Information on EC 2.5.1.31 - ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]

Word Map on EC 2.5.1.31
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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota

EC NUMBER
COMMENTARY hide
2.5.1.31
-
RECOMMENDED NAME
GeneOntology No.
ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
(2E,6E)-farnesyl diphosphate + 8 isopentenyl diphosphate = 8 diphosphate + ditrans,octacis-undecaprenyl diphosphate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
alkenyl group transfer
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Biosynthesis of secondary metabolites
-
-
di-trans,poly-cis-undecaprenyl phosphate biosynthesis
-
-
Terpenoid backbone biosynthesis
-
-
isoprenoid biosynthesis
-
-
SYSTEMATIC NAME
IUBMB Comments
(2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate cistransferase (adding 8 isopentenyl units)
Undecaprenyl pyrophosphate synthase catalyses the consecutive condensation reactions of a farnesyl diphosphate with eight isopentenyl diphosphates, in which new cis-double bonds are formed, to generate undecaprenyl diphosphate that serves as a lipid carrier for peptidoglycan synthesis of bacterial cell wall [3].
CAS REGISTRY NUMBER
COMMENTARY hide
52350-87-5
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
gene uppS
-
-
Manually annotated by BRENDA team
gene uppS1 containing a single-point mutation in the ribosome-binding site of the uppS gene, mutant strain HB13564
-
-
Manually annotated by BRENDA team
gene uppsS
UniProt
Manually annotated by BRENDA team
Salmonella newington
-
-
-
Manually annotated by BRENDA team
strains ATCC6538p (MSSA) and K24 (MRSA)
UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(2E,6E)-8-(N-methyl-2-aminobenzoyloxy)-3,7-dimethyl-2,6-octandien-1-diphosphate + 8 isopentenyl diphosphate
?
show the reaction diagram
-
a fluorescent analog of farnesyl diphosphate
-
-
?
(2E,6E)-farnesyl diphosphate + 8 isopentenyl diphosphate
8 diphosphate + ditrans,octacis-undecaprenyl diphosphate
show the reaction diagram
(2E,6E)-farnesyl diphosphate + isopentenyl diphosphate
diphosphate + di-trans,poly-cis-undecaprenyl diphosphate
show the reaction diagram
-
-
-
-
?
(2E,6E)-farnesyl diphosphate + isopentenyl diphosphate
diphosphate + ditrans,polycis-undecaprenyl diphosphate
show the reaction diagram
-
-
-
-
?
(2E,6E)-farnesyl thiodiphosphate + isopentenyl diphosphate
?
show the reaction diagram
-
weak activity, 10000000fold lower than with (2E,6E)-farnesyl diphosphate
-
-
?
(2E,6E,10E)-geranylgeranyl diphosphate + isopentenyl diphosphate
?
show the reaction diagram
(2Z,6E)-famesyl diphosphate + isopentenyl diphosphate
?
show the reaction diagram
-
-
-
-
?
(2Z,6E,10E)-geranylgeranyl diphosphate + isopentenyl diphosphate
?
show the reaction diagram
(2Z,6E,10E,14E)-farnesylgeranyl diphosphate + isopentenyl diphosphate
?
show the reaction diagram
-
-
-
-
?
(2Z,6Z,10E,14E)-farnesylgeranyl diphosphate + isopentenyl diphosphate
?
show the reaction diagram
-
-
-
-
?
(E)-3-methyl-3-pentenyl diphosphate + isopentenyl diphosphate
?
show the reaction diagram
-
reactive as substrate and competitive inhibition profile
-
-
?
