Information on EC 1.17.7.4 - 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase

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

EC NUMBER
COMMENTARY hide
1.17.7.4
-
RECOMMENDED NAME
GeneOntology No.
4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
dimethylallyl diphosphate + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O = (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
show the reaction diagram
isopentenyl diphosphate + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O = (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
-
-
-
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redox reaction
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-
-
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reduction
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-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Biosynthesis of antibiotics
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Biosynthesis of secondary metabolites
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Metabolic pathways
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methylerythritol phosphate pathway I
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methylerythritol phosphate pathway II
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Terpenoid backbone biosynthesis
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isoprenoid biosynthesis
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SYSTEMATIC NAME
IUBMB Comments
isopentenyl-diphosphate:ferredoxin oxidoreductase
An iron-sulfur protein that contains either a [3Fe-4S] [6] or a [4Fe-4S] [5] cluster. This enzyme forms a system with a ferredoxin or a flavodoxin and an NAD(P)H-dependent reductase. This is the last enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. This pathway, also known as the 1-deoxy-D-xylulose 5-phosphate (DOXP) or as the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway, is found in most bacteria and in plant chloroplasts. The enzyme acts in the reverse direction, producing a 5:1 mixture of isopentenyl diphosphate and dimethylallyl diphosphate.
CAS REGISTRY NUMBER
COMMENTARY hide
512789-14-9
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
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Manually annotated by BRENDA team
strain CCAP 19/30
Uniprot
Manually annotated by BRENDA team
strain CCAP 19/30
Uniprot
Manually annotated by BRENDA team
gene ispH, formerly lytB
-
-
Manually annotated by BRENDA team
BY-2 cells
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-
Manually annotated by BRENDA team
no activity in Homo sapiens
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-
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Manually annotated by BRENDA team
gene HDR
UniProt
Manually annotated by BRENDA team
induced in correlation with carotinoid production during fruit ripening and, in recombinant Arabidopsis thaliana, in correlation with deetiolation of seedlings
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-
Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
metabolism
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
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
dimethylallyl diphosphate + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
show the reaction diagram
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
isopentenyl diphosphate + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
show the reaction diagram
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H + H+
dimethylallyl diphosphate + NAD(P)+ + H2O
show the reaction diagram
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H + H+
isopentenyl diphosphate + NAD(P)+ + H2O
show the reaction diagram
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NADPH
dimethylallyl diphosphate + isopentenyl diphosphate + NADP+ + H2O
show the reaction diagram
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-
-
-
?
2 (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + 4 reduced ferredoxin [iron-sulfur] cluster + 4 H+
dimethylallyl diphosphate + isopentenyl diphosphate + 4 oxidized ferredoxin [iron-sulfur] cluster + 2 H2O
show the reaction diagram
isopentenyl diphosphate + NAD(P)+ + H2O
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H
show the reaction diagram
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
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
dimethylallyl diphosphate + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
show the reaction diagram
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
isopentenyl diphosphate + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
show the reaction diagram
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H + H+
dimethylallyl diphosphate + NAD(P)+ + H2O
show the reaction diagram
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H + H+
isopentenyl diphosphate + NAD(P)+ + H2O
show the reaction diagram
isopentenyl diphosphate + NAD(P)+ + H2O
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H
show the reaction diagram
additional information
?
