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
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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
Biosynthesis of secondary metabolites
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mono-trans, poly-cis decaprenyl phosphate biosynthesis
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Terpenoid backbone biosynthesis
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isoprenoid biosynthesis
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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
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?
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+
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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+
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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+
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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
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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
Mycobacterium tuberculosis
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pH 7.9, 37°C
11.5
(2Z,6E)-farnesyl diphosphate
Mycobacterium tuberculosis
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pH 7.9, 37°C
0.06
geranyl diphosphate
Mycobacterium tuberculosis
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pH 7.9, 37°C
0.03
geranylgeranyl diphosphate
Mycobacterium tuberculosis
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pH 7.9, 37°C
0.08
isopentenyl diphosphate
Mycobacterium tuberculosis
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pH 7.9, 37°C
0.16
neryl diphosphate
Mycobacterium tuberculosis
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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
Mycobacterium tuberculosis
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pH 7.9, 37°C
1810
0.122
geranyl diphosphate
Mycobacterium tuberculosis
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pH 7.9, 37°C
175
0.75
geranylgeranyl diphosphate
Mycobacterium tuberculosis
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pH 7.9, 37°C
231
0.899
isopentenyl diphosphate
Mycobacterium tuberculosis
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pH 7.9, 37°C
113
5.5
neryl diphosphate
Mycobacterium tuberculosis
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pH 7.9, 37°C
1451
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
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7
assay at; assay at
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.28
sequence calculation
8.13
sequence calculation
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
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
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)
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