2-amideanilinogeranyl diphosphate + isopentenyl diphosphate
?
show the reaction diagram
2-nitrileanilinogeranyl diphosphate + 9 isopentenyl diphosphate
9 diphosphate + 2-nitrileanilinobactoprenyl diphosphate
show the reaction diagram
7-(2,6-dimethyl-8-diphospho-2,6-octadienyloxy)-8-methyl-4-trifluoromethyl-chromen-2-one geranyl diphosphate + isopentenyl diphosphate
?
show the reaction diagram
-
fluorescent analogue of (2E,6E)-farnesyl diphosphate, alternative substrate and inhibitor
-
-
?
di-trans-poly-cis-decaprenyl diphosphate + isopentenyl diphosphate
diphosphate + di-trans-poly-cis-undecaprenyl diphosphate
show the reaction diagram
farnesyl diphosphate + 8 isopentenyl diphosphate
8 diphosphate + undecaprenyl diphosphate
show the reaction diagram
-
neither dimethylallyl diphosphate nor geranyl diphosphate act as priming substrate for the enzyme
-
-
?
farnesyl diphosphate + isopentenyl diphosphate
diphosphate + di-trans-poly-cis-undecaprenyl diphosphate
show the reaction diagram
farnesyl phosphate + isopentenyl diphosphate
phosphate + di-trans-poly-cis-undecaprenyl diphosphate
show the reaction diagram
-
low activity
-
-
?
geranyl diphosphate + isopentenyl diphosphate
?
show the reaction diagram
-
C10 GPP displays a 90fold larger Km value compared with (2E,6E)-farnesyl diphosphate
-
-
?
geranyl diphosphate + isopentenyl diphosphate
diphosphate + ?
show the reaction diagram
-
less effective than farnesyl diphosphate
-
-
?
geranylgeranyl diphosphate + isopentenyl diphosphate
?
show the reaction diagram
-
containing a larger C20 hydrocarbon tail, is an equally good substrate
-
-
?
geranylgeranyl diphosphate + isopentenyl diphosphate
diphosphate + ?
show the reaction diagram
-
as effective as farnesyl diphosphate
-
-
?
isopentenyl diphosphate + (E,E)-(2-diazo-3-trifluoropropionyloxy)geranyl diphosphate
(E,E)-(2-diazo-3-trifluoropropionyloxy)polyprenyl diphosphate + diphosphate
show the reaction diagram
isopentenyl diphosphate + DELTA3-isopentenyl diphosphate
?
show the reaction diagram
-
-
-
-
?
isopentenyl diphosphate + dimethylallyl diphosphate
?
show the reaction diagram
-
2% of the activity with farnesyl diphosphate
-
-
?
isopentenyl diphosphate + farnesyl diphosphate
C55-polyprenyl diphosphate + C50-polyprenyl diphosphate + diphosphate
show the reaction diagram
isopentenyl diphosphate + geranyl diphosphate
C55-polyprenyl diphosphate + C50-polyprenyl diphosphate + diphosphate
show the reaction diagram
isopentenyl diphosphate + geranylgeranyl diphosphate
C55-polyprenyl diphosphate + C50-polyprenyl diphosphate + diphosphate
show the reaction diagram
isopentenyl diphosphate + geranylneryl diphosphate
?
show the reaction diagram
-
cis,trans,trans-geranylneryl diphosphate
-
-
?
isopentenyl diphosphate + isopentenyl diphosphate
?
show the reaction diagram
-
-
-
-
?
isopentenyl diphosphate + neryl diphosphate
C55-polyprenyl diphosphate + C50-polyprenyl diphosphate + diphosphate
show the reaction diagram
isopentenyl diphosphate + S-farnesyl thiodiphosphate
?
show the reaction diagram
-
weak activity, 10000000fold lower than with farnesyl diphosphate
-
-
?
N-(4-benzoylphenyl)-4-hydroxy-2-oxo-5-phenethyl-2,5-dihydro-1H-pyrrole-3-carboxamide + isopentenyl diphosphate
?
show the reaction diagram
-
Photo-probe
-
-
?
neryl diphosphate + isopentenyl diphosphate
?
show the reaction diagram
-
-
-
-
?
