Menaquinol 6 (ECMDB21551) (M2MDB001946)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (5)Transporters (1)XML
Proteins (872)
Record Information
Version2.0
Creation Date2012-08-09 09:25:25 -0600
Update Date2015-06-03 17:21:46 -0600
Secondary Accession Numbers
  • ECMDB21551
Identification
Name:Menaquinol 6
DescriptionMenaquinol 6 is a polyprenylhydroquinone having a hexaprenyl moiety at position 2 and a methyl group at position 3. It is a substrate for Dimethyl sulfoxide reductase (dmsA). This enzyme catalyzes the reduction of dimethyl sulfoxide (DMSO) to dimethyl sulfide (DMS) using the following reaction: Dimethylsulfide + menaquinone + H2O = dimethylsulfoxide + menaquinol. DMSO reductase serves as the terminal reductase under anaerobic conditions, with DMSO being the terminal electron acceptor. Terminal reductase during anaerobic growth on various sulfoxides and N-oxide compounds. This enzyme allows E.coli to grow anaerobically on DMSO as respiratory oxidant. Menaquinol 6 is generated by Ubiquinone/menaquinone biosynthesis methyltransferase (ubiE). This enzyme is required for the conversion of demethylmenaquinone (DMKH2) to menaquinone (MKH2) and has the following catalytic activity: A demethylmenaquinone + S-adenosyl-L-methionine = a menaquinol + S-adenosyl-L-homocysteine.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • A Menaquinol
  • Menaquinol
  • Reduced menaquinone
  • Reduced vitamin K2
  • Vitamin K2 hydroquinone
Chemical Formula:C41H58O2
Weight:Average: 582.898
Monoisotopic: 582.4436811
InChI Key:ZVENTDGZQVBWNA-RCIYGOBDSA-N
InChI:InChI=1S/C41H58O2/c1-30(2)16-11-17-31(3)18-12-19-32(4)20-13-21-33(5)22-14-23-34(6)24-15-25-35(7)28-29-37-36(8)40(42)38-26-9-10-27-39(38)41(37)43/h9-10,16,18,20,22,24,26-28,42-43H,11-15,17,19,21,23,25,29H2,1-8H3/b31-18+,32-20+,33-22+,34-24+,35-28+
CAS number:39776-48-2
IUPAC Name:2-[(2E,6E,10E,14E,18E)-3,7,11,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaen-1-yl]-3-methylnaphthalene-1,4-diol
Traditional IUPAC Name:2-[(2E,6E,10E,14E,18E)-3,7,11,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaen-1-yl]-3-methylnaphthalene-1,4-diol
SMILES:[H]\C(CC\C(C)=C(/[H])CC\C(C)=C(/[H])CC\C(C)=C(/[H])CC\C(C)=C(/[H])CC1=C(O)C2=CC=CC=C2C(O)=C1C)=C(\C)CCC=C(C)C
Chemical Taxonomy
Description belongs to the class of organic compounds known as polyprenylphenols. Polyprenylphenols are compounds containing a polyisoprene chain attached to a phenol group.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassPolyprenylphenols
Direct ParentPolyprenylphenols
Alternative Parents
Substituents
  • Polyprenylphenol
  • Sesterterpenoid
  • Prenylbenzoquinol
  • 1-naphthol
  • Naphthalene
  • Hydroquinone
  • Benzenoid
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aromatic homopolycyclic compound
Molecular FrameworkAromatic homopolycyclic compounds
External Descriptors
Physical Properties
State:Not Available
Charge:0
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.00028 g/LALOGPS
logP9.29ALOGPS
logP12.9ChemAxon
logS-6.3ALOGPS
pKa (Strongest Acidic)9.38ChemAxon
pKa (Strongest Basic)-6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area40.46 ŲChemAxon
Rotatable Bond Count17ChemAxon
Refractivity194.77 m³·mol⁻¹ChemAxon
Polarizability74.45 ųChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Membrane
Reactions:
Protoporphyrinogen IX + 3 Menaquinone + 3 Menaquinone <> Protoporphyrin IX +3 Menaquinol 6
Demethylmenaquinol + S-Adenosylmethionine + Demethylmenaquinol <> Menaquinol 6 + S-Adenosylhomocysteine
Dimethyl sulfide + Menaquinone + Water > Dimethyl sulfoxide + Menaquinol 6
Protoporphyrinogen IX + 3 Menaquinone > Protoporphyrin IX +3 Menaquinol 6
