Information on EC 4.2.1.28 - propanediol dehydratase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
4.2.1.28
-
RECOMMENDED NAME
GeneOntology No.
propanediol dehydratase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
propane-1,2-diol = propanal + H2O
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
elimination
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
L-1,2-propanediol degradation
-
-
Propanoate metabolism
-
-
SYSTEMATIC NAME
IUBMB Comments
propane-1,2-diol hydro-lyase (propanal-forming)
Requires a cobamide coenzyme. Also dehydrates ethylene glycol to acetaldehyde.
CAS REGISTRY NUMBER
COMMENTARY hide
9026-90-8
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Acetobacterium sp.
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
strain DSM 20016, and strain F275 isolated from the human gut
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
Salmonella enterica produces a proteinaceous microcompartment for B12-dependent 1,2-propanediol utilization, Pdu MCP. The Pdu MCP consists of catabolic enzymes encased within a protein shell and its function is to sequester propionaldehyde, a toxic intermediate of 1,2-propanediol degradation, overview. A short N-terminal region of the medium subunit, PduD, is required for packaging the coenzyme B12-dependent diol dehydratase, PduCDE, into the lumen of the Pdu MCP. PduD subunit also mediates packaging of itself and other subunits of diol dehydratase, PduC and PduE, into the Pdu MCP
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(R)-propane-1,2-diol
propanal + H2O
show the reaction diagram
(R,S)-1,2-propanediol
propanal + H2O
show the reaction diagram
-
-
-
-
?
(S)-propane-1,2-diol
propanal + H2O
show the reaction diagram
1,2-butanediol
butanal + H2O
show the reaction diagram
-
-
-
-
?
1,2-butanediol
butyraldehyde
show the reaction diagram
1,2-ethanediol
acetaldehyde
show the reaction diagram
1,2-ethanediol
acetaldehyde + H2O
show the reaction diagram
1,2-propanediol
?
show the reaction diagram
-
-
-
-
-
1,2-propanediol
propanal
show the reaction diagram
1,2-propanediol
propanal + H2O
show the reaction diagram
1,2-propanediol
propionaldehyde + H2O
show the reaction diagram
-
-
-
-
?
1,3-butanediol
?
show the reaction diagram
-
low turnover
-
-
-
2,3-butanediol
methyl ethyl ketone
show the reaction diagram
3-butene-1,2-diol
?
show the reaction diagram
-
-
-
-
?
3-butyne-1,2-diol
?
show the reaction diagram
-
-
-
-
?
butane-1,2-diol
?
show the reaction diagram
ethane-1,2-diol
ethanal + H2O
show the reaction diagram
ethylene glycol
acetaldehyde
show the reaction diagram
Acetobacterium sp.
-
-
-
-
-
glycerol
?
show the reaction diagram
glycerol
beta-hydroxypropionaldehyde
show the reaction diagram
glycerol
beta-hydroxypropionaldehyde + H2O
show the reaction diagram
glycolaldehyde hydrate
ethandiol
show the reaction diagram
-
-
-
?
propane-1,2-diol
propanal + H2O
show the reaction diagram
thioglycerol
?
show the reaction diagram
-
-
-
-
?
additional information
?
-
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)-propane-1,2-diol
propanal + H2O
show the reaction diagram
(S)-propane-1,2-diol
propanal + H2O
show the reaction diagram
1,2-propanediol
?
show the reaction diagram
-
-
-
-
-
1,2-propanediol
propanal + H2O
show the reaction diagram
-
-
-
-
?
glycerol
?
