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Information on EC 4.1.1.98 - 4-hydroxy-3-polyprenylbenzoate decarboxylase
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4.1.1.98 4-hydroxy-3-polyprenylbenzoate decarboxylaseIUBMB Comments
The enzyme catalyses a step in prokaryotic ubiquinone biosynthesis, as well as in plastoquinone biosynthesis in cyanobacteria. The enzyme can accept substrates with different polyprenyl tail lengths in vitro, but uses a specific length in vivo, which is determined by the polyprenyl diphosphate synthase that exists in the specific organism. It requires a prenylated flavin cofactor that is produced by EC 2.5.1.129, flavin prenyltransferase.
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Word Map
- 4.1.1.98
- ubiquinone
- aeruginosa
-
fmn-free
-
colwellia
- psychrerythraea
-
fmn-bound
-
psychrophilic
- decarboxylases
- transposon
-
uniprotkb
- phenol
The expected taxonomic range for this enzyme is: Bacteria, Archaea
Synonyms
pa0254, cpsubix, slr1099, 3-octaprenyl-4-hydroxybenzoate carboxy-lyase, 3-octaprenyl-4-hydroxybenzoate decarboxylase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
3-octaprenyl-4-hydroxybenzoate carboxy-lyase
3-octaprenyl-4-hydroxybenzoate decarboxylase
flavin mononucleotide-dependent aromatic acid decarboxylase
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PAD1
slr1099
ubiD
ubiX
yigC
PAD1
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slr1099
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-
-
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ubiD
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-
-
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ubiX
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-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
a 4-hydroxy-3-polyprenylbenzoate = a 2-polyprenylphenol + CO2
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PATHWAY SOURCE
PATHWAYS
BRENDA
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, , , ,
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SYSTEMATIC NAME
IUBMB Comments
4-hydroxy-3-polyprenylbenzoate carboxy-lyase
The enzyme catalyses a step in prokaryotic ubiquinone biosynthesis, as well as in plastoquinone biosynthesis in cyanobacteria. The enzyme can accept substrates with different polyprenyl tail lengths in vitro, but uses a specific length in vivo, which is determined by the polyprenyl diphosphate synthase that exists in the specific organism. It requires a prenylated flavin cofactor that is produced by EC 2.5.1.129, flavin prenyltransferase.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
4-hydroxy-3-farnesylbenzoate
? + CO2
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highest activity with 4-hydroxy-3-farnesylbenzoate
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-
?
3-octaprenyl-4-hydroxybenzoate
2-octaprenylphenol + CO2
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-
-
?
a 4-hydroxy-3-polyprenylbenzoate
a 2-polyprenylphenol + CO2
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-
-
?
additional information
?
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analysis of the conformational changes upon FMN binding and the enzymatic mechanism at the molecular level, overview
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-
?
additional information
?
