Isoprenoid (prenyl) diphosphate biosynthesis (IPP/DMAPP -> GPP -> FPP -> GGPP)

The isoprenoid-diphosphate trunk converts the universal five-carbon isoprene units produced by the mevalonate pathway into the linear prenyl diphosphates that seed every downstream isoprenoid class. The mevalonate pathway (HMGCS1/HMGCR/MVK/PMVK/MVD, curated separately) delivers isopentenyl diphosphate (IPP). Isopentenyl-diphosphate delta-isomerase (IDI1, ubiquitous; IDI2, muscle-enriched paralog) reversibly interconverts IPP and its allylic isomer dimethylallyl diphosphate (DMAPP), balancing the two pools. Farnesyl diphosphate synthase (FDPS) then carries out two sequential head-to-tail (trans, 1'-4) condensations: DMAPP + IPP -> geranyl diphosphate (GPP, C10), and GPP + IPP -> farnesyl diphosphate (FPP, C15). FPP is the central branch point: it feeds sterol/cholesterol synthesis (via squalene, SQLE/ FDFT1), heme A, ubiquinone/CoQ side chains, dolichol (cis-prenyltransferase DHDDS/NUS1), and protein farnesylation (FTase). Geranylgeranyl diphosphate synthase (GGPS1) adds one more IPP to FPP giving geranylgeranyl diphosphate (GGPP, C20), the C20 donor for protein geranylgeranylation (GGTase-I and RabGGTase). All three enzymes are cytosolic Mg2+-dependent prenyltransferases/isomerases (IDI1/IDI2 also peroxisomal). The pathway is the pharmacological target of nitrogen bisphosphonates (FDPS); GGPS1 loss-of-function causes a muscular dystrophy / sensorineural hearing loss / ovarian insufficiency syndrome.

MODULE:isoprenoid_diphosphate_biosynthesisDRAFTMetabolic Pathwaymodules/isoprenoid_diphosphate_biosynthesis.yaml
isoprenoid biosynthetic processGO:0008299 farnesyl diphosphate biosynthetic processGO:0045337 geranylgeranyl diphosphate biosynthetic processGO:0033386
GO:0008299
isoprenoid biosynthetic process
IDI1/IDI2, FDPS and GGPS1 build the linear prenyl diphosphates of isoprenoid metabolism (GO:0008299).
GO:0045337
farnesyl diphosphate biosynthetic process
FDPS produces farnesyl diphosphate (GO:0045337) via GPP (GO:0033384).
GO:0033386
geranylgeranyl diphosphate biosynthetic process
GGPS1 produces geranylgeranyl diphosphate (GO:0033386).
file:human/IDI1/IDI1-ai-review.yaml
IDI1 gene review (human)
IPP<->DMAPP isomerase, ubiquitous (UniProtKB:Q13907, GO:0004452) matches the completed human IDI1 review.
file:human/IDI2/IDI2-ai-review.yaml
IDI2 gene review (human)
IPP<->DMAPP isomerase, muscle-enriched paralog (UniProtKB:Q9BXS1, GO:0004452) matches the completed human IDI2 review.
file:human/FDPS/FDPS-ai-review.yaml
FDPS gene review (human)
Farnesyl diphosphate synthase, DMAPP+IPP->GPP->FPP (UniProtKB:P14324, GO:0004337/GO:0004161) matches the completed human FDPS review.
file:human/GGPS1/GGPS1-ai-review.yaml
GGPS1 gene review (human)
Geranylgeranyl diphosphate synthase, FPP+IPP->GGPP (UniProtKB:O95749, GO:0004311) matches the completed human GGPS1 review.
4Nodes
3Parts
0Variant Sets
0Variants
3Annotons
2Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:isoprenoid_diphosphate_biosynthesis 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.

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

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

Gene Review Complete Deep research
FDPS P14324 ✓ ✓ ✗
GGPS1 O95749 ✓ ✓ ✗
IDI1 Q13907 ✓ ✓ ✗
IDI2 Q9BXS1 ✓ ✓ ✗

Details

Context
cytosolGO:0005829 peroxisomeGO:0005777
Isoprenoid (prenyl) diphosphate biosynthesisMetabolic Pathwayisoprenoid_diphosphate_biosynthesis
isoprenoid biosynthetic processGO:0008299 farnesyl diphosphate biosynthetic processGO:0045337 geranylgeranyl diphosphate biosynthetic processGO:0033386
Context
cytosolGO:0005829 peroxisomeGO:0005777

