Coenzyme Q10 (ubiquinone) biosynthesis (PDSS1/2, COQ2-COQ9)

Coenzyme Q10 (ubiquinone-10) is the lipophilic electron/proton carrier of the mitochondrial inner membrane that shuttles electrons from respiratory Complexes I and II (and from electron-transfer flavoprotein, dihydroorotate dehydrogenase and others) to Complex III, and is a membrane antioxidant. Its biosynthesis has two arms that meet at the matrix face of the inner membrane. First, the C50 polyisoprenoid tail is built: the all-trans-decaprenyl-diphosphate synthase, a heterotetramer of PDSS1 and PDSS2, condenses (2E,6E)-farnesyl diphosphate with isopentenyl diphosphate units to all-trans- decaprenyl diphosphate. The polytopic inner-membrane prenyltransferase COQ2 then attaches this tail to the ring precursor 4-hydroxybenzoate, committing it to the pathway. A series of ring modifications, carried out by a membrane-associated multienzyme assembly (the "COQ synthome"/complex Q), converts the polyprenyl-hydroxybenzoate to ubiquinol: FAD-dependent hydroxylation by COQ6, C-methylation by the SAM-dependent methyltransferase COQ5, Zn-dependent C1 decarboxylation by COQ4, di-iron C6 hydroxylation by COQ7 (whose lipophilic substrate is bound and presented by the lipid-binding protein COQ9), and the two O-methylation steps performed by COQ3 (not covered here). Assembly and activity of the synthome require the atypical UbiB-family kinase/ATPases COQ8A and COQ8B. The exact order of the head-group modifications in humans is not fully resolved, and the enzymes act within the synthome complex rather than as free-standing steps. Defects in any of these genes cause primary coenzyme Q10 deficiency, a clinically heterogeneous mitochondrial disease (encephalomyopathy, cerebellar ataxia, steroid-resistant nephrotic syndrome, Leigh syndrome), some forms of which are partially responsive to oral CoQ10.

MODULE:coenzyme_q10_biosynthesisDRAFTMetabolic Pathwaymodules/coenzyme_q10_biosynthesis.yaml
ubiquinone biosynthetic processGO:0006744
GO:0006744
ubiquinone biosynthetic process
PDSS1/2 and COQ2-COQ9 together carry out ubiquinone (CoQ10) biosynthesis (GO:0006744).
file:human/PDSS1/PDSS1-ai-review.yaml
PDSS1 gene review (human)
The decaprenyl-diphosphate synthase subunit (UniProtKB:Q5T2R2, GO:0097269) matches the completed human PDSS1 review.
file:human/PDSS2/PDSS2-ai-review.yaml
PDSS2 gene review (human)
The decaprenyl-diphosphate synthase subunit (UniProtKB:Q86YH6, GO:0097269) matches the completed human PDSS2 review.
file:human/COQ2/COQ2-ai-review.yaml
COQ2 gene review (human)
The 4-hydroxybenzoate polyprenyltransferase step (UniProtKB:Q96H96, GO:0008412) matches the completed human COQ2 review.
file:human/COQ6/COQ6-ai-review.yaml
COQ6 gene review (human)
The FAD-dependent ring hydroxylase step (UniProtKB:Q9Y2Z9, GO:0106364) matches the completed human COQ6 review.
file:human/COQ5/COQ5-ai-review.yaml
COQ5 gene review (human)
The C-methyltransferase step (UniProtKB:Q5HYK3, GO:0008425) matches the completed human COQ5 review.
file:human/COQ4/COQ4-ai-review.yaml
COQ4 gene review (human)
The Zn-dependent decarboxylase / synthome-organizer (UniProtKB:Q9Y3A0, GO:0120539) matches the completed human COQ4 review.
file:human/COQ7/COQ7-ai-review.yaml
COQ7 gene review (human)
The di-iron 3-demethoxyubiquinone hydroxylase step (UniProtKB:Q99807, GO:0160224) matches the completed human COQ7 review.
file:human/COQ9/COQ9-ai-review.yaml
COQ9 gene review (human)
The lipid-binding substrate-presenter for COQ7 (UniProtKB:O75208, GO:0008289/GO:0019840) matches the completed human COQ9 review.
file:human/COQ8A/COQ8A-ai-review.yaml
COQ8A gene review (human)
The atypical UbiB-family kinase/ATPase synthome regulator (UniProtKB:Q8NI60, GO:0006744) matches the completed human COQ8A review.
file:human/COQ8B/COQ8B-ai-review.yaml
COQ8B gene review (human)
The atypical UbiB-family kinase synthome regulator (UniProtKB:Q96D53, GO:0006744) matches the completed human COQ8B review.
9Nodes
8Parts
0Variant Sets
0Variants
8Annotons
7Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:coenzyme_q10_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 (10/10 grounded genes reviewed)