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
(2E,6E)-farnesyl diphosphate + 8 isopentenyl diphosphate
8 diphosphate + ditrans,octacis-undecaprenyl diphosphate
show the reaction diagram
farnesyl diphosphate + isopentenyl diphosphate
diphosphate + di-trans-poly-cis-undecaprenyl diphosphate
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
-
weak stimulation
KCl
-
activates at 50 mM
sulfate
-
2 molecules bound per enzyme dimer, 1 at each active site, binding structure
Triton
-
3 Triton (T1, T2, and T3) are located in the two monomers with one on the top portion of the active site tunnel in monomer A and the other two occupying the overall tunnel of monomer B
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(2E,6E)-farnesyl thiodiphosphate
(2E,6E,10E)-4-methylfarnesyl diphosphate
-
competitive inhibitor against (2Z,6E,10E)-geranylgeranyl diphosphate
(2S,3R,4S,5S,6R)-2-(3-((4-((3-(4,5-dihydro-1H-imidazol-2-yl)-phenyl)ethynyl)phenyl)ethynyl)phenoxy)-6-(hydroxymethyl)-tetrahydro-2H-pyran-3,4,5-triol
(2Z,6E,10E)-4-methyl-geranylgeranyl diphosphate
-
allylic substrate homologue, competitive inhibitor against the allylic primer. It also acts as a strong noncompetitive inhibitor against isopentenyl diphosphate
(4aS,8aS)-4-hydroxy-2-oxo-1,2,4a,5,6,7,8,8a-octahydro[1,6]naphthyridine-3-carboxylic acid (4-piperidin-1-ylphenyl)amide
-
-
(E)-3-methyl-3-pentenyl diphosphate
-
reactive as substrate and competitive inhibition profile
(E,E)-[1-3H]-(2-diazo-3-trifluoropropionyloxy)geranyl diphosphate
-
-
(S)-farnesyl thiodiphosphate
-
an extremely poor substrate for UPPs
1,2-Cyclohexanedione
1,4-bis(6-(1,4,5,6-tetrahydropyrimidin-2-yl)-1H-indol-2-yl)-benzene
1,4-bis(6-(4,5-dihydro-1H-imidazol-2-yl)-1H-indol-2-yl)benzene
2,2'-(5,5'-(1,3-phenylenebis(ethyne-2,1-diyl))bis(3-bromo-5,1-phenylene))diethanamine
2,2'-(E)-ethene-1,2-diylbis[6-(4,5-dihydro-1H-imidazol-2-yl)-1H-indole]
2-propanol
3-(2-chlorophenyl)-N-(4-isopropylphenyl-5-methylisoxazole-4-carboxamide)
i.e. UK-106051, a drug-like UPPs inhibitor, UK-106051 binds to a site in the middle of this binding cleft. Substrates FPP and IPP cannot bind simultaneously to UPPs-inhibitor binary complexes
3-desmethyl (2Z,6E,10E)-geranylgeranyl diphosphate
-
mixed inhibition with farnesyl diphosphate, competitive inhibition with reaction intermediate (2Z,6E,10E)-geranylgeranyl diphosphate
3-desmethyl farnesyl diphosphate
-
competitive with farnesyl diphosphate, mixed inhibition with reaction intermediate (2Z,6E,10E)-geranylgeranyl diphosphate; competitive with farnesyl diphosphate, mixed inhibition with reaction intermediate (Z,E,E)-geranylgeranyl diphosphate
3-desmethyl Z-geranylgeranyl diphosphate
-
mixed inhibition with farnesyl diphosphate, competitive inhibition with reaction intermediate (Z,E,E)-geranylgeranyl diphosphate
3-[5-(5,6-dihydrobenzimidazo[1,2-c]quinazolin-6-yl)-2,5-dihydrofuran-2-yl]benzenesulfonamide
4,4'-[pentane-1,5-diylbis(oxy)]dibenzenecarboximidamide
5-benzyl-4-hydroxy-5-methyl-2-oxo-2,5-dihydro-1H-pyrrole-3-carboxylic acid (4-cyclohexylphenyl)amide
-
-
