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Information on EC 1.17.7.4 - 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase and Organism(s) Aquifex aeolicus and UniProt Accession O67625
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1.17.7.4 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductaseIUBMB Comments
An iron-sulfur protein that contains either a [3Fe-4S] or a [4Fe-4S] 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 3-methylbut-3-en-1-yl diphosphate and prenyl diphosphate.
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Word Map
- 1.17.7.4
-
isoprenoids
-
dimethylallyl
- 4-phosphate
- methylerythritol
-
1-hydroxy-2-methyl-2-e-butenyl
-
2-c-methyl-d-erythritol
-
dmapp
- 1-deoxy-d-xylulose
- reductoisomerase
- 1-deoxy-d-xylulose-5-phosphate
-
e-4-hydroxy-3-methylbut-2-enyl
- isoprene
- bertoni
- rebaudiana
- steviol
-
methyl-jasmonate
- synthesis
The taxonomic range for the selected organisms is: Aquifex aeolicus
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
+
2
+
=
+
2
+
2
+
2
oxidized ferredoxin [iron-sulfur] cluster
+
=
+
2
reduced ferredoxin [iron-sulfur] cluster
+
2
Synonyms
4-hydroxy-3-methylbut-2-enyl diphosphate reductase, 1-hydroxy-2-methyl-2-(e)-butenyl 4-diphosphate reductase, 1-hydroxy-2-methyl-2-(e)-butenyl-4-diphosphate reductase, hshdr1, hshdr2, srhdr, (e)-4-hydroxy-3-methylbut-2-enyl diphosphate reductase, dshdr, isoprenoid synthesis h, chloroplast biogenesis6, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
reductase, (E)-4-hydroxy-3-methylbut-2-enyl diphosphate
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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+
reaction mechanism
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+
reaction mechanism, role of protein residues in the IspH mechanism, detailed overview
-
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+
reaction mechanism, role of protein residues in the IspH mechanism, detailed overview
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
redox reaction
-
-
-
-
oxidation
-
-
-
-
reduction
-
-
-
-
PATHWAY SOURCE
PATHWAYS
BRENDA
-
-, -
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 3-methylbut-3-en-1-yl diphosphate and prenyl diphosphate.
CAS REGISTRY NUMBER
COMMENTARY
512789-14-9
-
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
(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
-
producing a 5:1 mixture of isopentenyl diphosphate and dimethyallyl diphosphate
r
(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
-
producing a 5:1 mixture of isopentenyl diphosphate and dimethyallyl diphosphate
r
isopentenyl diphosphate + NAD(P)+ + H2O
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H + H+
dimethylallyl diphosphate + NAD(P)+ + H2O
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H + H+
isopentenyl diphosphate + NAD(P)+ + H2O
additional information
?
-
-
the IspH-catalyzed reaction involves formation of organometallic species, containing Fe-C bonds
-
-
?
isopentenyl diphosphate + NAD(P)+ + H2O
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H
part of isoprenoid biosynthesis
-
r
isopentenyl diphosphate + NAD(P)+ + H2O
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H
2-C-methyl-D-erithritol-4-phosphate pathway
-
r
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H + H+
dimethylallyl diphosphate + NAD(P)+ + H2O
-
formation of a mixture of isopentenyl diphosphate and dimethylallyl diphosphate in a ratio 1:5
-
-
r
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H + H+
dimethylallyl diphosphate + NAD(P)+ + H2O
-
HMBPP reductase catalyzes the 2H+/2e- reduction of (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate to form an approximately 5:1 mixture of isopentenyl diphosphate and dimethylallyl diphosphate, insights into IspH catalysis and inhibition, involving organometallic species. Residue E126 is essential for catalytic activity. Residue H124 is not a major contributor to substrate binding, but is essential for catalysis, it is involved in delivering H+ to E126 and the bound (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate. Residue H42 forms hydrogen bonds to the bound diphosphate ligand. Ligand binding structure spectral analysis and modelling, overview
-
-
r
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H + H+
dimethylallyl diphosphate + NAD(P)+ + H2O
-
HMBPP reductase catalyzes the 2H+/2e- reduction of (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate to form an approximately 5:1 mixture of isopentenyl diphosphate and dimethylallyl diphosphate, insights into IspH catalysis and inhibition, involving organometallic species, overview
-
-
r
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H + H+
isopentenyl diphosphate + NAD(P)+ + H2O
-
formation of a mixture of isopentenyl diphosphate and dimethylallyl diphosphate in a ratio 1:5
-
-
r
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H + H+
isopentenyl diphosphate + NAD(P)+ + H2O
-
HMBPP reductase catalyzes the 2H+/2e- reduction of (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate to form an approximately 5:1 mixture of isopentenyl diphosphate and dimethylallyl diphosphate, insights into IspH catalysis and inhibition, involving organometallic species. Residue E126 is essential for catalytic activity. Residue H124 is not a major contributor to substrate binding, but is essential for catalysis, it is involved in delivering H+ to E126 and the bound (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate. Residue H42 forms hydrogen bonds to the bound diphosphate ligand. Ligand binding structure spectral analysis and modelling, overview
-
-
r
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H + H+
isopentenyl diphosphate + NAD(P)+ + H2O
-
HMBPP reductase catalyzes the 2H+/2e- reduction of (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate to form an approximately 5:1 mixture of isopentenyl diphosphate and dimethylallyl diphosphate, insights into IspH catalysis and inhibition, involving organometallic species, overview
-
-
r
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
(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
-
-
r
isopentenyl diphosphate + NAD(P)+ + H2O
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H + H+
