Information on EC 1.3.99.6 - 3-oxo-5beta-steroid 4-dehydrogenase

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

EC NUMBER
COMMENTARY
1.3.99.6
-
RECOMMENDED NAME
GeneOntology No.
3-oxo-5beta-steroid 4-dehydrogenase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
a 3-oxo-5beta-steroid + acceptor = a 3-oxo-DELTA4-steroid + reduced acceptor
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
oxidation
-
-
-
-
redox reaction
-
-
-
-
reduction
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Metabolic pathways
-
-
Steroid hormone biosynthesis
-
-
SYSTEMATIC NAME
IUBMB Comments
3-oxo-5beta-steroid:acceptor DELTA4-oxidoreductase
-
SYNONYMS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
3-keto-DELTA4-steroid-5beta-reductase
-
-
-
-
3-oxo-5beta-steroid DELTA4-dehydrogenase
-
-
-
-
3-oxo-DELTA4-steroid-5beta-reductase
-
-
-
-
5beta-POR
-
-
5beta-POR
Q6PQJ9
-
5beta-POR
Q078S6
-
5beta-reductase
-
-
-
-
AKR1D1
-
-
Aldo-keto reductase family 1 member D1
-
-
-
-
Delta(4)-3-ketosteroid 5-beta-reductase
-
-
-
-
DELTA-3-ketosteroid-5beta-reductase
-
-
-
-
DELTA4-3-ketosteroid-5beta-reductase
-
-
-
-
DELTA4-3-oxosteroid 5beta-reductase
-
-
-
-
DELTA4-3-oxosteroid 5beta-reductase
-
-
DELTA4-5beta-DH
-
-
-
-
EC 1.3.1.3
Q078S6
related
progesterone 5beta-reductase
-
-
progesterone 5beta-reductase
Q6PQJ9
-
progesterone 5beta-reductase
-
-
progesterone 5beta-reductase
Q078S6
-
steroid 5beta reductase
-
-
-
-
steroid 5beta-reductase
-
-
steroid DELTA-5beta-dehydrogenase
-
-
-
-
testosterone 5beta-reductase
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
9067-97-4
-
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Clostridium innocuum
-
-
-
Manually annotated by BRENDA team
gene SRD5B1, enzyme AKR1D1, healthy persons and 3 different patients with neonatal onset cholestatic liver disease and normal gamma-glutamyl transpeptidase activity
-
-
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
17beta-hydroxy-5beta-androstan-3-one + menaphthone
testosterone + reduced acceptor
show the reaction diagram
-
acceptor: phenazine methosulfate
-
-
?
17beta-hydroxy-5beta-androstan-3-one + menaphthone
testosterone + reduced acceptor
show the reaction diagram
-
acceptor: 1,2-naphthoquinone, 1,4-naphthoquinone, 1,4-benzoquinone, menadione or coenzyme Q10
-
-
?
21-hydroxy-5beta-pregnan-3,20-dione + acceptor
21-hydroxy-pregn-4-en-3,20-dione + reduced acceptor
show the reaction diagram
-
acceptor: 1,2-naphthoquinone, 1,4-naphthoquinone, 1,4-benzoquinone, menadione or coenzyme Q10
-
-
?
3,12-dioxo-5beta-cholan-24-oic acid + menaphthone
3,12-dioxo-4-cholen-24-oic acid + reduced menaphthone
show the reaction diagram
-
-
-
-
?
3,12-dioxo-5beta-cholan-24-oic acid + phenazine methosulfate
3,12-dioxo-4-cholen-24-oic acid + reduced phenazine methosulphate
show the reaction diagram
-
-
-
-
?
3,12-dioxo-5beta-cholan-24-oic acid methyl ester + menaphthone
3,12-dioxo-4-cholen-24 oic acid methyl ester + reduced menaphthone
show the reaction diagram
-
-
-
-
?
3,12-dioxo-5beta-cholan-24-oic acid methyl ester + phenazine methosulfate
3,12-dioxo-4-cholen-24 oic acid methyl ester + reduced phenazine methosulfate
show the reaction diagram
-
-
-
-
?
