Information on EC 4.2.1.167 - (R)-2-hydroxyglutaryl-CoA dehydratase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
4.2.1.167
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RECOMMENDED NAME
GeneOntology No.
(R)-2-hydroxyglutaryl-CoA dehydratase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
(R)-2-hydroxyglutaryl-CoA = (E)-glutaconyl-CoA + H2O
show the reaction diagram
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
L-glutamate degradation V (via hydroxyglutarate)
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SYSTEMATIC NAME
IUBMB Comments
(R)-2-hydroxyglutaryl-CoA hydro-lyase ((E)-glutaconyl-CoA-forming)
The enzymes from the bacteria Acidaminococcus fermentans and Clostridium symbiosum are involved in the fermentation of L-glutamate. The enzyme contains [4F-4S] clusters, FMNH2 and riboflavin. It must be activated by an activator protein. Once activated, it can catalyse many turnovers.
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Clostridium microsporum
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Manually annotated by BRENDA team
Q9X5B8: subunit beta (hgdB), Q9X5B7: subunit alpha (hgdA)
Q9X5B8 AND Q9X5B7
UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(E)-glutaconyl-CoA + H2O
(R)-2-hydroxyglutaryl-CoA
show the reaction diagram
(R)-2-hydroxyadipyl-CoA
?
show the reaction diagram
(R)-2-hydroxyglutaryl-CoA
(E)-glutaconyl-CoA + H2O
show the reaction diagram
butynedioyl-CoA
?
show the reaction diagram
muconyl-CoA
?
show the reaction diagram
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hydration of butynedioyl-CoA most likely leads to 2-oxosuccinyl-CoA, which spontaneously hydrolyzes to oxaloacetate and CoASH
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r
oxalocrotonyl-CoA
?
show the reaction diagram
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r
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
(R)-2-hydroxyglutaryl-CoA
(E)-glutaconyl-CoA + H2O
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
4Fe-4S-center
P11569 and P11570
the enzyme contains [4F-4S] clusters
Ferredoxin
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alternative electron donor besides flavodoxin is a two [4Fe-4S]1+/2+-cluster-containing ferredoxin, with redox potentials of –405 mV and –340mV. The flavodoxin is the dominant electron donor protein under iron-limiting conditions. The concentration of ferredoxin increases stepwise from about 0.2 micromol/g at 7–13 microM Fe to 1.1 micromol/g at 17–45 microM Fe
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flavodoxin
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dominant electron donor protein under iron-limiting conditions
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riboflavin
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presence of trace amounts
riboflavin 5'-phosphate
[4Fe-4S]-center
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4Fe-4S centre
Q9X5B8 AND Q9X5B7
the enzyme contains two [4Fe4S]2+ clusters. It is likely that the alpha and beta subunits are bridged by a [4Fe4S]2+ cluster. The enzyme contains 7.5 non-heme iron and 8.1 acid labile sulfur/heterodimer, symmetric cube-type structures
Molybdenum
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protein contains about 0.1 molybdenum (VI) per heterodimer. The enzyme has to be activated by the extremely oxygensensitive [4Fe-4S]1+/2+-cluster-containing homodimeric component A, which generates Mo(V) by an ATP/Mg2+-induced one-electron transfer
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Activator protein
P11569 and P11570
the enzyme must be activated by an activator protein. Once activated, it can catalyse many turnovers
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activator protein HgdC
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additional information
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enzyme requires an activator protein HgdC for activity. Dehydratase activity is stimulated at least tenfold by cell-free extracts of Escherichia coli cells transformed with a plasmid carrying hgdC. On the chromosome the HgdC gene is located just before the catalytic subunits hgdA and hgdB
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.25
(E)-glutaconyl-CoA
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pH 8.0, 21°C
0.1
(R)-2-hydroxyadipyl-CoA
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pH 8.0, 21°C
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0.052
(R)-2-hydroxyglutaryl-CoA
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pH 8.0, 21°C
2.1
butynedioyl-CoA
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pH 8.0, 21°C
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0.57
muconyl-CoA
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pH 8.0, 21°C
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1.1
oxalocrotonyl-CoA
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pH 8.0, 21°C
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
27
(E)-glutaconyl-CoA
Clostridium symbiosum
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pH 8.0, 21°C
10074
440
(R)-2-hydroxyadipyl-CoA
Clostridium symbiosum
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pH 8.0, 21°C
206971
1600
(R)-2-hydroxyglutaryl-CoA
Clostridium symbiosum
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pH 8.0, 21°C
52055
1.4
butynedioyl-CoA
Clostridium symbiosum
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pH 8.0, 21°C
206974
0.8
muconyl-CoA
Clostridium symbiosum
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pH 8.0, 21°C
214078
820
oxalocrotonyl-CoA
Clostridium symbiosum
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pH 8.0, 21°C
214079
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.0558
P11569 and P11570
pH 7.0, 37°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7
P11569 and P11570
assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37
P11569 and P11570
assay at
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
42000
P11569 and P11570
2 * 55000 (alpha), + 2 * 42000 (beta), SDS-PAGE
55000
P11569 and P11570
2 * 55000 (alpha), + 2 * 42000 (beta), SDS-PAGE
100000
Q9X5B8 AND Q9X5B7
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
heterodimer
tetramer
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
the enzyme is oxygen sensitive with a half-life of 2 days under aerobic conditions
Q9X5B8 AND Q9X5B7
733766
under anaerobic conditions at 4°C for about 1 week without loss of activity
Q9X5B8 AND Q9X5B7
733766
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-80°C, frozen with liquid nitrogen, stable
Q9X5B8 AND Q9X5B7
4°C, 1 week, anaerobic conditions, stable
Q9X5B8 AND Q9X5B7
4°C, stable for several months
P11569 and P11570
homodimeric activator, in the presence of 5 mM MgCl2 and 1 mM ADP or ATP, can be stabilized and stored for 4 days at 4°C without loss of activity
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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Q9X5B8 AND Q9X5B7
expression in Escherichia coli
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