Glycolysis II — payoff phase (glyceraldehyde-3-phosphate → pyruvate); PGK/PGAM/enolase/PK deficiencies

The payoff (energy-yielding) phase of glycolysis is the second half of the cytosolic pathway, converting each glyceraldehyde-3-phosphate produced in the investment phase into pyruvate while generating ATP and NADH. Five steps: glyceraldehyde-3-phosphate dehydrogenase (GAPDH) oxidises and phosphorylates glyceraldehyde-3-phosphate to 1,3-bisphosphoglycerate, reducing NAD+ to NADH; phosphoglycerate kinase (PGK1) transfers a phosphate from 1,3-bisphosphoglycerate to ADP, forming 3-phosphoglycerate and the first ATP (substrate-level phosphorylation); phosphoglycerate mutase (muscle PGAM2) isomerises 3-phosphoglycerate to 2-phosphoglycerate; enolase (muscle ENO3) dehydrates 2-phosphoglycerate to phosphoenolpyruvate; and pyruvate kinase (liver/RBC PKLR, or muscle/other PKM) transfers the phosphate of phosphoenolpyruvate to ADP, forming pyruvate and the second ATP. Per glucose (two trioses) the payoff phase yields 4 ATP and 2 NADH, for a net glycolytic gain of 2 ATP + 2 NADH + 2 pyruvate. Because mature erythrocytes rely entirely on glycolytic ATP, defects here characteristically cause hereditary nonspherocytic hemolytic anemia, often combined with tissue-specific features: PGK1 deficiency (X-linked hemolytic anemia + myopathy + CNS disease); PGAM2 deficiency = glycogen storage disease type X (muscle); ENO3 deficiency = GSD type XIII (muscle); and PKLR deficiency = pyruvate kinase deficiency, the commonest glycolytic cause of hemolytic anemia.

MODULE:glycolysis_payoff_phaseDRAFTMetabolic Pathwaymodules/glycolysis_payoff_phase.yaml
glycolytic processGO:0006096
GO:0006096
glycolytic process
The module is grounded in the GO glycolytic process (GO:0006096); it covers the payoff-phase steps from glyceraldehyde-3-phosphate to pyruvate.
Reactome:R-HSA-70171
Glycolysis
Step order and reaction stoichiometries follow the human Reactome "Glycolysis" reactions R-HSA-70449 (GAPDH), R-HSA-71850 (PGK1), R-HSA-71654 (PGAM), R-HSA-71660 (enolase) and R-HSA-71670 (pyruvate kinase).
file:human/GAPDH/GAPDH-ai-review.yaml
GAPDH gene review (human)
The glyceraldehyde-3-phosphate dehydrogenase step (UniProtKB:P04406, GO:0004365) matches the previously completed human GAPDH review (already on main).
file:human/PGK1/PGK1-ai-review.yaml
PGK1 gene review (human)
The phosphoglycerate kinase step (UniProtKB:P00558, GO:0004618) matches the completed human PGK1 review.
file:human/PGAM2/PGAM2-ai-review.yaml
PGAM2 gene review (human)
The phosphoglycerate mutase step (UniProtKB:P15259, GO:0004619) matches the completed human PGAM2 review.
file:human/ENO3/ENO3-ai-review.yaml
ENO3 gene review (human)
The enolase step (UniProtKB:P13929, GO:0004634) matches the completed human ENO3 review.
file:human/PKLR/PKLR-ai-review.yaml
PKLR gene review (human)
The pyruvate kinase step (UniProtKB:P30613, GO:0004743) matches the completed human PKLR review.
file:human/PKM/PKM-ai-review.yaml
PKM gene review (human)
The muscle/other pyruvate kinase isozyme of the final step (UniProtKB:P14618, GO:0004743) matches the previously completed human PKM review (already on main).
6Nodes
5Parts
0Variant Sets
0Variants
5Annotons
4Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:glycolysis_payoff_phase 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