3-oxo-5beta-24-cholan-oic acid + phenazine methosulfate
3-oxo-4-cholen-24-oic acid + reduced phenazine methosulfate
show the reaction diagram
-
-
-
-
?
3-oxo-5beta-cholan-24-oic acid + menaphthone
3-oxo-4-cholen-24-oic acid + reduced menaphthone
show the reaction diagram
-
-
-
-
?
4-androstene-3,17-dione + NADPH
5beta-androstan-3,15-dione + NADP+
show the reaction diagram
Q078S6
-
-
-
?
4-androstene-3,17-dione + NADPH
5beta-androstan-3,15-dione + NADP+
show the reaction diagram
Q6PQJ9
-
-
-
?
4-pregnen-3,20-dione + NADH
5beta-pregnan-3,20-dione + NAD+
show the reaction diagram
-
-
-
-
?
4-pregnen-3,20-dione + NADH
5beta-pregnan-3,20-dione + NAD+
show the reaction diagram
Clostridium innocuum
-
i.e. progesterone
-
-
?
5beta-androst-3,17-dione + acceptor
androst-1,4-dien-3,17-dione + reduced acceptor
show the reaction diagram
-
acceptor: 1,2-naphthoquinone, 1,4-naphthoquinone, 1,4-benzoquinone, menadione or coenzyme Q10
-
-
?
5beta-androstan-3,17-dione + acceptor
4-androsten-3,17-dione + reduced acceptor
show the reaction diagram
-
acceptor: phenazine methosulfate
-
-
?
5beta-androstan-3,17-dione + acceptor
4-androsten-3,17-dione + reduced acceptor
show the reaction diagram
-
acceptor: nitroblue tetrazolium
-
-
?
5beta-androstan-3,17-dione + acceptor
4-androsten-3,17-dione + reduced acceptor
show the reaction diagram
-
acceptor: 1,2-naphthoquinone, 1,4-naphthoquinone, 1,4-benzoquinone, menadione or coenzyme Q10
-
-
?
5beta-androstane-3,17-dione + acceptor
androst-4-en-3,17-dione + reduced acceptor
show the reaction diagram
-
acceptor: 1,2-naphthoquinone, 1,4-naphthoquinone, 1,4-benzoquinone, menadione or coenzyme Q10
-
-
?
5beta-pregnan-3,20-dione + menaphthone
4-pregnen-3,20-dione + reduced menaphthone
show the reaction diagram
-
-
-
-
?
5beta-pregnan-3,20-dione + phenazine methosulfate
4-pregnen-3,20-dione + reduced menazine methosulfate
show the reaction diagram
-
-
-
-
?
cortexone + NADPH
21-trihydroxy-5beta-pregnane-3,20-dione + NADP+
show the reaction diagram
Q078S6
-
-
-
?
cortexone + NADPH
21-trihydroxy-5beta-pregnane-3,20-dione + NADP+
show the reaction diagram
Q6PQJ9
-
-
-
?
cortisol + NADPH
11beta,17,21-trihydroxy-5beta-pregnane-3,20-dione + NADP+
show the reaction diagram
Q078S6
-
-
-
?
progesterone + NADPH + H+
5beta-pregnane-3,20-dione + NADP+
show the reaction diagram
-
-
-
-
?
progesterone + NADPH + H+
5beta-pregnane-3,20-dione + NADP+
show the reaction diagram
Q078S6
-
-
-
ir
progesterone + NADPH + H+
5beta-pregnane-3,20-dione + NADP+
show the reaction diagram
-
-
-
-
?
progesterone + NADPH + H+
5beta-pregnane-3,20-dione + NADP+
show the reaction diagram
Q6PQJ9
5alpha-pregnane-3,20-dione, the 5alpha-isomer of the pregnane-3,20-dione is not formed
-
-
ir
progesterone + NADPH + H+
5beta-pregnane-3,20-dione + NADP+
show the reaction diagram
-
highest substrate specificity
-
-
ir
testosterone + NADH
17beta-hydroxy-5beta-androstan-3-one + NAD+
show the reaction diagram
Clostridium innocuum
-
-
-
-
-
testosterone + NADPH + H+
(5beta,17beta)-17-hydroxyandrostan-3-one + NADP+
show the reaction diagram
Q6PQJ9
-
-
-
?
cortisol + NADPH
11beta,17,21-trihydroxy-5beta-pregnane-3,20-dione + NADP+
show the reaction diagram
Q6PQJ9
-
-
-
?
additional information
?
