADPH

Processes

pentose-phosphate shunt, oxidative branchGO:0009051

Oxidatively decarboxylates 6-phosphogluconate to ribulose 5-phosphate and generates the second NADPH of the oxidative branch.

Part 2: non-oxidative pentose-phosphate rearrangements
Pentose phosphate non-oxidative branchMetabolic Pathwaynon_oxidative_branch
pentose-phosphate shunt, non-oxidative branchGO:0009052

Connections

Ribulose 5-phosphate from the oxidative branch is the substrate for ribose-5-phosphate isomerase.
Ribulose 5-phosphate from the oxidative branch is also the substrate for ribulose-phosphate 3-epimerase.
Ribose 5-phosphate is one substrate for the first transketolase step.
Xylulose 5-phosphate is the ketose donor for the first transketolase step.
Sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate from transketolase are the transaldolase substrates.
Erythrose 4-phosphate from transaldolase is used by the second transketolase step.
Xylulose 5-phosphate also supplies the second transketolase step.
Part 1: ribulose 5-phosphate to ribose 5-phosphate
Ribose-5-phosphate isomeraseReactionribose_5_phosphate_isomerase_step

Annotons

Ribose-5-phosphate isomerase
ribose_5_phosphate_isomerase_activity
Participant: Family: ribose-5-phosphate isomerase family
Family:
ribose-5-phosphate isomerase familyPANTHER:PTHR11934
Representative Members: PSEPK rpiA exemplarUniProtKB:Q88CN0

Function

ribose-5-phosphate isomerase activityGO:0004751
Substrates: D-ribulose 5-phosphate
Products: D-ribose 5-phosphate

Processes

pentose-phosphate shunt, non-oxidative branchGO:0009052

Interconverts ribulose 5-phosphate and ribose 5-phosphate, supplying one aldose substrate for transketolase and ribose carbon for nucleotide-biosynthesis exits.

Part 2: ribulose 5-phosphate to xylulose 5-phosphate
Ribulose-phosphate 3-epimeraseReactionribulose_phosphate_epimerase_step

Annotons

Ribulose-phosphate 3-epimerase
ribulose_phosphate_epimerase_activity
Participant: Family: ribulose-phosphate 3-epimerase family
Family:
ribulose-phosphate 3-epimerase familyPANTHER:PTHR11749
Representative Members: PSEPK rpe exemplarUniProtKB:Q88QS3

Function

D-ribulose-phosphate 3-epimerase activityGO:0004750
Substrates: D-ribulose 5-phosphate
Products: D-xylulose 5-phosphate

Processes

pentose-phosphate shuntGO:0006098

Interconverts ribulose 5-phosphate and xylulose 5-phosphate, supplying the ketose donor used in both transketolase steps.

Part 3: first two-carbon transfer
Transketolase: xylulose 5-phosphate plus ribose 5-phosphateReactiontransketolase_first_step

Annotons

Transketolase first PPP reaction
transketolase_first_activity
Participant: Family: bacterial transketolase family
Family:
bacterial transketolase familyPANTHER:PTHR43522
Representative Members: PSEPK tktA exemplarUniProtKB:Q88D62

Function

transketolase activityGO:0004802
Substrates: D-xylulose 5-phosphate D-ribose 5-phosphate
Products: sedoheptulose 7-phosphate D-glyceraldehyde 3-phosphate
Cofactors: thiamine diphosphate magnesium ion

Processes

pentose-phosphate shunt, non-oxidative branchGO:0009052

Thiamine-diphosphate-dependent transfer of a two-carbon ketol unit from xylulose 5-phosphate to ribose 5-phosphate.

Part 4: three-carbon transfer
TransaldolaseReactiontransaldolase_step

Annotons

Transaldolase
transaldolase_activity
Participant: Family: transaldolase family
Family:
transaldolase familyPANTHER:PTHR10683
Representative Members: PSEPK tal exemplarUniProtKB:Q88KX1

Function

transaldolase activityGO:0004801
Substrates: sedoheptulose 7-phosphate D-glyceraldehyde 3-phosphate
Products: D-erythrose 4-phosphate D-fructose 6-phosphate

Processes

pentose-phosphate shuntGO:0006098

Transfers a three-carbon unit from sedoheptulose 7-phosphate to glyceraldehyde 3-phosphate, producing erythrose 4-phosphate and fructose 6-phosphate.

Part 5: second two-carbon transfer
Transketolase: xylulose 5-phosphate plus erythrose 4-phosphateReactiontransketolase_second_step

Annotons

Transketolase second PPP reaction
transketolase_second_activity
Participant: Family: bacterial transketolase family
Family:
bacterial transketolase familyPANTHER:PTHR43522
Representative Members: PSEPK tktA exemplarUniProtKB:Q88D62

Function

transketolase activityGO:0004802
Substrates: D-xylulose 5-phosphate D-erythrose 4-phosphate
Products: D-fructose 6-phosphate D-glyceraldehyde 3-phosphate
Cofactors: thiamine diphosphate magnesium ion

Processes

pentose-phosphate shunt, non-oxidative branchGO:0009052

The same transketolase family performs the second PPP two-carbon transfer, converting xylulose 5-phosphate and erythrose 4-phosphate to fructose 6-phosphate and glyceraldehyde 3-phosphate.