10 complete review(s) · 0 with deep research · 0 missing review · 10 reviewed but lacking deep research

Gene Review Complete Deep research
COQ2 Q96H96 ✓ ✓ ✗
COQ4 Q9Y3A0 ✓ ✓ ✗
COQ5 Q5HYK3 ✓ ✓ ✗
COQ6 Q9Y2Z9 ✓ ✓ ✗
COQ7 Q99807 ✓ ✓ ✗
COQ8A Q8NI60 ✓ ✓ ✗
COQ8B Q96D53 ✓ ✓ ✗
COQ9 O75208 ✓ ✓ ✗
PDSS1 Q5T2R2 ✓ ✓ ✗
PDSS2 Q86YH6 ✓ ✓ ✗

Details

Context
mitochondrial inner membraneGO:0005743 mitochondrial matrixGO:0005759
Coenzyme Q10 (ubiquinone) biosynthesisMetabolic Pathwaycoenzyme_q10_biosynthesis
ubiquinone biosynthetic processGO:0006744
Context
mitochondrial inner membraneGO:0005743 mitochondrial matrixGO:0005759

Coenzyme Q10 (ubiquinone) biosynthesis (GO:0006744), grounded to ten completed human gene reviews. Tail: PDSS1 (Q5T2R2) + PDSS2 (Q86YH6) share PTHR12001 and form the heterotetrameric decaprenyl- diphosphate synthase (GO:0097269; complex GO:0032478). Ring commitment: COQ2 (Q96H96 PTHR11048, GO:0008412 4-HB polyprenyltransferase, inner membrane). Head-group modification (the membrane- associated "COQ synthome"/complex Q, GO:0110142): COQ6 (Q9Y2Z9 PTHR43876, GO:0106364 FAD monooxygenase), COQ5 (Q5HYK3 PTHR43591, GO:0008425 SAM C-methyltransferase), COQ4 (Q9Y3A0 PTHR12922, GO:0120539 Zn C1 decarboxylase + synthome scaffold — the catalytic role is from 2024 biochemistry, superseding the older "non-catalytic scaffold" view), COQ7 (Q99807 PTHR11237, GO:0160224 di-iron C6 hydroxylase — di-iron, NOT flavin), with COQ9 (O75208 PTHR21427) a non-catalytic lipid-binding protein that presents the DMQ substrate to COQ7. The two O-methylation steps (COQ3) are not covered (COQ3 is not in the dismech gene set). Assembly/activity of the synthome requires the atypical UbiB-family enzymes COQ8A (Q8NI60) and COQ8B (Q96D53), which share PTHR43851: COQ8A's demonstrated activity is an ATPase (it explicitly LACKS canonical in-trans protein-kinase activity — a NOT annotation), whereas COQ8B has a demonstrated COQ3-directed protein-kinase activity; both are ATP-binding and regulatory rather than pathway-metabolite enzymes, so they are modelled with `processes` (GO:0006744) not a catalytic `function`. CoQ10 is the electron carrier feeding the OXPHOS Complex III curated in the respiratory-chain modules. GO term ids/labels verified against the local go.db. Disorders: primary CoQ10 deficiency COQ10D1-D9 (COQ2 D1, PDSS1 D2, PDSS2 D3, COQ8A D4, COQ9 D5, COQ6 D6, COQ4 D7, COQ7 D8, COQ8B D9), variably CoQ10-responsive.