show the reaction diagram
propane-1,2-diol
propanal + H2O
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
adenosylcobalamin
cob(II)alamin
-
dependent on
Cobalamin
cobamide
coenzyme B12
additional information
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Cr2+
-
0.10 mol/mol of enzyme
Cu2+
-
0.16 mol/mol of enzyme
Divalent cations
-
-
Fe2+
-
0.09 mol/mol of enzyme
Li+
-
slight activation
Mn2+
-
0.09 mol/mol of enzyme
Zn2+
-
0.12 mol/mol of enzyme
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1,2-Butanediol
1,2-cyclohexanediol
-
-
1,2-ethanediol
-
weak
2,3-Butanediol
2-fluoroethanol
-
weak
3-butene-1,2-diol
-
holodiol dehydratase undergoes rapid and irreversible inactivation, the inactivation cleaves the Co-C bond of adenosylcobalamin irreversibly forming unidentified radicals and cob(II)alamin that resist oxidation even in the presence of oxygen, inactivation mechanism, overview
3-butyne-1,2-diol
-
holodiol dehydratase undergoes rapid and irreversible inactivation, the inactivation cleaves the Co-C bond of adenosylcobalamin irreversibly forming unidentified radicals and cob(II)alamin that resist oxidation even in the presence of oxygen, inactivation mechanism, overview
adenosylcobalamin
adenosylcobinamide 3-(2-methylbenzimidazolyl)propyl phosphate
-
competitive inhibitor with respect to coenzyme B12. Irreversible cleavage of the coenzyme Co-C bond during the inactivation
-
adenosylethylcobalamin
-
strong competitive inhibitor
adenosylmethylcobalamin
-
; catalytic efficiency (turnover number to Km-value) of the holoenzyme with adenosylmethylcobalamin is 0.15% of that for the regular coenzyme adenosylcobalamin, Km: 0.0017 mM
adenosylpentylcobalamin
-
strong competitive inhibitor
Chloroacetaldehyde
-
inactivates
CN-cobalamin
-
-
coenzyme B12
-
inactivation in absence of substrate
cyanocobalamin
ethylene glycol bis -N,N,N,N-tetraacetic acid
-
beta-aminoethyl ether
glycerol
glycoaldehyde
-
inactivates
glycolaldehyde hydrate
-
induces the formation of cob(II)alamin and 5'-deoxyadenosine from adenosylcobalamin at the active site of the enzyme, and the resulting complex is inactive
hydroxylamine
-
-
iodoacetamide
isopropanolamine
-
weak
K+
Acetobacterium sp.
-
16% inhibition at 40 mM
N-ethylmaleimide
-
apoenzyme completely inactivated
o-iodobenzoic acid
-
-
o-phenanthroline
-
-
O2
-
irreversible inactivation
p-chloromercuribenzoate
p-Chloromercuriphenylsulfonic acid
-
complete inhibition at 0.1 mM
p-hydroxymercuribenzoate
-
ternary complex stable, apoenzyme unstable
Propane-1,2-diol
Rb+
Acetobacterium sp.
-
35% inhibition at 40 mM
styrene glycol
-
competitive inhibitor, Ki: 50.2 mM
sulfhydryl compounds
thioglycerol
-
holodiol dehydratase undergoes rapid and irreversible inactivation, the inactivation cleaves the Co-C bond of adenosylcobalamin irreversibly forming unidentified radicals and cob(II)alamin that resist oxidation even in the presence of oxygen, inactivation mechanism, overview
additional information
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
diol dehydratase-reactivating factor
-
dithiothreitol
-
activates, 900% stimulation at 1 mM
additional information
-
ADP and ATP analogues are not able to substitute ATP significantly
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.47 - 3.9
(R)-Propane-1,2-diol
0.11 - 2.6
(S)-Propane-1,2-diol
2.5
1,2-Butanediol
-
pH 8.0, 37C
0.56 - 5.5
1,2-ethanediol
0.04 - 10
1,2-propanediol
0.64
2,3-Butanediol
-
-
0.00082 - 0.0027
adenosylcobinamide 3-benzimidazolylpropyl phosphate
0.00099
adenosylcobinamide 3-imidazolylpropyl phosphate
-
-
0.00029
adenosylcobinamide 3-pyridylpropyl phosphate
-
-
0.26 - 0.9
Cobalamin
0.00096
cobeta-adenosyl-coalpha-benzimidazolylcobamide
-
-
0.00104
cobeta-adenosyl-coalpha-imidazolylcobamide
-
-
0.0008 - 0.008
coenzyme B12
10.5
ethane-1,2-diol
-
at pH 8.6 and 37C
0.73 - 16
glycerol
0.12 - 1.9
Propan-1,2-diol
0.22 - 1.3
