Information on EC 2.5.1.86 - trans,polycis-decaprenyl diphosphate synthase

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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria

EC NUMBER
COMMENTARY hide
2.5.1.86
-
RECOMMENDED NAME
GeneOntology No.
trans,polycis-decaprenyl diphosphate synthase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
(2Z,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + trans,octacis-decaprenyl diphosphate
show the reaction diagram
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
mono-trans, poly-cis decaprenyl phosphate biosynthesis
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isoprenoid biosynthesis
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Terpenoid backbone biosynthesis
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Biosynthesis of secondary metabolites
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SYSTEMATIC NAME
IUBMB Comments
(2Z,6E)-farnesyl-diphosphate:isopentenyl-diphosphate farnesylcistransferase (adding 7 isopentenyl units)
The enzyme is involved in the biosynthesis of decaprenyl phosphate, which plays a central role in the biosynthesis of essential mycobacterial cell wall components, such as the mycolyl-arabinogalactan-peptidoglycan complex and lipoarabinomannan [2].
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
gene NCgl2203 or uppS2
UniProt
Manually annotated by BRENDA team
gene NCgl2203 or uppS2
UniProt
Manually annotated by BRENDA team
gene SlDPS
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-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
metabolism
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requirement for two long-chain prenyl diphosphate synthases in the tomato, i.e. SlSPS, a solanesyl diphosphate synthase, EC 2.5.1.85, and SlDPS, a decaprenyl diphosphate synthase
physiological function
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)-farnesyl diphosphate + isopentenyl diphosphate
diphosphate + decaprenyl diphosphate + nonaprenyl diphosphate + octaprenyl diphosphate
show the reaction diagram
(2Z,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate
7 diphosphate + (2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E)-decaprenyl diphosphate
show the reaction diagram
(2Z,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate
7 diphosphate + trans,octacis-decaprenyl diphosphate
show the reaction diagram
(2Z,6E)-farnesyl diphosphate + isopentenyl diphosphate
diphosphate + trans,octacis-decaprenyl diphosphate
show the reaction diagram
geranyl diphosphate + isopentenyl diphosphate
diphosphate + decaprenyl diphosphate + nonaprenyl diphosphate + octaprenyl diphosphate
show the reaction diagram
geranylgeranyl diphosphate + isopentenyl diphosphate
diphosphate + decaprenyl diphosphate + octaprenyl diphosphate + nonaprenyl diphosphate
show the reaction diagram
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the major product synthesized is octaprenyl diphosphate, followed by nonaprenyl diphosphate, decaprenyl diphosphate, and heptaprenyl diphosphate
-
?
neryl diphosphate + isopentenyl diphosphate
diphosphate + decaprenyl diphosphate + nonaprenyl diphosphate + octaprenyl diphosphate
show the reaction diagram
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decaprenyl diphosphate, nonaprenyl diphosphate, and octaprenyl diphosphate are synthesized. The relative amounts of both decaprenyl diphosphate and octaprenyl diphosphate are greater than that of nonaprenyl diphosphate
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?
additional information
?
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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
(2Z,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate
7 diphosphate + (2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E)-decaprenyl diphosphate
show the reaction diagram
(2Z,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate
7 diphosphate + trans,octacis-decaprenyl diphosphate
show the reaction diagram
(2Z,6E)-farnesyl diphosphate + isopentenyl diphosphate
diphosphate + trans,octacis-decaprenyl diphosphate
show the reaction diagram
additional information
?
