Metabolic Modeling Tutorial
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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MetaCyc Compound Class: a menaquinone

Abbrev Name: MQ

Synonyms: a vitamin K2

Superclasses: a redox electron carrier Membrane-Electron-Carriers an electron-transfer-related quinone
a vitamin a vitamin K
an aldehyde or ketone a ketone a cyclic ketone a quinone an electron-transfer-related quinone

Summary:
Menaquinones and demethylmenaquinones are isoprenoid quinones of the naphthalene series, and are constituents of bacterial plasma membranes, where they play important roles in electron transfer and oxidative phosphorylation. Menaquinones are the most widespread respiratory quinones in biological system [Fujimoto12]. Menaquinones and demethylmenaquinones are named MK-n or DMK-n, respectively, where the n refers to the number of prenyl units present in the side chain. The most common length of the side chain in bacteria is 8, although minor amounts of MK-1 through MK-14 have been found [Collins81].

Many bacteria and archaea have dehydrogenated menaquinones, which are named MK-n(H2). The degree and location of dehydrogenation depends on the species. Some organisms have menaquinones with modifications of the head group, for example Thermoplasma possess both thermoplasmaquinones (TPQ), which contains an extra methyl group, and methionaquinones (MTK), which contains a methylthio group [Shimada01].

Menaquinones are also known as vitamin K2. Vitamin K is a name given to a group of derivatives of 2-methyl-1,4-naphthoquinone that are required by mammals for the posttranslational modification of certain proteins, mostly involved in blood coagulation. These compounds, while essential for mammals, are not synthesized by them, and are thus considered vitamins.

The natural forms of the vitamin are vitamin K1 (phylloquinone) and vitamin K2 (menaquinone). Since menaquinones produced by different organisms have different tail lengths there are many variations of vitamin K2, usually specified based on the number of carbons in their tails, such as in Vitamin K2(45).

The reduced form of menaquinone is called a menaquinol.

Child Classes: a dihidromenaquinone (2) , a modified menaquinone (0)

Instances:
menaquinone-1 ,
menaquinone-2 ,
menaquinone-3 ,
menaquinone-4 ,
menaquinone-5 ,
menaquinone-6 ,
menaquinone-7 ,
menaquinone-8 ,
menaquinone-9 ,
menaquinone-10 ,
menaquinone-11 ,
menaquinone-12 ,
menaquinone-13 ,
methionaquinone-7 ,
thermoplasmaquinone-7

SMILES: CC(C[R])=CCC1(C(C2(C(C(C=1C)=O)=CC=CC=2))=O)

Unification Links: KEGG:C00828

Reactions known to consume the compound:

formate to dimethyl sulfoxide electron transfer , formate to trimethylamine N-oxide electron transfer , nitrate reduction III (dissimilatory) :
formate[periplasmic space] + a menaquinone[inner membrane] + 2 H+ → CO2[periplasmic space] + a menaquinol[inner membrane] + H+[periplasmic space]

glycerol-3-phosphate to fumarate electron transfer :
sn-glycerol 3-phosphate + a menaquinone[inner membrane] → dihydroxyacetone phosphate + a menaquinol[inner membrane]

heme biosynthesis II (anaerobic) :
protoporphyrinogen IX + 3 a menaquinone → protoporphyrin IX + 3 a menaquinol

NADH to dimethyl sulfoxide electron transfer , NADH to fumarate electron transfer , NADH to trimethylamine N-oxide electron transfer , nitrate reduction VIII (dissimilatory) :
NADH + a menaquinone[inner membrane] + 5 H+ → NAD+ + a menaquinol[inner membrane] + 4 H+[periplasmic space]

sulfite oxidation V (SoeABC) :
sulfite + a menaquinone + H2O → sulfate + a menaquinol

TCA cycle VIII (helicobacter) :
(S)-malate + a menaquinone → oxaloacetate + a menaquinol

Not in pathways:
a menaquinone[inner membrane] + 2 H+ + H2[periplasmic space] → a menaquinol[inner membrane] + 2 H+[periplasmic space]
(S)-dihydroorotate + a menaquinone[inner membrane] → orotate + a menaquinol[inner membrane]

(5R)-carbapenem carboxylate biosynthesis , citrulline biosynthesis , L-Nδ-acetylornithine biosynthesis , proline degradation :
L-proline + an electron-transfer-related quinone[inner membrane] → (S)-1-pyrroline-5-carboxylate + an electron-transfer-related quinol[inner membrane] + H+