-
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very low specific activity with 4-hydroxy-3-octaprenylbenzoate
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-
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
a 4-hydroxy-3-polyprenylbenzoate
a 2-polyprenylphenol + CO2
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-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
FMN
enzyme uses a prenylated FMN cofactor. Formation of holoUbiD requires reconstitution in vitro of the apoUbiD with reduced prenylated FMN. A proton-coupled electron transfer may precede formation of the fully oxidized prenylated FMN
FMN
wild-type CpsUbiX has an FMN:protein molar ratio of 1.028:1. The protein with a V47S single mutation cannot bind FMN and has an FMN:protein molar ratio of 0.086:1
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
the addition of divalent cations does not stimulate the enzyme activity
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Protamine sulfate
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treatment of cell extract with 90% of the volume of protamine sulfate solution needed to completely precipitate nucleic acids results in a loss of more than 95% of the total enzyme activity
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
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not activated by thiamine diphosphate, coenzyme A, pyridoxamine phosphate, pyridoxall 5'-phosphate, biotin, ascorbic acid, NADH, NADPH, folic acid, FAD, FMN, or glutamate
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
UbiX belongs to the FMN-dependent decarboxylase family
malfunction
metabolism
physiological function
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the enzyme is required for production of coenzyme Q8 and growth on succinate media
malfunction
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disruption of the slr1099 gene results in reduced growth rates and plastoquinone contents
malfunction
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the Escherichia coli ubiX null mutant accumulates 4-hydroxy-3-octaprenylbenzoic acid, a coenzyme Q8 precursor, and shows decreased UbiG O-methyltransferase activity
metabolism
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the enzyme is involved in the decarboxylation step in coenzyme Q biosynthesis
metabolism
a set of enzymes, UbiA, UbiB, UbiC, UbiD, UbiE, UbiF, UbiG, UbiH and UbiX, catalyze the synthesis of ubiquinone from the compound chorismate. Enzyme UbiX catalyzes and regulates ubiquinone biosynthesis
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
256300
57614
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2 * 57614, SeMet-substituted protein, calculated from amino acid sequence
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dodecamer
homodimer
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2 * 57614, SeMet-substituted protein, calculated from amino acid sequence
homododecamer
homododecamer
12 * 23175, electron spray ionization mass spectrometry
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant His6-tagged wild-type (FMN-bound) and V47S mutant (FMN-free) enzymes, hanging drop vapour diffusion method, mixing of 800 nl of 21 mg/ml protein solution with 800 nl of reservoir solution containing 200 mM sodium chloride, 100 mM potassium phosphate monobasic/sodium phosphate dibasic, pH 5.8, and 11% w/v PEG 8000, for the wild-type enzyme and 0.1 M trisodium citrate, pH 5.4, 0.5 M ammonium sulfate, and 1.2 M lithium sulfate for the mutant enzyme, 20°C, 3 days, method optimization, X-ray diffraction structrue determination and analysis at 2.0 A and 1.76 A resolution, respectively
sitting drop vapor diffusion method, using 0.1 M trisodium citrate pH 5.4, 0.5 M ammonium sulfate, 1.2 M lithium sulfate
structures of an FMN-bound wild type form and an FMN-unbound V47S mutant form. UbiX is a dodecameric enzyme, and each monomer possesses a typical Rossmann-fold structure. The FMN-binding domain of UbiX is composed of three neighboring subunits. The highly conserved Gly15, Ser41, Val47, and Tyr171 residues play important roles in FMN binding. The FMN-bound wild type form and the FMN-free form show a significant conformational difference in the C-terminal loop region (comprising residues 170-176 and 195-206)
hanging drop vapor diffusion method, using 15% (w/v) PEG 4000, 0.2 M LiSO4, and 0.1 M Hepes buffer (pH 7.0)
structures of holoUbiD reveal a relatively open active site potentially occluded from solvent through domain motion
sitting drop vapor diffusion method, using 1 M (NH4)2SO4, 0.1 M Bis-Tris, pH 5.5, 1% (w/v) PEG 3350 or 0.1 M HEPES, pH 7.5, 0.2 M MgCl2, 10% (w/v) PEG 400
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
V47S
V47S
site-directed mutagenesis, the single mutation results in a loss of FMN binding, resulting in the production of FMN-free CpsUbiX protein. The mutation is likely to destabilize FMN-protein interactions without affecting the overall structural folding. The mutant enzyme has an FMN:protein molar ratio of 0.086:1. Wild-type CpsUbiX protein has a yellowish colour, while the V47S mutant does not
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Ni-NTA agarose bead chromatography and Sephacryl S200 gel filtration
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Ni-NTA resin column chromatography and Superdex 200 gel filtration
recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, gel filtration, and ultrafiltration
UbiD cannot be isolated in an active holoenzyme form. Formation of holoUbiD requires reconstitution in vitro of the apoUbiD with reduced prenylated FMN. The apoenzyme can be readily reconstituted and activated, but in vitro oxidation to the mature prenylated FMN cofactor stalls at formation of a radical prenylated FMN species in holoUbiD
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3) cells
gene ubiX, recombinant expression of His6-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Pfaff, C.; Glindemann, N.; Gruber, J.; Frentzen, M.; Sadre, R.
