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Information on EC 1.1.1.30 - 3-hydroxybutyrate dehydrogenase and Organism(s) Pseudomonas fragi and UniProt Accession Q5KST5

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IUBMB Comments
Also oxidizes other 3-hydroxymonocarboxylic acids.
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This record set is specific for:
Pseudomonas fragi
UNIPROT: Q5KST5
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The taxonomic range for the selected organisms is: Pseudomonas fragi
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Synonyms
beta-hydroxybutyrate dehydrogenase, 3-hydroxybutyrate dehydrogenase, d-beta-hydroxybutyrate dehydrogenase, d-3-hydroxybutyrate dehydrogenase, beta-hydroxybutyric dehydrogenase, dhrs6, 3-hydroxybutyrate dehydrogenase-2, beta-hydroxybutyric acid dehydrogenase, 3-hbdh, 3hbdh, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D-3-hydroxybutyrate dehydrogenase
-
3-D-hydroxybutyrate dehydrogenase
-
-
-
-
3-HBDH
-
-
-
-
3-hydroxybutyrate dehydrogenase
-
-
-
-
BDH
-
-
-
-
beta-hydroxybutyrate dehydrogenase
-
-
-
-
beta-hydroxybutyric acid dehydrogenase
-
-
-
-
beta-hydroxybutyric dehydrogenase
-
-
-
-
D-(-)-3-hydroxybutyrate dehydrogenase
-
-
-
-
D-3-hydroxybutyrate dehydrogenase
-
-
-
-
D-beta-hydroxybutyrate dehydrogenase
-
-
-
-
hydroxybutyrate oxidoreductase
-
-
-
-
NAD-beta-hydroxybutyrate dehydrogenase
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
redox reaction
-
-
-
-
PATHWAY SOURCE
PATHWAYS
-
-, -
SYSTEMATIC NAME
IUBMB Comments
(R)-3-hydroxybutanoate:NAD+ oxidoreductase
Also oxidizes other 3-hydroxymonocarboxylic acids.
CAS REGISTRY NUMBER
COMMENTARY hide
9028-38-0
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(R)-3-hydroxybutanoate + NAD+
acetoacetate + NADH
show the reaction diagram
-
-
-
?
(R)-3-hydroxybutanoate + NADP+
acetoacetate + NADPH
show the reaction diagram
activity with NADP+ is 2% of the activity with NAD+
-
-
?
D-3-hydroxybutyrate + NAD+
acetoacetate + NADH + H+
show the reaction diagram
-
-
-
r
L-threonine + NAD+
?
show the reaction diagram
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NADP+
2% of the activity with NAD+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
cacodylate
competitive
dimethyl malonate
-
DL-2-hydroxybutyrate
-
L-3-hydroxybutyrate
is a competitive inhibitor
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.2
(R)-3-hydroxybutanoate
-
0.37 - 32
acetoacetate
0.8 - 100
D-3-hydroxybutyrate
388
L-threonine
-
0.12 - 2.2
NAD+
0.01 - 1.5
NADH
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
4.5 - 125
acetoacetate
6.1 - 705
D-3-hydroxybutyrate
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5.6
cacodylate
-
80
dimethyl malonate
-
0.81
DL-2-hydroxybutyrate
-
0.9
DL-lactate
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
Q5KST5_PSEFR
260
1
26684
TrEMBL
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
27000
x * 27000, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 27000, SDS-PAGE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystals of ternary complex of HBDH-NAD+-L-3-hydroxybutyrate and the binary complex of HBDH-NAD+. The former structure shows a closed-form conformation, which is considered an active form for catalysis, while the latter stays mostly in a open-form conformation. Crystals of mutants T190S and T190A
hanging-drop vapor-diffusion method, ligand-free enzyme and enzyme-NAD+ complex, 2.0 A resolution
hanging-drop vapour-diffusion method using PEG 3000 as a precipitating agent. The crystals belong to the orthorhombic group P2(1)2(1)2, with unit-cell parameters a = 64.3, b = 99.0, c = 110.2 A. The crystals are most likely to contain two tetrameric subunits in the asymmetric unit
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
H144A
catalytic efficiency (kcat/Km) is 0.2% of the activity of wild-type HBDH
K152A
no activity
K152E
very low activity
K152Q
very low activity
K152R
retains a significant level of activity
L215A
both Km and kcat values are largely affected and the catalytic efficiency (kcat/Km) is less than 3% that of the wild-type enzyme
L215V
Km values increase 3.5- and 4.3fold and the kcat values are 73-118% those of the wild-type toward D-3-hydroxybutyrate and acetoacetate, respectively. Mutation does not significantly change Km and kcat toward NAD+ and NADH
Q196A
kcat/Km value is 0.6% that of the wild-type
Q196E
substantially reduced activity
Q196N
substantially reduced activity
Q94A
catalytic efficiency (kcat/Km) is 1.4% of the activity of wild-type HBDH
T190A
activity decreases to 0.1% that of the wild-type enzyme
T190C
decreased activity
T190S
retains 37% of the activity
W187A
very low activity
W187F
shows significant activity levels, 65% that of the wild-type enzyme
W187T
shows faint activity
W187Y
shows significant activity levels, 41% that of the wild-type enzyme
W257A
no activity
W257F
shows low activity levels, 2% that of the wild-type enzyme
W257Y
shows low activity levels, 1% that of the wild-type enzyme
Y155F
no activity
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
wild-type and mutants purified by metal chelating affinity chromatography followed by ion-exchange chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
efficiently expressed in Escherichia coli cells harboring pHBDH11
wild-type and mutants expressed in Escherichia coli XL1Blue harbouring pHBDH11. Wild-type HBDH and mutants containing an N-terminal His-tag expressed in Escherichia coli XL1Blue using pQE30 as a vector
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Nakajima, Y.; Ito, K.; Ichihara, E.; Ogawa, K.; Egawa, T.; Xu, Y.; Yoshimoto, T.
Crystallization and preliminary X-ray characterization of D-3-hydroxybutyrate dehydrogenase from Pseudomonas fragi
Acta Crystallogr. Sect. F
61
36-38
2005
Pseudomonas fragi (Q5KST5), Pseudomonas fragi
Manually annotated by BRENDA team
Ito, K.; Nakajima, Y.; Ichihara, E.; Ogawa, K.; Katayama, N.; Nakashima, K.; Yoshimoto, T.
D-3-hydroxybutyrate dehydrogenase from Pseudomonas fragi: molecular cloning of the enzyme gene and crystal structure of the enzyme
J. Mol. Biol.
355
722-733
2006
Pseudomonas fragi (Q5KST5), Pseudomonas fragi
Manually annotated by BRENDA team
Nakashima, K.; Ito, K.; Nakajima, Y.; Yamazawa, R.; Miyakawa, S.; Yoshimoto, T.
Closed complex of the D-3-hydroxybutyrate dehydrogenase induced by an enantiomeric competitive inhibitor
J. Biochem.
145
467-479
2009
Pseudomonas fragi (Q5KST5), Pseudomonas fragi
Manually annotated by BRENDA team