6 gene-function check(s) reflected in core functions · 0 conflict(s) · 1 evidence or coverage gap(s) (11 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
gapdh_activity GAPDH (human)
UniProtKB:P04406
Family Representative 		glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
GO:0004365 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
pgk_activity PGK1 (human, somatic)
UniProtKB:P00558
Family Representative 		phosphoglycerate kinase activity
GO:0004618 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
pgam_activity PGAM2 (human, muscle isozyme)
UniProtKB:P15259
Family Representative 		phosphoglycerate mutase activity
GO:0004619 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
enolase_activity ENO3 (human, muscle beta-enolase)
UniProtKB:P13929
Family Representative 		phosphopyruvate hydratase activity
GO:0004634 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
pk_activity PKLR (human, liver/red-cell isozyme)
UniProtKB:P30613
Family Representative 		pyruvate kinase activity
GO:0004743 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
pk_activity PKM (human, muscle/M1-M2 isozyme)
UniProtKB:P14618
Family Representative 		pyruvate kinase activity
GO:0004743 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
gapdh_activity Glyceraldehyde-3-phosphate dehydrogenase family (GAPDH/GAPDHS)
PANTHER:PTHR10836
Family 		glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
GO:0004365 		Family Supported
Family review supports GO:0004365 FAMILY_WIDE. Asserted by emp_glycolysis, gluconeogenesis and glycolysis_payoff_phase; accepted by the S. cerevisiae, S. pombe, human and mouse reviews.
pgk_activity Phosphoglycerate kinase family (PGK1/PGK2)
PANTHER:PTHR11406
Family 		phosphoglycerate kinase activity
GO:0004618 		Family Supported
Family review supports GO:0004618 FAMILY_WIDE. Asserted by emp_glycolysis, gluconeogenesis and glycolysis_payoff_phase; accepted by S. cerevisiae PGK1, S. pombe pgk1, human PGK1 and P. putida Pgk.
pgam_activity Cofactor-dependent phosphoglycerate mutase family (PGAM1/PGAM2/BPGM)
PANTHER:PTHR11931
Family 		phosphoglycerate mutase activity
GO:0004619 		Family Scope Restricted
GO:0004619 is SUBFAMILY_ONLY; this family grounding does not establish the allowed subfamily scope. The active PGM subfamilies. The emp_glycolysis, gluconeogenesis and glycolysis_payoff_phase modules select the base family, which also takes in BPGM and GPM2/GPM3. SF11 (BPGM) is listed because BPGM has a genuine minor phosphoglycerate mutase activity (EC 5.4.2.11), kept as non-core in its review.
enolase_activity Enolase family (ENO1/ENO2/ENO3)
PANTHER:PTHR11902
Family 		phosphopyruvate hydratase activity
GO:0004634 		Family Supported
Family review supports GO:0004634 FAMILY_WIDE. The modules (emp_glycolysis, gluconeogenesis, glycolysis_payoff_phase) select the whole family for this activity, and PAINT puts it at the family root. Experimental seeds cover every major lineage and include yeast ERR2 and ERR3. ERR1 and ENO4 hold the activity by homology only. For ERR1 the active-site residues are intact, so neither is treated as an exception.
pk_activity Pyruvate kinase family (PKM/PKLR)
PANTHER:PTHR11817
Family 		pyruvate kinase activity
GO:0004743 		Family Supported
Family review supports GO:0004743 FAMILY_WIDE. All modules that use the family (emp_glycolysis, glycolysis_payoff_phase, bacterial_pyruvate_metabolism) select the base family for this activity. That is safe for every characterized member. The only known loss is the Drosophila SF3 paralog set, which PAINT already excludes by IKR, so module selectors that rely on IBA inherit the correct exclusion. A module that selects SF3 or the family by sequence alone would include those paralogs.