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the enzyme can utilize geranyl, farnesyl or geranylgeranyl diphosphates in the synthesis of C45 and C50 prenyl diphosphates
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
-
absolute requirement for divalent cations. Enzyme activity is optimal in the presence of 1 mM Mg2+. MnCl2 at 0.1 mM also supports the activity. CaCl2 and ZnCl2 are much less effective
Mn2+
-
absolute requirement for divalent cations. Enzyme activity is optimal in the presence of 1 mM Mg2+. MnCl2 at 0.1 mM also supports the activity. CaCl2 and ZnCl2 are much less effective
Zn2+
-
absolute requirement for divalent cations. Enzyme activity is optimal in the presence of 1 mM Mg2+. MnCl2 at 0.1 mM also supports the activity. CaCl2 and ZnCl2 are much less effective
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-(2-methyl-1,3-dioxa-8-azaspiro[4.5]dec-8-yl)-8-nitro-6-(trifluoromethyl)-4H-1,3-benzothiazin-4-one
i.e. BTZ043. Benzothiazinones mediate killing of Corynebacterineae by blocking decaprenyl phosphate recycling involved in cell wall biosynthesis. In the presence of benzothiazinones (BTZ), the bacilli accumulate decaprenyl-phosphoribose and fail to recycle decaprenyl phosphate, which results in the depletion of decaprenyl phosphate and ultimately leads to cell death. Overexpression of Z-decaprenyl-diphosphate synthase gene NCgl2203 in wild-type Corynebacterium glutamicum increases resistance to benzothiazinone BTZ043. BTZ043 targets DprE1, which is a FAD-containing oxidoreductase involved in the epimerization of decaprenyl-phosphoribose to decaprenyl-phosphoarabinose
BPH-640
; a bisphosphonate inhibitor, three-dimensional structure from crystal structure, dimeric DPPS structure with one bound BPH-640 molecule in each monomer, overview. BPH-640 occupies a dimer interface binding site, sandwiched between residues G77, N78, G79, R80, T83, R89, and R127 of monomer A and residues R292 and F293 of monomer B
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
dithiothreitol
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stimulates activity
Triton X-100
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detergent stimulates activity, maximally active in presence of 0.1% Triton X-100
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.084
(2E,6E)-farnesyl diphosphate
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pH 7.9, 37°C
0.29
(2Z,6E)-farnesyl diphosphate
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pH 7.9, 37°C
0.49
geranyl diphosphate
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pH 7.9, 37°C
0.04
geranylgeranyl diphosphate
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pH 7.9, 37°C
0.089
isopentenyl diphosphate
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pH 7.9, 37°C
0.029
neryl diphosphate
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pH 7.9, 37°C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.07
(2E,6E)-farnesyl diphosphate
-
pH 7.9, 37°C
11.5
(2Z,6E)-farnesyl diphosphate
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pH 7.9, 37°C
0.06
geranyl diphosphate
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pH 7.9, 37°C
0.03
geranylgeranyl diphosphate
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pH 7.9, 37°C
0.08
isopentenyl diphosphate
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pH 7.9, 37°C
0.16
neryl diphosphate
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pH 7.9, 37°C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
39.66
(2Z,6E)-farnesyl diphosphate
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pH 7.9, 37°C
0.122
geranyl diphosphate
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pH 7.9, 37°C
0.75
geranylgeranyl diphosphate
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pH 7.9, 37°C
0.899
isopentenyl diphosphate
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pH 7.9, 37°C
5.5
neryl diphosphate
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pH 7.9, 37°C
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00041
BPH-640
Mycobacterium tuberculosis;
P9WFF7
pH and temperature not specified in the publication
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7
M9VRD0;, M9VU49;
assay at; assay at
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.28
M9VRD0;, M9VU49;
sequence calculation
8.13
M9VRD0;, M9VU49;
sequence calculation
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
UNIPROT
ORGANISM
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv);
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
36000
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x * 36000, SDS-PAGE
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystallization using sparse matrix screens and vapor diffusion, structures of Rv2361c in the apo form, with isopentyl diphosphate bound and with a substrate analogue, citronellyl diphosphate
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in complex with BPH-640, hanging drop vapor diffusion method, using; purified recombinant enzyme in complex with inhibitor BPH-640, X-ray diffraction structure determination and analysis at 1.8-1.9 A resolution
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant GST-tagged subunit from Escherichia coli strain BL21(DE3) by glutathione affinity chromatography, tag cleavage with factor Xa, and ultrafiltration; recombinant GST-tagged subunit from Escherichia coli strain BL21(DE3) by glutathione affinity chromatography, tag cleavage with factor Xa, and ultrafiltration
M9VRD0;, M9VU49;
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
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gene AgDPPS1, two cDNAs encoding the two subunits of an aphid long-chain PDDS, designated as AgDPPS1 and AgDPPS2, AgDPPS1 encodes subunit 1, DNA and amino acid sequence determination and analysis, sequence comparisons and phylogenetic analysis, recombinant overexpression of GST-tagged subunit in Escherichia coli strain BL21(DE3); gene AgDPPS2, two cDNAs encoding the two subunits of an aphid long-chain PDDS, designated as AgDPPS1 and AgDPPS2, AgDPPS2 encodes subunit 2, DNA and amino acid sequence determination and analysis, sequence comparisons and phylogenetic analysis, recombinant overexpression of GST-tagged subunit in Escherichia coli strain BL21(DE3)
M9VRD0;, M9VU49;
gene NCgl2203 or uppS2, recombinant overexpression in wild-type Corynebacterium glutamicum eliciting an increase in decaprenyl phosphate synthesis
gene Rv2361c, recombinant expression
gene SlDPS, recombinant expression in Escherichia coli
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
drug development