Connections

The decaprenyl diphosphate made by PDSS1/2 is the prenyl donor for COQ2.
ring_prenylation -> c5_hydroxylation Provides Input For
3-decaprenyl-4-hydroxybenzoate enters the COQ synthome for ring modification (the precise order of hydroxylations, methylations and decarboxylation, including the COQ3 O-methylation steps not modelled here, is not fully resolved in humans).
c5_hydroxylation -> c2_methylation Provides Input For
The hydroxylated ring intermediate is C-methylated by COQ5.
c2_methylation -> c1_decarboxylation Provides Input For
The methylated ring intermediate is decarboxylated by COQ4.
c1_decarboxylation -> c6_hydroxylation Provides Input For
The decarboxylated demethoxyubiquinol is the substrate for the COQ7 di-iron hydroxylase.
substrate_presentation -> c6_hydroxylation Positively Regulates
COQ9 binds and presents the lipophilic DMQ substrate to COQ7, activating hydroxylation.
synthome_regulation -> c1_decarboxylation Positively Regulates
The COQ8A/COQ8B atypical kinase/ATPases are required for assembly and activity of the COQ synthome (represented here on the COQ4 organizer node); loss destabilises the whole complex.
Part 1: decaprenyl (C50) tail synthesis
Decaprenyl-diphosphate synthase (PDSS1 + PDSS2)Reactiondecaprenyl_pp_synthesis

Annotons

PDSS1/PDSS2: all-trans-decaprenyl-diphosphate synthase
pdss_activity
Participant: Family: PDSS / trans-polyprenyl-diphosphate synthase family
Family:
PDSS / trans-polyprenyl-diphosphate synthase familyPANTHER:PTHR12001
Representative Members: PDSS1 (human)UniProtKB:Q5T2R2 PDSS2 (human)UniProtKB:Q86YH6

Function

all-trans-decaprenyl-diphosphate synthase activityGO:0097269
Substrates: (2E,6E)-farnesyl diphosphate isopentenyl diphosphate (7x)
Products: all-trans-decaprenyl diphosphate diphosphate

Locations

mitochondrial matrixGO:0005759

Builds the all-trans-decaprenyl (C50) tail of CoQ10.

Part 2: ring prenylation
4-hydroxybenzoate polyprenyltransferase (COQ2)Reactionring_prenylation

Annotons

COQ2: 4-hydroxybenzoate polyprenyltransferase
coq2_activity
Participant: Family: COQ2 / UbiA prenyltransferase family
Family:
COQ2 / UbiA prenyltransferase familyPANTHER:PTHR11048
Representative Members: COQ2 (human)UniProtKB:Q96H96

Function

4-hydroxybenzoate polyprenyltransferase activityGO:0008412
Substrates: 4-hydroxybenzoate all-trans-decaprenyl diphosphate (Mg2+)
Products: 3-decaprenyl-4-hydroxybenzoate diphosphate

Locations

mitochondrial inner membraneGO:0005743

Attaches the decaprenyl tail to 4-hydroxybenzoate.

Part 3: ring C5 hydroxylation
Ubiquinone biosynthesis monooxygenase (COQ6)Reactionc5_hydroxylation

Annotons

COQ6: FAD-dependent ring hydroxylase
coq6_activity
Participant: Family: COQ6 / ubiquinone biosynthesis monooxygenase family
Family:
COQ6 / ubiquinone biosynthesis monooxygenase familyPANTHER:PTHR43876
Representative Members: COQ6 (human)UniProtKB:Q9Y2Z9

Function

4-hydroxy-3-all-trans-polyprenylbenzoate oxygenase activityGO:0106364
Substrates: 3-decaprenyl-4-hydroxybenzoate ring intermediate O2 (FAD; electrons via ferredoxin FDX2/FDXR)
Products: hydroxylated (C5) ring intermediate

Locations

mitochondrial inner membraneGO:0005743

FAD-dependent hydroxylation of the CoQ ring intermediate.