dimethylallyl diphosphate + NAD(P)+ + H2O
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H + H+
isopentenyl diphosphate + NAD(P)+ + H2O
isopentenyl diphosphate + NAD(P)+ + H2O
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H
part of isoprenoid biosynthesis
-
r
isopentenyl diphosphate + NAD(P)+ + H2O
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H
2-C-methyl-D-erithritol-4-phosphate pathway
-
r
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H + H+
dimethylallyl diphosphate + NAD(P)+ + H2O
-
formation of a mixture of isopentenyl diphosphate and dimethylallyl diphosphate in a ratio 1:5
-
-
r
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H + H+
dimethylallyl diphosphate + NAD(P)+ + H2O
-
HMBPP reductase catalyzes the 2H+/2e- reduction of (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate to form an approximately 5:1 mixture of isopentenyl diphosphate and dimethylallyl diphosphate, insights into IspH catalysis and inhibition, involving organometallic species. Residue E126 is essential for catalytic activity. Residue H124 is not a major contributor to substrate binding, but is essential for catalysis, it is involved in delivering H+ to E126 and the bound (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate. Residue H42 forms hydrogen bonds to the bound diphosphate ligand. Ligand binding structure spectral analysis and modelling, overview
-
-
r
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H + H+
isopentenyl diphosphate + NAD(P)+ + H2O
-
formation of a mixture of isopentenyl diphosphate and dimethylallyl diphosphate in a ratio 1:5
-
-
r
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H + H+
isopentenyl diphosphate + NAD(P)+ + H2O
-
HMBPP reductase catalyzes the 2H+/2e- reduction of (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate to form an approximately 5:1 mixture of isopentenyl diphosphate and dimethylallyl diphosphate, insights into IspH catalysis and inhibition, involving organometallic species. Residue E126 is essential for catalytic activity. Residue H124 is not a major contributor to substrate binding, but is essential for catalysis, it is involved in delivering H+ to E126 and the bound (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate. Residue H42 forms hydrogen bonds to the bound diphosphate ligand. Ligand binding structure spectral analysis and modelling, overview
-
-
r
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Fe2+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
-
alkyne diphosphates are potent IspH inhibitors that form metallacycle complexes. Identification of inhibitors using the metallacycle model
-
additional information
-
analysis of alkynyl diphosphate inhibitors, inhibition model based on an electrostatic interaction with the active site E126, model for alkyne inhibition involving pi (or pi/sigma) metallacycle complex formation with the unique 4th Fe in the Fe4S4 cluster, computational docking and quantum chemical calculations, overview
-
additional information
-
pyridine inhibitors of IspH directly bind to the unique fourth Fe in the 4Fe-4S cluster, spectral binding structure analysis and inhibitor design, overview
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.59
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate
recombinant enzyme, pH 7.5, 60°C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
3.7
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate
recombinant enzyme, pH 7.5, 60°C
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
10
propargyl alcohol
-
above, pH not specified in the publication, temperature not specified in the publication
0.97
propargyl diphosphate
-
pH not specified in the publication, temperature not specified in the publication
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0091
2-(pyridin-3-yl)ethyl diphosphate
Aquifex aeolicus
-
pH not specified in the publication, temperature not specified in the publication
0.00045
but-3-ynyl diphosphate
Aquifex aeolicus
-
pH not specified in the publication, temperature not specified in the publication
1.2
pyridin-2-ylmethyl diphosphate
Aquifex aeolicus
-
pH not specified in the publication, temperature not specified in the publication
0.149
pyridin-4-ylmethyl trihydrogen diphosphate
Aquifex aeolicus
-
pH not specified in the publication, temperature not specified in the publication
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
physiological function
-
IspH is a 4Fe-4S protein that carries out an essential reduction step in isoprenoid biosynthesis
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
E126A
-
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
-
site-directed mutagenesis, the mutant shows an increased Km and a 5fold decreased Vmax compared to the wild-type enzyme
H42A
-
site-directed mutagenesis, the mutant shows a decreased Vmax but unaltered Km compared to the wild-type enzyme
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
highly sensitive to O2, 21% remaining activity after incubation in air for 10 min
639340
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, purified enzyme, 20 mM Tris-HCl, pH 8.0, 95% remaining activity after 2 weeks
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged protein from Escherichia coli strain Xl1-Blue, to 95% homogeneity
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene lytB, expression as His-tagged enzyme in Escherichia coli strain XL1-Blue
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Altincicek, B.; Duin, E.C.; Reichenberg, A.; Hedderich, R.; Kollas, A.K.; Hintz, M.; Wagner, S.; Wiesner, J.; Beck, E.; Jomaa, H.
LytB protein catalyzes the terminal step of the 2-C-methyl-D-erythritol-4-phosphate pathway of isoprenoid biosynthesis
FEBS Lett.
532
437-440
2002
Aquifex aeolicus (O67625)
Wang, K.; Wang, W.; No, J.H.; Zhang, Y.; Zhang, Y.; Oldfield, E.
Inhibition of the Fe(4)S(4)-cluster-containing protein IspH (LytB): electron paramagnetic resonance, metallacycles, and mechanisms
J. Am. Chem. Soc.
132
6719-6727
2010
Aquifex aeolicus
Wang, W.; Li, J.; Wang, K.; Smirnova, T.I.; Oldfield, E.
Pyridine inhibitor binding to the 4Fe-4S protein A. aeolicus IspH (LytB): a HYSCORE Investigation
J. Am. Chem. Soc.
133
6525-6528
2011
Aquifex aeolicus
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