-
-
no activity with: NAD+, NADP+, FMN and FAD, inducible by 3-oxo-5beta-cholan-24-oic acid
-
-
-
additional information
?
-
-
inducible by testosterone and progesterone
-
-
-
additional information
?
-
-
enzyme is involved in bile acid biosynthesis
-
-
-
additional information
?
-
-
enzyme is essential in bile acids formation, analysis of bile acid contents in urine and plasma from healthy persons and 3 different patients with neonatal onset cholestatic liver disease, physiolgical role of the enzyme, overview
-
-
-
additional information
?
-
Q6PQJ9
pregnenolone, 21-OH-pregenenolone and isoprogesterone are not accepted by recombinant 5beta-POR
-
-
-
additional information
?
-
-
the recombinant enzyme catalyzes the stereospecific reduction of the delta4-double bond of several steroids with a 3-oxo,delta4,5 structure
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
additional information
?
-
-
inducible by 3-oxo-5beta-cholan-24-oic acid
-
-
-
additional information
?
-
-
inducible by testosterone and progesterone
-
-
-
additional information
?
-
-
enzyme is involved in bile acid biosynthesis
-
-
-
additional information
?
-
-
enzyme is essential in bile acids formation, analysis of bile acid contents in urine and plasma from healthy persons and 3 different patients with neonatal onset cholestatic liver disease, physiolgical role of the enzyme, overview
-
-
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
NADH
Clostridium innocuum, Clostridium paraputrificum
-
required
NADPH
-
cannot be replaced by NADH
NADPH
Q078S6
-
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
formaldehyde
-
30 mM
iodoacetate
-
50 mM, partial
Merthiolate
-
1.0 mM
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
FMNH2
Clostridium innocuum, Clostridium paraputrificum
-
slightly stimulatory in combination with NADH
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.228
4-androstene-3,17-dione
-
-
2.193
4-androstene-3,17-dione
Q078S6
-
0.042
4-pregnen-3,20-dione
Clostridium innocuum
-
-
1.597
cortexone
-
-
2.373
cortexone
Q078S6
-
0.291
cortisol
-
-
2.079
cortisol
Q078S6
-
0.0079
NADPH
-
-
0.008
NADPH
-
-
0.015
NADPH
Q078S6
-
0.0391
progesterone
-
-
0.12
progesterone
-
-
0.12
progesterone
-
purified wild type enzyme
0.215
progesterone
Q078S6
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
1.89
-
purified wild type enzyme, using progesterone as substrate
additional information
-
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5
Clostridium innocuum
-
-
7.8
-
with progesterone as substrate
8.5 - 10.5
-
pH 8.5: about 40% of maximal activity, pH 10.5: about 20% of maximal activity
9
-
above pH 9.0, the rate of DELTA4-5beta-dehydrogenase reaction increases with pH to the limit where accurate measurement can be made, pH 9.0
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
40
-
with progesterone as substrate
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
31 - 43
-
31°C: about 70% of maximal activity, 43°C: about 60% of maximal activity
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
-
lowest expression
Manually annotated by BRENDA team
-
from patients late in pregnancy, before term labour, during term labour and within the first 24 h postpartum
Manually annotated by BRENDA team
-
maximally transcribed in mature flowers
Manually annotated by BRENDA team
-
maximally transcribed
Manually annotated by BRENDA team
-
of alcohol-fed animals
Manually annotated by BRENDA team
-
relative expression decreases significantly in association with labour by about 10fold
Manually annotated by BRENDA team
-
mRNA is expressed in hepatocyte-like cells of rats treated with copper depletion regimen but not in the normal pancreas of rat fed a normal diet
Manually annotated by BRENDA team
-
most highly expressed, relative expression decreases significantly in association with labour by about 2fold
Manually annotated by BRENDA team
-
at the base of the rosette
Manually annotated by BRENDA team
-
at the basal part of the leaf, lowest amount
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
32000
-
gel filtration
391402
80000
Clostridium innocuum
-
gel filtration
287079
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
?
