Information on EC 3.1.1.75 - poly(3-hydroxybutyrate) depolymerase

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

EC NUMBER
COMMENTARY hide
3.1.1.75
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RECOMMENDED NAME
GeneOntology No.
poly(3-hydroxybutyrate) depolymerase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
[(R)-3-hydroxybutanoate]n + H2O = [(R)-3-hydroxybutanoate]n-x + [(R)-3-hydroxybutanoate]x; x: 1-5
show the reaction diagram
denatured, extracellular granules either have no surface layer or a damaged surface layer and are partially crystalline; Reaction also occurs with esters of other short-chain-length, C1-C5, hydroxyalkanoic acids, HA. There are two types of polymers: native, intracellular granules are amorphous and have an intact surface layer; x=1-5
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
carboxylic ester hydrolysis
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Butanoate metabolism
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SYSTEMATIC NAME
IUBMB Comments
poly[(R)-3-hydroxybutanoate] hydrolase
Reaction also occurs with esters of other short-chain-length (C1-C5) hydroxyalkanoic acids (HA). There are two types of polymers: native (intracellular) granules are amorphous and have an intact surface layer; denatured (extracellular) granules either have no surface layer or a damaged surface layer and are partially crystalline.
CAS REGISTRY NUMBER
COMMENTARY hide
9014-11-3
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
strains W1 and W5, degradation of BIOPOL only, strain W6, degradation of poly[(R)-3-hydroxybutanoate]n, BIOPOL and other polyhydroxyalkanoic acids
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Manually annotated by BRENDA team
a thermotolerant fungal soil isolate
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
N-18-25-9
SwissProt
Manually annotated by BRENDA team
subsp. israelensis ATCC 35646
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
Cupriavidus necator H16 / ATCC 23440 / NCIB 10442 / S-10-1
DS9701-09a
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Manually annotated by BRENDA team
DS9701-D2
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Manually annotated by BRENDA team
DS9713a-01
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Manually annotated by BRENDA team
strains W2, W3 and W4, degradation of BIOPOL
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Manually annotated by BRENDA team
GK13
UniProt
Manually annotated by BRENDA team
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SwissProt
Manually annotated by BRENDA team
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SwissProt
Manually annotated by BRENDA team
sp. nov., gene fkbU
UniProt
Manually annotated by BRENDA team
sp. nov., gene fkbU
UniProt
Manually annotated by BRENDA team
isolated from soil, gene phaZSomSO2
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Manually annotated by BRENDA team
isolated from soil, gene phaZSomSO2
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Manually annotated by BRENDA team
isolated from sludge, gene phaZSroSL3
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Manually annotated by BRENDA team
isolated from sludge, gene phaZSroSL3
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Manually annotated by BRENDA team
soil isolate
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Manually annotated by BRENDA team
fragment
UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(3-hydroxy-phenylalkanoic acid)n + H2O
(3-hydroxy-phenylalkanoic acid)n-x + 3-hydroxy-phenylalkanoic acid
show the reaction diagram
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novel natural aromatic plastic with an even number of carbon atoms
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?
(R)-3-[[(3'R)-3'-hydroxybutanoyl]oxy]butanoic acid + H2O
(R)-3-hydroxybutanoic acid
show the reaction diagram
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-
?
4-nitrophenyl acetate + H2O
4-nitrophenol + acetate
show the reaction diagram
4-nitrophenyl butanoate + H2O
4-nitrophenol + butanoate
show the reaction diagram
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wild type lipase activity is rather low
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?
4-nitrophenyl butyrate + H2O
4-nitrophenol + butyrate
show the reaction diagram
4-nitrophenyl hexanoate + H2O
4-nitrophenol + hexanoate
show the reaction diagram
4-nitrophenyl octanoate + H2O
4-nitrophenol + octanoate
show the reaction diagram
4-nitrophenyl pentanoate + H2O
4-nitrophenol + pentanoate
show the reaction diagram
4-nitrophenyl propionate + H2O
4-nitrophenol + propionate
show the reaction diagram
4-nitrophenyl valerate + H2O
4-nitrophenol + valerate
show the reaction diagram
methyl (3R)-3-[[(3'R)-3'-hydroxybutanoyl]oxy]butanoate + H2O
(R)-3-hydroxybutanoic acid + methyl-(R)-3-hydroxybutanoate + (R)-3-[[(3'R)-3'-hydroxybutanoyl]oxy]butanoic acid
show the reaction diagram
methyl (3R)-3-[[(3'R)-3'-methoxybutanoyl]oxy]butanoate + H2O
(R)-3-methoxybutanoic acid + methyl-(R)-3-hydroxybutanoate + methyl-[[(R)-3-methoxybutanoyl]oxy]butanoate
show the reaction diagram
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?