7-(2,6-dimethyl-8-diphospho-2,6-octadienyloxy)-8-methyl-4-trifluoromethyl-chromen-2-one geranyl diphosphate
-
competitive inhibitor, substrate analogue prepared and utilized to study ligand interactions
BPH-629
Butanedione
clomiphene
dihydropyridin-2-one
-
diphosphate
product inhibition
farnesyl thiodiphosphate
-
-
isopentyl thiodiphosphate
-
substrate analogue
Mg2+
-
inhibitory at high concentrations of e.g. 50 mM; inhibitory at high concentrations of e.g. 50 mM
N,N'-bis(6-chloro-1,3-benzothiazol-2-yl)methanedisulfonamide
N-[2-[(2-[1-[(3-amino-3-iminopropyl)amino]ethenyl]-1-methyl-1H-imidazol-4-yl)acetyl]-1-methyl-1H-imidazol-4-yl]-N2-(diaminomethylidene)glycinamide
N-[3-(4,5-dihydro-1H-imidazol-2-yl)phenyl]-N'-(3-phenoxyphenyl)biphenyl-4,4'-dicarboxamide
N1,N4-bis(4-(4,5-dihydro-1H-imidazol-2-yl)phenyl)-2-nitroterephthalamide
-
N1,N4-bis(4-(4,5-dihydro-1H-imidazol-2-yl)phenyl)-2-nitroterephthalamide dihydrochloride
N4,N4'-bis(3-(1,4,5,6-tetrahydropyrimidin-2-yl)phenyl)biphenyl-4,4'-dicarboxamide
N4,N4'-bis(3-(4,5-dihydro-1H-imidazol-2-yl)phenyl)-[1,1'-biphenyl]-4,4'-bicarboxamide
N4,N4'-bis(3-(4,5-dihydro-1H-imidazol-2-yl)phenyl)biphenyl-4,4'-bis(carbothioamide)
N4-(3-(4,5-dihydro-1H-imidazol-2-yl)phenyl)-N4'- (3-(((2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl)oxy)phenyl)-[1,1-biphenyl]-4,4-dicarboxamide
-
-
N4-(3-(4,5-dihydro-1H-imidazol-2-yl)phenyl)-N4'-(3-(hexyloxy)-phenyl)-[1,1-biphenyl]-4,4-dicarboxamide
N4-(3-(4,5-dihydro-1H-imidazol-2-yl)phenyl)-N4'-(3-methoxyphenyl)-[1,1-biphenyl]-4,4-dicarboxamide
N4-(3-(4,5-dihydro-1H-imidazol-2-yl)phenyl)-N4'-3(-(((2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl)oxy)phenyl)-[1,1-biphenyl]-4,4-dicarboxamide
-
-
-
NH4+
-
20 mM, 20% inhibition
Phenylglyoxal
S-farnesyl thiodiphosphate
-
-
SO42-
-
competitive inhibitor with respect to (2E,6E)-farnesyl diphosphate; competitive inhibitor with respect to farnesyl diphosphate
spirohexaline
tetramic acid
Triton X-100
viridicatumtoxin
viridicatumtoxin B
the inhibitor shows antimicrobial activity, particularly against Gram-positive bacteria including methicillin-resistant Staphylococcus aureus (MRSA), via inhibition of the UPP synthase activity
-
[1-hydroxy-2-(3-[3-[3-(2-hydroxy-2,2-bis-phosphono-ethyl)-biphenyl-3-ylsulfamoyl]-benzenesulfonylamino]-biphenyl-3-yl)-1-phosphono-ethyl]-phosphonic acid
additional information
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
capric acid
-
enhancement factor: 0.04 in absence of Triton X-100, 1.0 in presence of 0.1% Triton X-100
cardiolipin
cetyl sulfate
deoxycholate
dipalmitoylphosphatidic acid
-
enhancement factor: 0.2 in absence of Triton X-100, 1.2 in presence of 0.1% Triton X-100
Dodecyl sulfate
lauric acid
-
enhancement factor: 0.1 in absence of Triton X-100, 2.3 in presence of 0.1% Triton X-100
lecithin
lysophosphatidylglycerol
-
weak effect in activating lipid-depleted enzyme
myristic acid
oleic acid
palmitic acid
-
enhancement factor: 0.8 in absence of Triton X-100, 1.4 in presence of 0.1% Triton X-100
phosphatidic acid
phosphatidylglycerol
-