Gene-review completeness (6/6 grounded genes reviewed)

6 complete review(s) · 2 with deep research · 0 missing review · 4 reviewed but lacking deep research

Gene Review Complete Deep research
ENO3 P13929 ✓ ✓ ✗
GAPDH P04406 ✓ ✓ ✓
PGAM2 P15259 ✓ ✓ ✗
PGK1 P00558 ✓ ✓ ✗
PKLR P30613 ✓ ✓ ✗
PKM P14618 ✓ ✓ ✓

Details

Context
cytosolGO:0005829
Glycolysis (payoff phase)Metabolic Pathwayglycolysis_payoff_phase
glycolytic processGO:0006096
Context
cytosolGO:0005829

Five-step payoff phase of glycolysis grounded to the human enzymes GAPDH (UniProtKB:P04406, GO:0004365), phosphoglycerate kinase PGK1 (P00558, GO:0004618), phosphoglycerate mutase PGAM2 (P15259, GO:0004619), beta-enolase ENO3 (P13929, GO:0004634) and pyruvate kinase PKLR (P30613) / PKM (P14618) (GO:0004743). 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 the tissue isozymes and orthologs (PGAM node covers PGAM1/PGAM2/BPGM; enolase node ENO1/ENO2/ENO3; pyruvate-kinase node PKLR + PKM). GAPDH and PKM were reviewed previously (already on main) and are cross-linked via file: evidence; PGK1/PGAM2/ENO3/PKLR are the reviews new in this batch. Upstream, the two glyceraldehyde-3-phosphate molecules come from the glycolysis investment phase (hexokinase -> GPI -> PFK -> aldolase -> TPI); downstream, pyruvate feeds the pyruvate-metabolism module (PDC/PC) and lactate fermentation (LDHA/LDHB, a separate module), while the reverse reactions (except the PFK/PK/hexokinase committed steps) serve gluconeogenesis. Moonlighting roles (GAPDH; PGK1 extracellular reductase; PKM2 nuclear/protein-kinase) are captured non-core in the individual gene reviews. Disorders: PGK1 (X-linked hemolytic anemia + myopathy + CNS); PGAM2 (GSD X); ENO3 (GSD XIII); PKLR (pyruvate kinase deficiency, hemolytic anemia).

Connections

gapdh_step -> pgk_step Provides Input For
1,3-bisphosphoglycerate from GAPDH is the substrate for PGK1.
pgk_step -> pgam_step Provides Input For
3-phosphoglycerate from PGK1 is isomerised by PGAM.
pgam_step -> enolase_step Provides Input For
2-phosphoglycerate from PGAM is dehydrated by enolase.
enolase_step -> pk_step Provides Input For
Phosphoenolpyruvate from enolase is converted to pyruvate by pyruvate kinase.
Part 1: oxidative phosphorylation of the triose (NAD+ reduction)
D-glyceraldehyde-3-phosphate + NAD+ + Pi to 1,3-bisphosphoglycerate + NADHReactiongapdh_step

Annotons

GAPDH: glyceraldehyde-3-phosphate dehydrogenase
gapdh_activity
Participant: Family: Glyceraldehyde-3-phosphate dehydrogenase family (GAPDH/GAPDHS)
Family:
Glyceraldehyde-3-phosphate dehydrogenase family (GAPDH/GAPDHS)PANTHER:PTHR10836
Representative Members: GAPDH (human)UniProtKB:P04406

Function

glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activityGO:0004365
Substrates: D-glyceraldehyde 3-phosphate NAD+ phosphate
Products: 1,3-bisphospho-D-glycerate NADH

Locations

cytosolGO:0005829

Couples oxidation of glyceraldehyde-3-phosphate to formation of the high-energy acyl-phosphate 1,3-bisphosphoglycerate and reduction of NAD+ to NADH (reviewed previously; also a well-known moonlighting protein).