Chorismate pyruvate-lyase and 4-hydroxy-3-solanesylbenzoate decarboxylase are required for plastoquinone biosynthesis in the cyanobacterium Synechocystis sp. PCC6803
J. Biol. Chem.
289
2675-2686
2014
Synechocystis sp.
brenda
Liu, J.; Liu, J.H.
Ubiquinone (coenzyme Q) biosynthesis in Chlamydophila pneumoniae AR39: identification of the ubiD gene
Acta Biochim. Biophys. Sin. (Shanghai)
38
725-730
2006
Chlamydia pneumoniae, Chlamydia pneumoniae AR39
brenda
Do, H.; Lee, C.W.; Han, S.J.; Lee, S.G.; Kim, H.J.; Park, H.; Lee, J.H.
Purification, crystallization and preliminary X-ray crystallographic studies of FMN-bound and FMN-free forms of aromatic acid decarboxylase (CpsUbiX) from the psychrophilic bacterium Colwellia psychrerythraea 34H
Acta Crystallogr. Sect. F
70
215-220
2014
Colwellia psychrerythraea (Q489U8)
brenda
Gulmezian, M.; Hyman, K.R.; Marbois, B.N.; Clarke, C.F.; Javor, G.T.
The role of UbiX in Escherichia coli coenzyme Q biosynthesis
Arch. Biochem. Biophys.
467
144-153
2007
Escherichia coli
brenda
Leppik, R.; Young, I.; Gibson, F.
Membrane associated reactions in ubiquinone biosynthesis in Escherichia coli. 3-Octaprenyl-4-hydroxybenzoate carboxy lyase
Biochim. Biophys. Acta
436
800-810
1976
Escherichia coli
brenda
Jacewicz, A.; Izumi, A.; Brunner, K.; Schnell, R.; Schneider, G.
Structural insights into the UbiD protein family from the crystal structure of PA0254 from Pseudomonas aeruginosa
PLoS ONE
8
e63161
2013
Pseudomonas aeruginosa
brenda
Rangarajan, E.S.; Li, Y.; Iannuzzi, P.; Tocilj, A.; Hung, L.W.; Matte, A.; Cygler, M.
Crystal structure of a dodecameric FMN-dependent UbiX-like decarboxylase (Pad1) from Escherichia coli O157: H7
Protein Sci.
13
3006-3016
2004
Escherichia coli (P69772)
brenda
Do, H.; Lee, C.W.; Han, S.J.; Lee, S.G.; Kim, H.J.; Park, H.; Lee, J.H.
Purification, crystallization and preliminary X-ray crystallographic studies of FMN-bound and FMN-free forms of aromatic acid decarboxylase (CpsUbiX) from the psychrophilic bacterium Colwellia psychrerythraea 34H
Acta Crystallogr. Sect. F
70
215-220
2014
Colwellia psychrerythraea (Q489U8)
brenda
Marshall, S.; Fisher, K.; Cheallaigh, A.; White, M.; Payne, K.; Parker, D.; Rigby, S.; Leys, D.
Oxidative maturation and structural characterization of prenylated FMN binding by UbiD, a decarboxylase involved in bacterial ubiquinone biosynthesis
J. Biol. Chem.
292
4623-4637
2017
Escherichia coli (P0AAB4)
brenda
Do, H.; Kim, S.; Lee, C.; Kim, H.; Park, H.; Kim, H.; Park, H.; Park, H.; Lee, J.
Crystal structure of UbiX, an aromatic acid decarboxylase from the psychrophilic bacterium Colwellia psychrerythraea that undergoes FMN-induced conformational changes
Sci. Rep.
5
8196
2015
Colwellia psychrerythraea (Q489U8), Colwellia psychrerythraea
brenda
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