Propane-1,2-diol
0.6
R-1,2-propanediol
-
-
0.3
RS-1,2-propanediol
-
-
0.186
S-1,2-propanediol
-
-
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
7.2 - 7.8
1,2-Butanediol
286
1,2-ethanediol
Klebsiella pneumoniae
-
-
337 - 366
1,2-propanediol
15.1
2,3-Butanediol
Klebsiella pneumoniae
-
-
7.7 - 336
CN-cobalamin
317 - 371
glycerol
4
meso-2,3-butanediol
Klebsiella pneumoniae
-
-
0.03 - 354
Propane-1,2-diol
additional information
additional information
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.97
1,2-Butanediol
-
pH 8.0, 37C
0.03
3-butene-1,2-diol
-
pH 8.0, 37C
0.02
3-butyne-1,2-diol
-
pH 8.0, 37C
0.0027
adenosylcobinamide 3-(2-methylbenzimidazolyl)propyl phosphate
-
-
-
0.0015
adenosylethylcobalamin
-
-
0.0011
adenosylmethylcobalamin
-
-
0.00014 - 0.463
CN-cobalamin
0.0264
cyanocobalamin
-
-
50.2
styrene glycol
-
competitive inhibitor
0.1
thioglycerol
-
pH 8.0, 37C
additional information
additional information
-
kinetic analysis with inhibitory substrate analogues 3-butene-1,2-diol, 3-butyne-1,2-diol or thioglycerol
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.22
-
37C, pH 7.2, crude extract
0.77
-
37C, pH 7.2, purified enzyme
11
-
acitvating kation: K+; activating kation: (NH4)+
95
-
membrane-associated enzyme
106
-
membrane-associated enzyme
additional information
-
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.5 - 9.5
-
-
7.5
-
assay at
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.5 - 10.5
-
less than 10% activity is observed at pH 4.5 and pH 10.5
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25
Acetobacterium sp.
-
enzyme assay at
30
-
enzyme assay at
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
16 - 50
-
the enzyme retains more than 70% of its activity between 30 and 40C but less than 20% of its activity at 16 and 50C
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
additional information
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
Acetobacterium sp.
-
65% of activity
Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
14000
-
F consisits of one polypeptide, S of at least four subunits, x * 60000, x * 23000, x * 15500, x * 14000, Cys, Lys, His, andArg residues essential for catalysis
15500
-
F consisits of one polypeptide, S of at least four subunits, x * 60000, x * 23000, x * 15500, x * 14000, Cys, Lys, His, andArg residues essential for catalysis
19000
-
alpha2beta2gamma2, 2 * 60000, 2 * 30000, 2 * 19000, SDS-PAGE, recombinant enzyme, beta2 is F component, alpha2gamma2 is S component, mutual effects on folding
19173
-
x * 28071, x * 60348, x * 24113, x * 19173, estimated from nucleotide sequences of cloned genes
19800
-
2 * 61100 + 2 * 35000 + 2 * 19800, SDS-PAGE
22000
-
alpha2beta2gamma2, 2 * 63000 + 2 * 28000 + 2 * 22000, SDS-PAGE
23000
-
F consisits of one polypeptide, S of at least four subunits, x * 60000, x * 23000, x * 15500, x * 14000, Cys, Lys, His, andArg residues essential for catalysis
24113
-
x * 28071, x * 60348, x * 24113, x * 19173, estimated from nucleotide sequences of cloned genes
26000
-
1 * 26000, 1 * 200000, components F, S
28000
-
alpha2beta2gamma2, 2 * 63000 + 2 * 28000 + 2 * 22000, SDS-PAGE
28071
-
x * 28071, x * 60348, x * 24113, x * 19173, estimated from nucleotide sequences of cloned genes
30000
-
alpha2beta2gamma2, 2 * 60000, 2 * 30000, 2 * 19000, SDS-PAGE, recombinant enzyme, beta2 is F component, alpha2gamma2 is S component, mutual effects on folding
35000
-
2 * 61100 + 2 * 35000 + 2 * 19800, SDS-PAGE
60348
-
x * 28071, x * 60348, x * 24113, x * 19173, estimated from nucleotide sequences of cloned genes
61100
-
2 * 61100 + 2 * 35000 + 2 * 19800, SDS-PAGE
63000
-
alpha2beta2gamma2, 2 * 63000 + 2 * 28000 + 2 * 22000, SDS-PAGE
180000
-
gel filtration
200000
-
1 * 26000, 1 * 200000, components F, S
207000
210000
-
gel filtration
220000 - 240000
-
gel filtration, sedimentation equilibrium of cell-free extracts
220000
-