4-hydroxymandelate degradation :
(S)-4-hydroxymandelate + an electron-transfer-related quinone → 2-(4-hydroxyphenyl)-2-oxoacetate + an electron-transfer-related quinol

alanine degradation I :
D-alanine + an electron-transfer-related quinone[inner membrane] + H2O → ammonium + pyruvate + an electron-transfer-related quinol[inner membrane]

sulfide oxidation I (sulfide-quinone reductase) :
hydrogen sulfide + an electron-transfer-related quinone → intracellular S0 + an electron-transfer-related quinol

TCA cycle IV (2-oxoglutarate decarboxylase) , TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase) , TCA cycle VII (acetate-producers) :
succinate[in] + an electron-transfer-related quinone[CCO-OUT-CCO-IN] → fumarate[in] + an electron-transfer-related quinol[CCO-OUT-CCO-IN]

trans-4-hydroxy-L-proline degradation I :
trans-4-hydroxy-L-proline[in] + an electron-transfer-related quinone → pyrroline-hydroxy-carboxylate[in] + an electron-transfer-related quinol + H+[in]

trans-lycopene biosynthesis II (plants) :
7,9,9'-cis-neurosporene + an electron-transfer-related quinone → prolycopene + an electron-transfer-related quinol
9,9'-di-cis-ζ-carotene + an electron-transfer-related quinone → 7,9,9'-cis-neurosporene + an electron-transfer-related quinol


(S)-dihydroorotate + an electron-transfer-related quinone[inner membrane] → orotate + an electron-transfer-related quinol[inner membrane]
NADPH + an electron-transfer-related quinone + H+ → NADP+ + an electron-transfer-related quinol
a D-amino acid[in] + an electron-transfer-related quinone[CCO-OUT-CCO-IN] + H2O[in] → a 2-oxo carboxylate[in] + ammonium[in] + an electron-transfer-related quinol[CCO-OUT-CCO-IN]
D-glucopyranose[out] + an electron-transfer-related quinone + 2 H+[in] → D-glucono-1,5-lactone[out] + an electron-transfer-related quinol + 2 H+[out]
sn-glycerol 3-phosphate[in] + an electron-transfer-related quinone[CCO-OUT-CCO-IN] → dihydroxyacetone phosphate[in] + an electron-transfer-related quinol[CCO-OUT-CCO-IN]

quinate degradation I :
L-quinate + a quinone → 3-dehydroquinate + a quinol

shikimate degradation I :
shikimate + a quinone → 3-dehydroshikimate + a quinol

TCA cycle I (prokaryotic) , TCA cycle VII (acetate-producers) :
(S)-malate + a quinone → oxaloacetate + a quinol

thiosulfate oxidation II (to tetrathionate) :
2 thiosulfate + a quinone → tetrathionate + a quinol


a quinone + NAD(P)H + H+ → a quinol + NAD(P)+
a cyclic alcohol + a quinonea cyclic ketone + a quinol


a cyclic alcohol + a quinonea cyclic ketone + a quinol

Reactions known to produce the compound:

formate to dimethyl sulfoxide electron transfer , NADH to dimethyl sulfoxide electron transfer :
dimethyl sulfoxide[periplasmic space] + a menaquinol[inner membrane] → dimethyl sulfide[periplasmic space] + a menaquinone[inner membrane] + H2O[periplasmic space]

formate to trimethylamine N-oxide electron transfer , NADH to trimethylamine N-oxide electron transfer :
trimethylamine N-oxide[periplasmic space] + a menaquinol[inner membrane] + H+[periplasmic space] → trimethylamine[periplasmic space] + a menaquinone[inner membrane] + H2O[periplasmic space]

nitrate reduction III (dissimilatory) , nitrate reduction VIII (dissimilatory) :
nitrate + a menaquinol[inner membrane] + 2 H+ → nitrite + a menaquinone[inner membrane] + H2O + 2 H+[periplasmic space]

nitrate reduction VII (denitrification) :
2 nitric oxide + a menaquinol → nitrous oxide + a menaquinone + H2O

