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.