gel filtration, membrane-associated recombinant enzyme
230000
250000
-
gel filtration of membrane extracts
additional information
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
heptamer
-
2 * 60000, 1 * 51000, 2 * 29000, 2 * 15000, SDS-PAGE, subunit stoichiometry confirmed by N-terminal amino acid analysis
heterohexamer
hexamer
oligomer
tetramer
-
1 * 60000, 1 * 51000, 1 * 29000, 1 * 15000, SDS-PAGE
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
as complexes with coenzyme analogs in the substrate-bound and substrate-free forms
-
complexed with cyanocobalamin and glycerol, sandwich-drop vapor diffusion method, using 20 mM Tris/HCl buffer (pH 8.0) containing 14%-18% (w/v) poly(ethylene glycol) 6000, 0.23-0.25 M ammonium sulfate and 0.2% lauryl dimethylamine oxide
sandwich-drop vapor diffusion method, 4C
-
cyanocobalamin-enzyme complexes, X-ray studies
-
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
40
-
apoenzyme labile above
60
-
50% loss of activity, 30 min
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
10-20% glycerol stabilizes component F at 0C
-
calcium-deprived apoenzyme is unstable when incubated at 37C in the absence of both Ca2+ and substrate
-
limited proteolysis of the enzyme with trypsin converts the enzyme into a highly soluble form without loss of activity
-
sensitive to most solubilization procedures, dithiothreitol stabilizes
-
ternary complex photostable, coenzyme alone photolabile
-
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
50% loss of activity after 4 h under air
Acetobacterium sp.
-
5633
apoenzyme-coenzyme-substrate-analog complex relatively stable to O2 compared with holoenzyme, analogues: 1,2-butanediol, styrene glycol, and others to a lesser extent
-
5612
D- and DL-2,3-Butanediols protect holoenzyme from O2 inactivation
-
5619
extremely O2 sensitive
-
5628
O2 causes irreversible inactivation
-
696252
oxygen lability only if components F and S are associated
-
5613
total inactivation after aerobic incubation, substrate and analogues protect
-
5623
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4C, phosphate buffer, pH 7.0, at least 24 h
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ammonium sulfate precipitation and gel filtration
-
chromatography on DEAE-cellulose
-
DEAE-cellulose column chromatography
membrane-associated enzyme, higher yield than from cell-free extracts, 60000 subunit
-
native enzyme by ammonium sulfate fractionation and gel filtration
-
native enzyme by repeated immunoprecipitation on protein A-Sepharose beads, proteins fused to the N-terminus of PduD are encapsulated within the shell of the Pdu MCP
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
beta-subunit DNA and amino acid sequence determination and analysis, sequence comparison, and expression of wild-type and chimeric mutants, in Escherichia coli strain BL21(DE3), distribution of the chimeric mutants in recombinant bacterial cells, overview
catabolite-responsive element sequence immediately upstream of the pdu operon encoding diol dehydratase and metabolosome structural genes
-
expressed in Escherichia coli
-
expressed in Escherichia coli JM109 cells
expressed in Escherichia coli Rosetta (DE3) cells
-
expression in E.coli
-
expression in Escherichia coli
expression in Escherichia coli of the three genes encoding the subunits of the enzyme. Recombinant protein cannot form an active complex
-
expression in Escherichia coli strain JM109
-
expression of fusion protein PduD1-18-eGFP from a plasmid in a pduCDE deletion mutant
-
expression of wild-type and mutant enzymes in Escherichia coli
-
gene pduC, DNA and amino acid sequence determination and analysis, genetic organization in the pdu operon, overview, and recombinant enzyme expression in Escherichia coli strain JM109; gene pduD, DNA and amino acid sequence determination and analysis, genetic organization in the pdu operon, overview, and recombinant enzyme expression in Escherichia coli strain JM109; gene pduE, DNA and amino acid sequence determination and analysis, genetic organization in the pdu operon, overview, and recombinant enzyme expression in Escherichia coli strain JM109