marked effect in activating lipid-depleted enzyme
phosphatidylserine
-
enhancement factor: 0.05 in absence of Triton X-100, 0.4 in presence of 0.1% Triton X-100
Phospholipid
Polyamines
-
stimulate in presence of Mg2+
-
putrescine
-
stimulates
stearic acid
-
enhancement factor: 0.07 in absence of Triton X-100, 0.8 in presence of 0.1% Triton X-100
trans,trans,trans-geranylgeranyl diphosphate
-
stimulates activity with farnesyl diphosphate as substrate
trans,trans-farnesyl diphosphate
-
stimulates activity with farnesyl diphosphate as substrate
Triton
-
0.01 microM of UPPs with 5 microM of (2E,6E)-farnesyl diphosphate and 50 microM of isopentenyl diphosphate, 0.5 mM MgCl2, and 50 mM KCl in Hepes buffer (pH 7.5) is 190fold less active (0.013 s-1) for the IPP consumption in the absence of Triton; the UPPs steady-state kcat value in the presence of 0.1% Triton is 190fold larger than in the absence of Triton
Triton X-100
Triton X-102
-
stimulates
-
Triton X-114
-
stimulates
Triton X-45
-
stimulates
-
Tween 80
additional information
-
enzyme is inactive in absence of added effectors
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0011 - 0.0015
(2E,6E)-8-(N-methyl-2-aminobenzoyloxy)-3,7-dimethyl-2,6-octandien-1-diphosphate
-
pH 7.5, 25C
0.00011 - 18
(2E,6E)-farnesyl diphosphate
0.0088 - 0.064
(2E,6E,10E)-geranylgeranyl diphosphate
0.0043 - 18.1
(2Z,6E,10E)-geranylgeranyl diphosphate
0.0588
(2Z,6E,10E,14E)-farnesylgeranyl diphosphate
-
pH 8.5, 37C
0.0526
(2Z,6Z,10E,14E)-farnesylgeranyl diphosphate
-
pH 8.5, 37C
0.00017
(E,E)-(2-Diazo-3-trifluoropropionyloxy)geranyl diphosphate
-
pH 7.5, 35C
0.00013 - 0.103
(E,E)-farnesyl diphosphate
0.008 - 0.037
(E,E,E)-geranylgeranyl diphosphate
0.0189 - 0.305
(Z,E)-farnesyl diphosphate
0.0023 - 0.134
(Z,E,E)-Geranylgeranyl diphosphate
0.0588
(Z,E,E,E)-farnesylgeranyl diphosphate
-
pH 8.5, 37C
0.0526
(Z,Z,E,E)-farnesylgeranyl diphosphate
-
pH 8.5, 37C
0.00069
7-(2,6-dimethyl-8-diphospho-2,6-octadienyloxy)-8-methyl-4-trifluoromethyl-chromen-2-one geranyl diphosphate
-
alternative substrate, pH 7.5, 25C
0.00011 - 0.155
farnesyl diphosphate
0.0032 - 0.036
geranyl diphosphate
0.0003 - 0.0075
geranylgeranyl diphosphate
0.00041 - 252.5
isopentenyl diphosphate
0.0267 - 0.032
neryl diphosphate
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
11.2
(2E,6E)-8-(N-methyl-2-aminobenzoyloxy)-3,7-dimethyl-2,6-octandien-1-diphosphate
Escherichia coli
-
pH 7.5, 25C
0.0000633 - 3.5
(2E,6E)-farnesyl diphosphate
0.00000031
(2E,6E)-farnesyl thiodiphosphate
Escherichia coli
-
much smaller than using (2E,6E)-farnesyl diphosphate, pH 7.5, 25C
0.002 - 1.77
(2Z,6E,10E)-geranylgeranyl diphosphate
0.002 - 1.77
(Z,E,E)-Geranylgeranyl diphosphate
0.02
7-(2,6-dimethyl-8-diphospho-2,6-octadienyloxy)-8-methyl-4-trifluoromethyl-chromen-2-one geranyl diphosphate
Escherichia coli
-
alternative substrate, pH 7.5, 25C
0.00006 - 2.5
farnesyl diphosphate
1.7
geranyl diphosphate
Escherichia coli
-
25C, pH 7.5
0.18 - 2.1
geranylgeranyl diphosphate
0.0002 - 2.5
isopentenyl diphosphate
additional information
additional information
-