Part 2: first substrate-level ATP generation
1,3-bisphosphoglycerate + ADP to 3-phosphoglycerate + ATPReactionpgk_step

Annotons

PGK1/PGK2: phosphoglycerate kinase
pgk_activity
Participant: Family: Phosphoglycerate kinase family (PGK1/PGK2)
Family:
Phosphoglycerate kinase family (PGK1/PGK2)PANTHER:PTHR11406
Representative Members: PGK1 (human, somatic)UniProtKB:P00558

Function

phosphoglycerate kinase activityGO:0004618
Substrates: 1,3-bisphospho-D-glycerate ADP
Products: 3-phospho-D-glycerate ATP

Locations

cytosolGO:0005829

Generates the first ATP of glycolysis by substrate-level phosphorylation (reverse direction in gluconeogenesis). X-linked PGK1 deficiency causes hemolytic anemia with myopathy and CNS disease; PGK2 is testis-specific.

Part 3: phosphoglycerate isomerisation
3-phosphoglycerate to 2-phosphoglycerateReactionpgam_step

Annotons

PGAM1/PGAM2: phosphoglycerate mutase
pgam_activity
Participant: Family: Cofactor-dependent phosphoglycerate mutase family (PGAM1/PGAM2/BPGM)
Family:
Cofactor-dependent phosphoglycerate mutase family (PGAM1/PGAM2/BPGM)PANTHER:PTHR11931
Representative Members: PGAM2 (human, muscle isozyme)UniProtKB:P15259

Function

phosphoglycerate mutase activityGO:0004619
Substrates: 3-phospho-D-glycerate
Products: 2-phospho-D-glycerate

Locations

cytosolGO:0005829

Interconverts 3- and 2-phosphoglycerate (dimer of the muscle PGAM2/M and brain PGAM1/B subunits; muscle = PGAM2 homodimer). PGAM2 deficiency = GSD type X (exercise intolerance, myoglobinuria).

Part 4: dehydration to the high-energy enol phosphate
2-phosphoglycerate to phosphoenolpyruvate + H2OReactionenolase_step

Annotons

ENO1/ENO2/ENO3: enolase (phosphopyruvate hydratase)
enolase_activity
Participant: Family: Enolase family (ENO1/ENO2/ENO3)
Family:
Enolase family (ENO1/ENO2/ENO3)PANTHER:PTHR11902
Representative Members: ENO3 (human, muscle beta-enolase)UniProtKB:P13929

Function

phosphopyruvate hydratase activityGO:0004634
Substrates: 2-phospho-D-glycerate
Products: phosphoenolpyruvate water

Locations

cytosolGO:0005829

Mg2+-dependent dehydration of 2-phosphoglycerate to phosphoenolpyruvate. Tissue isozymes ENO1 (alpha, ubiquitous), ENO2 (gamma, neuronal), ENO3 (beta, muscle); ENO3 deficiency = GSD type XIII.

Part 5: second substrate-level ATP generation (final, committed)
phosphoenolpyruvate + ADP to pyruvate + ATPReactionpk_step

Annotons

PKM/PKLR: pyruvate kinase
pk_activity
Participant: Family: Pyruvate kinase family (PKM/PKLR)
Family:
Pyruvate kinase family (PKM/PKLR)PANTHER:PTHR11817
Representative Members: PKLR (human, liver/red-cell isozyme)UniProtKB:P30613 PKM (human, muscle/M1-M2 isozyme)UniProtKB:P14618

Function

pyruvate kinase activityGO:0004743
Substrates: phosphoenolpyruvate ADP
Products: pyruvate ATP

Locations

cytosolGO:0005829

Final, essentially irreversible glycolytic step generating the second ATP; homotetramer, Mg2+/K+-dependent, allosterically activated by fructose-1,6-bisphosphate. PKLR (liver/RBC) deficiency = pyruvate kinase deficiency (commonest glycolytic hemolytic anemia); PKM = muscle/other.