Isoprenoid (prenyl) diphosphate biosynthesis trunk (GO:0008299), grounded to four completed human gene reviews; the bridge between the mevalonate pathway (HMGCS1/HMGCR/MVK/PMVK/MVD, separate) and the sterol, dolichol, ubiquinone and protein-prenylation branches. IDI1 (Q13907 PTHR10885, ubiquitous) + IDI2 (Q9BXS1 PTHR10885, muscle-enriched paralog) reversibly isomerize IPP<->DMAPP (GO:0004452; cytosol + peroxisome via PTS1). FDPS (P14324 PTHR11525) does two sequential trans condensations DMAPP+IPP->GPP (GO:0004161) then GPP+IPP->FPP (GO:0004337) — the central C15 branch point; it is the nitrogen-bisphosphonate drug target. GGPS1 (O95749 PTHR12001, homohexamer) adds one IPP to FPP -> GGPP (GO:0004311), the C20 donor for GGTase-I/RabGGTase (see protein_prenylation_caax_processing module). All cytosolic, Mg2+-dependent. GGPS1 loss-of-function -> muscular dystrophy/sensorineural hearing loss/ovarian insufficiency. FDPS/GGPS1 partial-reaction EC activities (GO:0004161/GO:0004337 shared active site) kept non-core where redundant. GO term ids/labels verified against the local go.db; module passes structural + term-label validation.

Connections

ipp_isomerization -> fpp_synthesis Provides Input For
IDI supplies the DMAPP primer (and balances IPP) that FDPS condenses to GPP/FPP.
fpp_synthesis -> ggpp_synthesis Provides Input For
FDPS-made FPP is the substrate GGPS1 elongates to GGPP.
Part 1: IPP/DMAPP isomerization
Isopentenyl-diphosphate delta-isomerase (IDI1 / IDI2)Reactionipp_isomerization

Annotons

IDI1/IDI2: isopentenyl-diphosphate delta-isomerase
idi_activity
Participant: Family: IDI / isopentenyl-diphosphate delta-isomerase (type 1) family
Family:
IDI / isopentenyl-diphosphate delta-isomerase (type 1) familyPANTHER:PTHR10885
Representative Members: IDI1 (human; ubiquitous)UniProtKB:Q13907 IDI2 (human; muscle-enriched)UniProtKB:Q9BXS1

Function

isopentenyl-diphosphate delta-isomerase activityGO:0004452
Substrates: isopentenyl diphosphate (IPP)
Products: dimethylallyl diphosphate (DMAPP)

Locations

cytosolGO:0005829 peroxisomeGO:0005777

Interconvert IPP and DMAPP to balance the isoprene-unit pools.

Part 2: GPP + FPP synthesis (trans-prenyltransferase)
Farnesyl diphosphate synthase (FDPS)Reactionfpp_synthesis

Annotons

FDPS: farnesyl diphosphate synthase (DMAPP+IPP->GPP->FPP)
fdps_activity
Participant: Family: FDPS / farnesyl pyrophosphate synthase family
Family:
FDPS / farnesyl pyrophosphate synthase familyPANTHER:PTHR11525
Representative Members: FDPS (human)UniProtKB:P14324

Function

(2E,6E)-farnesyl diphosphate synthase activityGO:0004337
Substrates: dimethylallyl diphosphate (DMAPP) isopentenyl diphosphate (IPP; Mg2+)
Products: (2E,6E)-farnesyl diphosphate (FPP) geranyl diphosphate (GPP; intermediate) diphosphate

Locations

cytosolGO:0005829

Elongate DMAPP with two IPP units to the C15 branch-point precursor FPP.

Part 3: GGPP synthesis (trans-prenyltransferase)
Geranylgeranyl diphosphate synthase (GGPS1)Reactionggpp_synthesis

Annotons

GGPS1: geranylgeranyl diphosphate synthase (FPP+IPP->GGPP)
ggps1_activity
Participant: Family: GGPS1 / geranylgeranyl pyrophosphate synthase family
Family:
GGPS1 / geranylgeranyl pyrophosphate synthase familyPANTHER:PTHR12001
Representative Members: GGPS1 (human)UniProtKB:O95749

Function

geranylgeranyl diphosphate synthase activityGO:0004311
Substrates: (2E,6E)-farnesyl diphosphate (FPP) isopentenyl diphosphate (IPP; Mg2+)
Products: (2E,6E,10E)-geranylgeranyl diphosphate (GGPP) diphosphate

Locations

cytosolGO:0005829

Elongate FPP with one IPP unit to the C20 donor GGPP.