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production of isopentenyl diphosphate and dimethylallyl diphosphate is key step in controlling the production of plastidial isoprenoid precursors and carotenoid biosynthesis in plant cells
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
deazaflavin
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requires a reducing system, e.g. flavodoxin/flavodoxin reductase or NADPH or the photoreduced deazaflavin radical
FAD
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requires a reducing system, e.g. flavodoxin/flavodoxin reductase or NADPH or the photoreduced deazaflavin radical
Ferredoxin
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NADP+
NADPH
additional information
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enzyme possesses a dioxygen-sensitive [4Fe-4S] cluster as prosthetic group
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
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Co2+ and Mn2+, at 0.5 mM, lower the content of isopentenyl diphosphate in the mixture of both products, isopentenyl diphosphate and dimethylallyl diphosphate
Iron
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(3FE-4S)+ cluster, 2.6 mol of iron per mol of subunit, wild-type, 0.6 mol per mol of subunit, mutant C12S, 0.9 mol per mol of subunit, mutant C92S, 1.4 mol, mutant C197S
Iron-sulfur cluster
Mn2+
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activates; Co2+ and Mn2+, at 0.5 mM, lower the content of isopentenyl diphosphate in the mixture of both products, isopentenyl diphosphate and dimethylallyl diphosphate
additional information
-
no addition of divalent kations required
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(E)-4-amino-3-methylbut-2-en-1-yl diphosphate
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(E)-4-mercapto-3-methyl-but-2-en-1-yl diphosphate
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2-(pyridin-3-yl)ethyl diphosphate
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i.e. BPH-1027
BPH-1029
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BPH-293
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but-3-ynyl diphosphate
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Ca2+
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inhibitory
Fe2+
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inhibitory
Imidazol
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Mg2+
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inhibitory
Mn2+
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inhibitory
N-methylpyridinium
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-
Ni2+
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inhibitory
propargyl alcohol
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weak inhibition, binding structure, overview
propargyl diphosphate
pyridin-2-ylmethyl diphosphate
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i.e. BPH-1029
pyridin-3-ylmethyl diphosphate
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i.e. BPH-293
pyridin-4-ylmethyl trihydrogen diphosphate
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i.e. BPH-1030
pyridine-N-oxide
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Zn2+
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complete inhibition
additional information
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.006 - 0.59
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.11 - 3.7
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
52.35 - 518.3
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate
5327
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.000054
(E)-4-amino-3-methylbut-2-en-1-yl diphosphate
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pH 8, 37C
0.00002
(E)-4-mercapto-3-methyl-but-2-en-1-yl diphosphate
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pH 8, 37C
10
propargyl alcohol
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above, pH not specified in the publication, temperature not specified in the publication
0.97
propargyl diphosphate
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pH not specified in the publication, temperature not specified in the publication
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0091
2-(pyridin-3-yl)ethyl diphosphate
Aquifex aeolicus
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pH not specified in the publication, temperature not specified in the publication
0.00045
but-3-ynyl diphosphate
Aquifex aeolicus
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pH not specified in the publication, temperature not specified in the publication
1.2
pyridin-2-ylmethyl diphosphate
Aquifex aeolicus
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pH not specified in the publication, temperature not specified in the publication
0.149
pyridin-4-ylmethyl trihydrogen diphosphate
Aquifex aeolicus
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pH not specified in the publication, temperature not specified in the publication
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.002
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purified apoenzyme, with FAD and NADPH as reducing cofactors
0.011
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purified apoenzyme, with photoreduced deazaflavin as reducing cofactor
0.03
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reconstituted purified enzyme, with photoreduced deazaflavin as reducing cofactor
0.044
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reconstituted purified enzyme, with FAD and NADPH as reducing cofactors
6.6
recombinant enzyme
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5
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assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
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assay at
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
48 - 72
half-maximal activity at 48C and 72C
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.81
sequence calculation
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
additional information
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enzyme is detected in all tissues analyzed
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
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N-terminal bipartite sequence is required for targeting proteins to the apicoplast lumen
Manually annotated by BRENDA team
additional information
no transmembrane regions in the SmHDR1 polypeptide
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Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
UNIPROT
Aquifex aeolicus (strain VF5)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
36000
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x * 36000, SDS-PAGE
36591