-
x * 37000, SDS-PAGE
?
-
x * 40000, SDS–PAGE
?
-
x * 43963, sequence analysis, x * 43000, purified enzyme, SDS–PAGE
?
Q078S6
x * 45000, SDS–PAGE
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
5beta-POR, in the presence and absence of the cofactor NADP+, hanging drop vapour diffusion method, using 15% polyethylene glycol 4000, 0.1 M ammonium acetate, and 0.1 M sodium citrate, pH 5.6
-
by the hanging-drop method, at 2.7 A resolution, crystals belong to space group P43212, contain a single 5beta-POR molecule in the asymmetric unit and tend to diffract anisotropically, identification of six out of eight possible Se-atom positions
-
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
58
-
half-life: 10 min
391381
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
glycerol stabilizes
-
phenazine methosulfate stabilizes
-
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
oxygen-sensitive
Clostridium innocuum, Clostridium paraputrificum
-
287079
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-70°C, 20% glycerol, 1 week, less than 30% loss of activity
Clostridium innocuum
-
4°C, in neutral buffer, 20% glycerol, about 50% loss of activity after 1 month
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
by Ni-NTA affinity chromatography
-
nickel-Sepharose affinity column chromatography and Superdex 75 gel filtration
-
to homogeneity by Ni–NTA affinity chromatography
-
to apparent homogeneity by affinity chromatography
-
by Ni-NTA affinity chromatography
Q078S6
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli strain M15
-
overproduced by the pQE expression system and transformed into Escherichia coli strain B834(DE3)
-
Sph1/Sal1 5beta-POR fragment cloned into the pQE vector and transformed into Escherichia coli strain M15(pREP4)
-
full-length P5betaR cDNA overexpressed in Escherichia coli as a fusion protein with MBP or His-tag
-
gene SRD5B1, DNA sequence determination and analysis from healthy persons and 3 different patients with neonatal onset cholestatic liver disease and normal gamma-glutamyl transpeptidase activity, parents and siblings
-
SPHI /SALI IC5beta-POR fragment cloned into the pQE vector system and transformed into Escherichai coli strain M15(pREP4)
Q078S6
expression in Escherichia coli
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Y179A
-
inactive
Y179F
-
inactive
P198L
-
naturally occurring mutation of C662T in patient MS, homozygous, patient shows giant cell hepatitis
L106F
-
naturally occurring mutation of C385T in patient RM, homozygous, patient shows giant cell hepatitis and prominent extramedullary haemopoiesis
additional information
-
in patient BH naturally occurs a frame shift due to a base deletion, 511delT, resulting in a premature stop codon in exon 5, patient shows giant cell hepatitis and prominent extramedullary haemopoiesis
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
-
determination of the concentration of chenodeoxycholic acid by an enzyme kit consisting of 3alpha-hydroxysteroid dehydrogenase, 3-keto-5beta-steroid-DELTA4-dehydrogenase, NAD+, nitroblue tetrazolium, diaphorase and some other reagents
additional information
-
5beta-POR is highly conserved within the genus Digitalis and the respective genes and proteins share considerable homology to putative progesterone reductases from other plant species
additional information
-
inspection of the MAD-phased electron-density map shows that 5beta-POR is a Rossmann-type reductase and the quality of the map is such that it is anticipated that a complete atomic model of 5beta-POR may readily be built
additional information
-
P5betaR belongs to the short-chain dehydrogenase/reductase (SDR) superfamily, bearing no structural homology to its mammalian counterpart, which is a member of the aldo-keto reductase (AKR) superfamily
additional information
Q078S6
significant homology to the putative progesterone 5beta-reductases isolated from other plant species, such as Digitalis lanata (ca. 98% identical) and Arabidopsis thaliana (ca. 69% identical)