Part 4: ring C2 methylation
2-methoxy-6-polyprenyl-1,4-benzoquinol methylase (COQ5)Reactionc2_methylation

Annotons

COQ5: C-methyltransferase (SAM)
coq5_activity
Participant: Family: COQ5 / 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase family
Family:
COQ5 / 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase familyPANTHER:PTHR43591
Representative Members: COQ5 (human)UniProtKB:Q5HYK3

Function

2-methoxy-6-polyprenyl-1,4-benzoquinol methyltransferase activityGO:0008425
Substrates: 2-methoxy-6-polyprenyl-1,4-benzoquinol S-adenosyl-L-methionine
Products: C2-methylated ring intermediate S-adenosyl-L-homocysteine

Locations

mitochondrial matrixGO:0005759

SAM-dependent C-methylation of the CoQ ring.

Part 5: ring C1 decarboxylation (+ synthome organization)
COQ4 (Zn decarboxylase / synthome organizer)Reactionc1_decarboxylation

Annotons

COQ4: 4-hydroxy-3-methoxy-5-polyprenylbenzoate decarboxylase
coq4_activity
Participant: Family: COQ4 family
Family:
COQ4 familyPANTHER:PTHR12922
Representative Members: COQ4 (human)UniProtKB:Q9Y3A0

Function

4-hydroxy-3-methoxy-5-polyprenylbenzoate decarboxylase activityGO:0120539
Substrates: 4-hydroxy-3-methoxy-5-polyprenylbenzoate ring intermediate (Zn2+)
Products: C1-decarboxylated ring intermediate CO2

Locations

mitochondrial inner membraneGO:0005743

Zn-dependent C1 decarboxylation; scaffolds the COQ synthome.

Part 6: ring C6 hydroxylation
3-demethoxyubiquinone hydroxylase (COQ7)Reactionc6_hydroxylation

Annotons

COQ7: di-iron 3-demethoxyubiquinone 3-hydroxylase
coq7_activity
Participant: Family: COQ7 / di-iron demethoxyubiquinone hydroxylase family
Family:
COQ7 / di-iron demethoxyubiquinone hydroxylase familyPANTHER:PTHR11237
Representative Members: COQ7 (human)UniProtKB:Q99807

Function

3-demethoxyubiquinone 3-hydroxylase (NADH) activityGO:0160224
Substrates: 3-demethoxyubiquinol (DMQ) O2 (carboxylate-bridged di-iron center)
Products: 3-demethylubiquinol

Locations

mitochondrial inner membraneGO:0005743

Di-iron C6 hydroxylation of demethoxyubiquinol (penultimate step).

Part 7: substrate presentation to COQ7
Lipid-binding presenter (COQ9)Reactionsubstrate_presentation

Annotons

COQ9: lipid-binding substrate presenter
coq9_activity
Participant: Family: COQ9 family
Family:
COQ9 familyPANTHER:PTHR21427
Representative Members: COQ9 (human)UniProtKB:O75208

Processes

ubiquinone biosynthetic processGO:0006744

Locations

mitochondrial inner membraneGO:0005743

Non-catalytic lipid-binding protein; binds and presents the lipophilic DMQ substrate to COQ7 (COQ7:COQ9 module), activating the penultimate hydroxylation. Deficiency = COQ10D5.

Part 8: synthome assembly/activation
Atypical UbiB-family kinase/ATPase (COQ8A + COQ8B)Reactionsynthome_regulation

Annotons

COQ8A/COQ8B: atypical kinase/ATPase synthome regulator
coq8_activity
Participant: Family: COQ8 / ADCK (UbiB) atypical kinase family
Family:
COQ8 / ADCK (UbiB) atypical kinase familyPANTHER:PTHR43851
Representative Members: COQ8A (human)UniProtKB:Q8NI60 COQ8B (human)UniProtKB:Q96D53

Processes

ubiquinone biosynthetic processGO:0006744

Locations

mitochondrial matrixGO:0005759

ATP-binding UbiB-family enzymes required for assembly/activity of the COQ synthome. COQ8A's demonstrated activity is an ATPase (not canonical protein kinase); COQ8B has a COQ3-directed protein-kinase activity. COQ8A -> COQ10D4/ARCA2 ataxia; COQ8B -> COQ10D9 steroid-resistant nephrotic syndrome.