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Information on EC 4.2.1.167 - (R)-2-hydroxyglutaryl-CoA dehydratase and Organism(s) Acidaminococcus fermentans and UniProt Accession P11570
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4.2.1.167 (R)-2-hydroxyglutaryl-CoA dehydrataseIUBMB Comments
The enzymes from the bacteria Acidaminococcus fermentans and Clostridium symbiosum are involved in the fermentation of L-glutamate. The enzyme contains [4Fe-4S] clusters, FMNH2 and riboflavin. It must be activated by an activator protein. Once activated, it can catalyse many turnovers.
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The taxonomic range for the selected organisms is: Acidaminococcus fermentans
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
(r)-2-hydroxyglutaryl-coa dehydratase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
hgdAB
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 [4Fe-4S] clusters, FMNH2 and riboflavin. It must be activated by an activator protein. Once activated, it can catalyse many turnovers.
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
additional information
?
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in the presence of ATP one electron is transferred from flavodoxin hydroquinone via the [4Fe-4S]1+/2+ cluster of the activator protein to Mo(VI) of heterodimeric dehydratase, which is thereby reduced to Mo(V)
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-
?
(R)-2-hydroxyglutaryl-CoA
(E)-glutaconyl-CoA + H2O
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-
-
?
(R)-2-hydroxyglutaryl-CoA
(E)-glutaconyl-CoA + H2O
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-
-
?
(R)-2-hydroxyglutaryl-CoA
(E)-glutaconyl-CoA + H2O
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-
-
r
(R)-2-hydroxyglutaryl-CoA
(E)-glutaconyl-CoA + H2O
the enzyme is involved in the fermentation of L-glutamate
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-
?
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
(R)-2-hydroxyglutaryl-CoA
(E)-glutaconyl-CoA + H2O
the enzyme is involved in the fermentation of L-glutamate
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-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Ferredoxin
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 713 microM Fe to 1.1 micromol/g at 1745 microM Fe
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flavodoxin
dominant electron donor protein under iron-limiting conditions
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riboflavin 5'-phosphate
1 mol per mol of heterodimeric dehydratase
riboflavin 5'-phosphate
the actual dehydration is mediated by component D, which contains 1.0 [4Fe-4S]2+ cluster, 1.0 reduced riboflavin-5'-phosphate and about 0.1 molybdenum (VI) per heterodimer
[4Fe-4S]-center
each active component contains an oxygen sensitive diamagnetic [4Fe-4S]2+ cluster. Reduction of the [4Fe-4S]2+ cluster of the activator protein with dithionite yields a paramagnetic [4Fe-4S]1+ cluster with the unusual electron spin ground state S=3/2. Under air the activator protein looses its activity within seconds due to irreversible degradation of its [4Fe-4S]2+ cluster to a [2Fe-2S]2+ cluster. The [4Fe-4S]2+ cluster of the heterodimeric dehydratase cannot be reduced to a [4Fe-4S]1+ cluster
[4Fe-4S]-center
the actual dehydration is mediated by component D, which contains 1.0 [4Fe-4S]2+ cluster, 1.0 reduced riboflavin-5'-phosphate and about 0.1 molybdenum (VI) per heterodimer
[4Fe-4S]-center
the reduced [4Fe-4S]+ cluster containing activator protein transfers one electron to the dehydratase driven by ATP hydrolysis, which activates the enzyme. With a tenfold excess of titanium(III) citrate at pH 8.0 the activator can be further reduced, yielding about 50% of a superreduced [4Fe-4S]0 cluster in the all-ferrous state. The superreduced cluster has apparent spectroscopic similarities with the corresponding [4Fe-4S]0 cluster described for the nitrogenase Fe-protein. Only one-electron transfer steps are involved in dehydratase catalysis
[4Fe-4S]-center
the [4Fe-4S](1+/2+) cluster of the activator protein is exposed to the solvent. Upon exchange of the bound ADP by ATP, the chelation rate by iron chelators is 8fold enhanced, indicating a large conformational change. Oxidized activator exhibits ATPase activity of 6 s(-1), which is completely abolished upon reduction by one electron
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Molybdenum
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
LITERATURE
IMAGE
Activator protein
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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the enzyme is activated by ATP, MgCl2, and Ti(III)citrate by an activator protein (HgdC) that is present in the organism at very low concentrations. It is suggested that during the activation step, the electron of this cycle is fed into the enzyme by Ti(III)citrate and energized by hydrolysis of ATP. Both functions are apparently catalysed by the activator. The enzyme remains in this activated state for several turnovers
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additional information
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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additional information
-
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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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
P11569 i.e. subunit alpha, P11570 i.e. subunit beta
UniProt
P11569 i.e. subunit alpha, P11570 i.e. subunit beta, P11568 i.e. activator protein
UniProt
P11569: alpha-subunit, P11570: beta-subunit
UniProt
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
the enzyme is involved in the fermentation of L-glutamate
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
42000
55000
42000
2 * 55000 (alpha), + 2 * 42000 (beta), SDS-PAGE
55000
2 * 55000 (alpha), + 2 * 42000 (beta), SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
tetramer
2 * 55000 (alpha), + 2 * 42000 (beta), SDS-PAGE
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
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
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Buckel, W.