Not in pathways:
S-adenosyl-L-methionine + a demethylmenaquinone → S-adenosyl-L-homocysteine + a menaquinone
2 a menaquinol + oxygen[in] + 8 H+[in] → 2 a menaquinone + 8 H+[out] + 2 H2O[in]
2 an oxidized c-type cytochrome[out] + a menaquinol → 2 a reduced c-type cytochrome[out] + a menaquinone + 2 H+[in]

methane oxidation to methanol II :
methane + an electron-transfer-related quinol + oxygen → methanol + an electron-transfer-related quinone + H2O

TCA cycle VI (obligate autotrophs) :
succinate[in] + an electron-transfer-related quinone[CCO-OUT-CCO-IN] ← fumarate[in] + an electron-transfer-related quinol[CCO-OUT-CCO-IN]


2 an oxidized c-type cytochrome[out] + an electron-transfer-related quinol → 2 a reduced c-type cytochrome[out] + an electron-transfer-related quinone + 2 H+[in]

cuticular wax biosynthesis :
a secondary alcohol + an oxidized electron acceptor → a ketone + a reduced electron acceptor


a secondary alcohol + oxygen → a ketone + hydrogen peroxide


a nitroalkane + oxygen + H2O → an aldehyde or ketone + nitrite + hydrogen peroxide + H+

Reactions known to both consume and produce the compound:

glycerol-3-phosphate to fumarate electron transfer , incomplete reductive TCA cycle , mixed acid fermentation , NADH to fumarate electron transfer , pyruvate fermentation to propionate I , reductive TCA cycle I , reductive TCA cycle II , TCA cycle VIII (helicobacter) :
fumarate[in] + a menaquinol[CCO-OUT-CCO-IN] ↔ succinate[in] + a menaquinone[CCO-OUT-CCO-IN]

nitrate reduction I (denitrification) , nitrate reduction VII (denitrification) :
nitrate[in] + an electron-transfer-related quinol ↔ nitrite[in] + an electron-transfer-related quinone + H2O[in]

Not in pathways:
a quinone + NADPH ↔ a semiquinone + NADP+

In Reactions of unknown directionality:

Not in pathways:
a menaquinone + H2 = a menaquinol


9,9'-di-cis-ζ-carotene + 2 an electron-transfer-related quinone = prolycopene + 2 an electron-transfer-related quinol
formate + an electron-transfer-related quinone + H+ = CO2 + an electron-transfer-related quinol
NADH + an electron-transfer-related quinone + H+ = NAD+ + an electron-transfer-related quinol
an (R)-2-hydroxyacid + an electron-transfer-related quinone = a 2-oxo acid + an electron-transfer-related quinol
an oxidized coenzyme F420 + an electron-transfer-related quinol = a reduced coenzyme F420 + an electron-transfer-related quinone


phenylacetyl-CoA + 2 a quinone + H2O = 2 a quinol + phenylglyoxylyl-CoA
a quinone + NADH = a semiquinone + NAD+
1-(β-D-ribofuranosyl)-1,4-dihydronicotinamide + a quinone + H+ = a quinol + 1-(β-D ribofuranosyl)nicotinamide


a ketone + NADP+ = an enone + NADPH + H+
a secondary alcohol + an oxidized coenzyme F420 = a ketone + a reduced coenzyme F420
a secondary alcohol + NADP+ = a ketone + NADPH + H+
a secondary alcohol + NAD+ = a ketone + NADH + H+

In Redox half-reactions:
a menaquinone + 2 H+[in] + 2 e- → a menaquinol ,
a menaquinone + 2 H+[out] + 2 e- → a menaquinol ,
an electron-transfer-related quinone + 2 H+[in] + 2 e- → an electron-transfer-related quinol

This compound has been characterized as a cofactor or prosthetic group of the following enzymes: putrescine oxidase

Credits:
Revised 17-Aug-2009 by Caspi R , SRI International


References

Collins81: Collins MD, Jones D (1981). "Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication." Microbiol Rev 45(2);316-54. PMID: 7022156

Fujimoto12: Fujimoto N., Kosaka T., Yamada M. (2012). "Menaquinone as Well as Ubiquinone as a Crucial Component in the Escherichia coli Respiratory Chain." Chapter 10 in Chemical Biology, edited by D Ekinci, ISBN 978-953-51-0049-2.

Shimada01: Shimada H, Shida Y, Nemoto N, Oshima T, Yamagishi A (2001). "Quinone profiles of Thermoplasma acidophilum HO-62." J Bacteriol 183(4);1462-5. PMID: 11157962


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Fri Nov 28, 2014, biocyc13.