N-terminal truncations (20 or 16 amino acid residues) of either or both of the beta and gamma subunits are expressed on a high level in Escherichia coli. All the mutant enzymes obtained are expressed in a soluble, active form. The mutant enzyme with the N-terminal truncations of both beta and gamma subunits are indistinguishable in catalytic properties from recombinant wild-type enzyme of the enzyme purified from Klebsiella oxytoca in a soluble form
-
overexpression in Escherichia coli strain JM109
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D335A
-
does not form (alpha-beta-gamma)complex; inactive mutant
D335N
-
inactive mutant
E170A
-
inactive mutant
E170H
-
does not form (alpha-beta-gamma)complex
E221A
-
does not form (alpha-beta-gamma)complex
H143A
-
only very little activity
Halpha143A
-
site-directed mutagenesis, the mutant shows residual activity compared to the wild-type enzyme
Halpha143E
-
site-directed mutagenesis, the mutant is inactive and does not form (alphabeta)2 complexes
Halpha143K
-
site-directed mutagenesis, the mutant is inactive and does not form (alphabeta)2 complexes
Halpha143L
-
site-directed mutagenesis, the mutant shows residual activity compared to the wild-type enzyme
Halpha143Q
-
site-directed mutagenesis, the mutant shows residual activity compared to the wild-type enzyme, irreversible inactivation by O2 in the absence of substrate at a much lower rate than the wild type, preference of the Halpha143Q mutant for (R)- and (S)-1,2-propanediols, kinetic parameters for each enantiomer, overview
Kbeta135A
-
site-directed mutagenesis, the mutant shows 42% reduced activity compared to the wild-type enzyme, the mutant is less sensitive to inhibitor CN-cobalamin
Kbeta135E
-
site-directed mutagenesis, the mutant shows 98% reduced activity compared to the wild-type enzyme
Kbeta135Q
-
site-directed mutagenesis, the mutant shows 27% reduced activity compared to the wild-type enzyme, the mutant is less sensitive to inhibitor CN-cobalamin
Kbeta135R
-
site-directed mutagenesis, the mutant shows 24% reduced activity compared to the wild-type enzyme
Q141A
-
partial activity
Q296A
-
increased Km for substrate(1,2-propanediol) by a factor of 250
Q336A
the mutant shows decreased activity (21%) compared to the wild type enzyme
S301A
the mutant shows decreased activity (76%) compared to the wild type enzyme
S301A/Q336A
the mutant shows lowest activity (9.8%) compared to the wild type enzyme
S362A
-
partial activity
Salpha224A
-
site-directed mutagenesis, the mutant shows 81% reduced activity compared to the wild-type enzyme, mechanism-based complete inactivation of the Salpha224A holoenzyme during catalysis by propan-1,2-diol leading to accumulation of cobalamin, mechanism, overview
Salpha224N
-
site-directed mutagenesis, the mutant shows 95% reduced activity compared to the wild-type enzyme
Q336A
-
the mutant shows decreased activity (21%) compared to the wild type enzyme
-
S301A
-
the mutant shows decreased activity (76%) compared to the wild type enzyme
-
S301A/Q336A
-
the mutant shows lowest activity (9.8%) compared to the wild type enzyme
-
additional information
Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
inactivated holoenzymes undergo reactivation by diol dehydratase-reactivating factor in the presence of ATP, Mg2+ and adenosylcobalamin
-
reconstitution of calcium-containing apoenzyme from calcium-deprived apoenzyme and Ca2+, overview
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
degradation
Acetobacterium sp.
-
possible use in anaerobic polyethylene glycol degradation
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