The reversible dehydration of (R)-2-hydroxyglutarate to (E)-glutaconate
Eur. J. Biochem.
106
439-447
1980
Acidaminococcus fermentans, Acidaminococcus fermentans (P11569 and P11570), Acidaminococcus fermentans DSM 20731 (P11569 and P11570), [Clostridium] symbiosum
Schweiger, G.; Dutscho R.; Buckel, W.
Purification of 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. An iron-sulfur protein
Eur. J. Biochem.
169
441-448
1987
Acidaminococcus fermentans (P11569 and P11570), Acidaminococcus fermentans, Acidaminococcus fermentans DSM 20731 (P11569 and P11570)
Hans, M.; Buckel, W.; Bill, E.
The iron-sulfur clusters in 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. Biochemical and spectroscopic investigations
Eur. J. Biochem.
267
7082-7093
2000
Acidaminococcus fermentans (P11569 and P11570 and P11568), Acidaminococcus fermentans DSM 20731 (P11569 and P11570 and P11568)
Thamer, W.; Cirpus, I.; Hans, M.; Pierik, A.J.; Selmer, T.; Bill, E.; Linder, D.; Buckel, W.
A two [4Fe-4S]-cluster-containing ferredoxin as an alternative electron donor for 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans
Arch. Microbiol.
179
197-204
2003
Acidaminococcus fermentans (P11569 and P11570), Acidaminococcus fermentans DSM 20731 (P11569 and P11570)
Hans, M.; Bill, E.; Cirpus, I.; Pierik, A.J.; Hetzel, M.; Alber, D.; Buckel, W.
Adenosine triphosphate-induced electron transfer in 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans
Biochemistry
41
5873-5882
2002
Acidaminococcus fermentans (P11569 and P11570), Acidaminococcus fermentans DSM 20731 (P11569 and P11570)
Muller, U.; Buckel, W.
Activation of (R)-2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans
Eur. J. Biochem.
230
698-704
1995
Acidaminococcus fermentans, Acidaminococcus fermentans ATCC 25085
Bendrat, K.; Mueller, U.; Klees, A.G.; Buckel, W.
Identification of the gene encoding the activator of (R)-2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans by gene expression in Escherichia coli
FEBS Lett.
329
329-331
1993
Acidaminococcus fermentans (P11569 and P11570 and P11568), Acidaminococcus fermentans, Acidaminococcus fermentans DSM 20731 (P11569 and P11570 and P11568)
Hans, M.; Buckel, W.; Bill, E.
Spectroscopic evidence for an all-ferrous [4Fe-4S]0 cluster in the superreduced activator of 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans
J. Biol. Inorg. Chem.
13
563-574
2008
Acidaminococcus fermentans (P11569 and P11570 and P11568), Acidaminococcus fermentans DSM 20731 (P11569 and P11570 and P11568)
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