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2 * 36591, recombinant His-tagged enzyme, amino acid sequence determination
37000
x * 37000, recombinant enzyme, SDS-PAGE
48000
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Western blot
49900
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calculated from cDNA
51330
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calculated from cDNA
51860
x * 51860, sequence calculation
72000
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recombinant His-tagged enzyme, gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
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2 * 36591, recombinant His-tagged enzyme, amino acid sequence determination
monomer
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
purified recombinant IspH, sitting drop vapour diffusion method at 20C, 0.004 ml of 35 /ml protein in 50 mM Tris-HCl, pH 8.0, is mixed with 0.004 ml of reservoir solution containing 100 mM Bis-Tris-HCl, pH 6.5, 200 mM lithium sulfate and 25% PEG 3350, final pH is 6.8, crystal soaking in 2 M lithium sulfate, pH 6.5, before freezing, X-ray diffraction structure determination and analysis at 1.4 A resolution, molecular replacement, modelling
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crystallized under anaerobic conditions. Its structure is determined by the multiple anomalous dispersion method and refined to final R/Rfree factors of 17.5/19.5% at 2.2 A resolution. LytB is a momoner which is essentially composed of three related alpha/beta-domains arranged in a cloverleaf form with the Fe/S-cluster in its center
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
IspH is more stable in its closed conformation with a substrate molecule bound to the cluster, compared to its open conformation in solution
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OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
enzyme possesses a O2-sensitive [4Fe-4S] cluster
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639341
highly sensitive to O2, 21% remaining activity after incubation in air for 10 min
639340
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, purified enzyme, 20 mM Tris-HCl, pH 8.0, 95% remaining activity after 2 weeks
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
purified by using Strep-tactin chromatography
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recombinant His-tagged apoprotein from Escherichia coli strain M15, to homogeneity
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recombinant His-tagged IspH from strain XL-1 Blue by nickel affinity and anion exchange chromatography followed by dialysis, over 99% purity
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recombinant His-tagged protein from Escherichia coli strain Xl1-Blue, to 95% homogeneity
recombinant His-tagged protein from Escherichia coli strain XL1-Blue, to homogeneity
using Ni-NTA chromatography
using Ni-NTA chromatpgraphy
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cloning from genomic DNA and expression as His-tagged protein in Escherichia coli strain XL-1 Blue
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expressed as a Strep-tagged fusion protein in Escherichia coli
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expressed in a Escherichia coli mutant strain MG1655 ara<>ispH
expressed in Escherichia coli
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expressed in Escherichia coli as a His-tagged fusion protein
expression in Escherichia coli
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gene HDR, DNA and amino acid sequence determination and analysis, phylogenetic analysis and tree, functional complementation by SmHDR1 of the Escherichia coli HDR mutant MG1655 ara/ispH, overexpression of SmHDR1 accelerates the biosynthesis of beta-carotene and enhances the production of tanshinones in cultured hairy roots of Salvia miltiorrhiza Bge. f. alba, transformation using Agrobacterium rhizogenes strain ACCC10060
gene HsHDR1, DNA and amino acid sequence determination and analysis, phylogenetic analysis; gene HsHDR2, DNA and amino acid sequence determination and analysis, phylogenetic analysis
gene ispH, expression as His-tagged protein in Escherichia coli strain XL1-Blue, construction of a synthetic operon containing ispH, ispG and gepE
gene ispH, the IspH domain of the Arabidopsis thaliana enzyme HDR corresponding to the full-length IspH of Escherichia coli fails to complement the Escherichia coli ispH mutant
gene lytB, expression as His-tagged enzyme in Escherichia coli strain XL1-Blue
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
expression of gene SmHDR1 is induced by 0.1 mM methyl-jasmonate and salicylic acid, but not by 0.1 mM abscisic acid, in hairy roots
GATA box is involved in light mediated gene regulation of SrHDR in stevia
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Salinity up-shift (9-18% NaCl) and/or nitrate depletion resulted in an increase of DsHDR steady-state mRNA, 36 h upon the stress onset
up-regulated preceding and during the increase in monoterpenol precursor volatile organic compounds (PVOCs)
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E126A
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site-directed mutagenesis, the mutant is almost inactive, formation of an organometallic species with HMBPP, a pi/sigma metallacycle or nu2-alkenyl complex, overview
H124A
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site-directed mutagenesis, the mutant shows an increased Km and a 5fold decreased Vmax compared to the wild-type enzyme
H42A
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site-directed mutagenesis, the mutant shows a decreased Vmax but unaltered Km compared to the wild-type enzyme
C12S
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decrease in iron content, dramatic decrease in activity
C197S
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decrease in iron content, dramatic decrease in activity
C92S
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decrease in iron content, dramatic decrease in activity
E126Q
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inactive mutant used to trap a paramagnetic reaction intermediate representing the 3-CH2OH-rotated weak pi-complex, intermediate II
additional information
Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
reconstitution of purified apoenzyme with prosthetic group [Fe4-S4] cluster
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
synthesis
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recombinant expression of enzyme can be greatly enhanced by coexpression of genes from the isc operon which are required for the assembly of iron-sulfur clusters
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