A demethylmenaquinone + S-adenosyl-L-methionine > Menaquinol 6 + S-Adenosylhomocysteine
Menaquinone + Water + Dimethyl sulfide <> Menaquinol 6
Protoporphyrinogen IX + menaquinone-8 > Protoporphyrin IX + Menaquinol 6
SMPDB Pathways:
Porphyrin metabolismPW000936 ThumbThumb?image type=greyscaleThumb?image type=simple
Sulfur metabolismPW000922 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-0223090000-23a445bdcbe0768e162dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-054y-0549220000-1badad58095ed0f65faeView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0k92-2159410000-e96cf420729fd4eb7066View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-001i-0000090000-e521a6b39bcfc988308dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-0100090000-c01fde52bc298d1c3773View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-01b9-1703190000-697d8ca95a75ab4e5b61View in MoNA
MSMass Spectrum (Electron Ionization)Not AvailableView in JSpectraViewer
References
References:
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID18151
HMDB IDNot Available
Pubchem Compound ID6441040
Kegg IDC05819
ChemSpider ID4945264
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. Protoporphyrinogen oxidase
General function:
Involved in FMN binding
Specific function:
Catalyzes the 6-electron oxidation of protoporphyrinogen-IX to form protoporphyrin-IX. Does not use oxygen directly. Is coupled to the respiratory chain
Gene Name:
hemG
Uniprot ID:
P0ACB4
Molecular weight:
21226
Reactions
Protoporphyrinogen IX + 3 menaquinone = protoporphyrin IX + 3 menaquinol.
Protein Details
2. Anaerobic dimethyl sulfoxide reductase chain A
General function:
Involved in dimethyl sulfoxide reductase activity
Specific function:
Terminal reductase during anaerobic growth on various sulfoxide and N-oxide compounds. Allows E.coli to grow anaerobically on Me(2)SO as respiratory oxidant
Gene Name:
dmsA
Uniprot ID:
P18775
Molecular weight:
90398
Reactions
Dimethylsulfide + menaquinone + H(2)O = dimethylsulfoxide + menaquinol.
Protein Details
3. Anaerobic dimethyl sulfoxide reductase chain B
General function:
Involved in electron carrier activity
Specific function:
Electron transfer subunit of the terminal reductase during anaerobic growth on various sulfoxide and N-oxide compounds
Gene Name:
dmsB
Uniprot ID:
P18776
Molecular weight:
22869
Protein Details
4. Anaerobic dimethyl sulfoxide reductase chain C
General function:
Involved in anaerobic electron transport chain
Specific function:
Terminal reductase during anaerobic growth on various sulfoxide and N-oxide compounds. DmsC anchors the dmsAB dimer to the membrane and stabilizes it
Gene Name:
dmsC
Uniprot ID:
P18777
Molecular weight:
30826
Protein Details
5. Ubiquinone/menaquinone biosynthesis methyltransferase ubiE
General function:
Involved in methyltransferase activity
Specific function:
Methyltransferase required for the conversion of dimethylmenaquinone (DMKH2) to menaquinone (MKH2) and the conversion of 2-polyprenyl-6-methoxy-1,4-benzoquinol (DDMQH2) to 2-polyprenyl-3-methyl-6-methoxy-1,4-benzoquinol (DMQH2)
Gene Name:
ubiE
Uniprot ID:
P0A887
Molecular weight:
28073
Reactions
A demethylmenaquinone + S-adenosyl-L-methionine = a menaquinol + S-adenosyl-L-homocysteine.
S-adenosyl-L-methionine + 2-methoxy-6-all-trans-polyprenyl-1,4-benzoquinol = S-adenosyl-L-homocysteine + 6-methoxy-3-methyl-2-all-trans-polyprenyl-1,4-benzoquinol.

Transporters

Protein Details
1. Protein PhsC homolog
General function:
respiratory electron transport chain
Specific function:
Not Available
Gene Name:
ydhU
Uniprot ID:
P77409
Molecular weight:
29582
Reactions
=