methyl (3R)-3-[[(3'R)-3'-[[(3''R)-3''-hydroxybutanoyl]oxy]butanoyl]oxy]butanoate + H2O
(R)-3-hydroxybutanoic acid + methyl-(R)-3-hydroxybutanoate + (R)-3-[[(3'R)-3'-hydroxybutanoyl]oxy]butanoic acid + methyl (3R)-3-[[(3'R)-3'-hydroxybutanoyl]oxy]butanoate + (R)-3-[[(3'R)-3'-[[(3''R)-3''-hydroxybutanoyl]oxy]butanoyl]oxy]butanoic acid
show the reaction diagram
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?
methyl (3R)-3-[[(3'R)-3'-[[(3''R)-3''-[[(3'''R)-3'''-hydroxybutanoyl]oxy]butanoyl]oxy]butanoyl]oxy]butanoate + H2O
(R)-3-hydroxybutanoic acid + methyl-(R)-3-hydroxybutanoate + (R)-3-[[(3'R)-3'-hydroxybutanoyl]oxy]butanoic acid + methyl (3R)-3-[[(3'R)-3'-hydroxybutanoyl]oxy]butanoate + (R)-3-[[(3'R)-3'-[[(3''R)-3''-hydroxybutanoyl]oxy]butanoyl]oxy]butanoic acid + methyl (3R)-3-[[(3'R)-3'-[[(3''R)-3''-[[(3'''R)-3'''-hydroxybutanoyl]oxy]butanoyl]oxy]butanoyl]oxy]butanoate
show the reaction diagram
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?
p-nitrophenyl acetate + H2O
4-nitrophenol + acetate
show the reaction diagram
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?
p-nitrophenyl acetate + H2O
p-nitrophenol + acetate
show the reaction diagram
p-nitrophenyl butyrate + H2O
4-nitrophenol + butyrate
show the reaction diagram
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?
p-nitrophenyl butyrate + H2O
p-nitrophenol + butyrate
show the reaction diagram
p-nitrophenyl laurate + H2O
p-nitrophenol + laurate
show the reaction diagram
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?
p-nitrophenyl myristate + H2O
4-nitrophenol + myristate
show the reaction diagram
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?
p-nitrophenyl palmitate + H2O
4-nitrophenol + palmitate
show the reaction diagram
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?
p-nitrophenyl valerate + H2O
4-nitrophenol + pentanoate
show the reaction diagram
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?
p-nitrophenyl-decanoate + H2O
p-nitrophenol + decanoate
show the reaction diagram
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wild type lipase activity is rather low
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?
p-nitrophenyl-palmitate + H2O
p-nitrophenol + palmitate
show the reaction diagram
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wild type lipase activity is rather low
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?
p-nitrophenyldecanoate + H2O
p-nitrophenol + decanoate
show the reaction diagram
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?
PEG containing poly(3-hydroxybutyrate-co-3-hydroxyvalerate) + H2O
?
show the reaction diagram
poly (3-hydroxybutyrate) + H2O
?
show the reaction diagram
poly((R)-3-hydroxybutyrate) + H2O
?
show the reaction diagram
poly(3-hydroxybutyrate) + H2O
3-hydroxybutyrate + 3-hydroxybutyryl-3-hydroxybutyrate
show the reaction diagram
poly(3-hydroxybutyrate) + H2O
?
show the reaction diagram
poly(3-hydroxybutyrate-co-3-hydroxyvalerate) + H2O
?
show the reaction diagram
poly(3-hydroxybutyrate-co-3-hydroxyvalerate)n + H2O
poly(3-hydroxybutyrate-co-3-hydroxyvalerate)n-x + poly(3-hydroxybutyrate-co-3-hydroxyvalerate)
show the reaction diagram
poly(3-hydroxybutyrate-co-4-hydroxybutyrate) + H2O
?
show the reaction diagram
poly(3-hydroxybutyrate-co-[12%]3-hydroxyvalerate)n + H2O
poly(3-hydroxybutyrate-co-[12%]3-hydroxyvalerate)n-x + poly(3-hydroxybutyrate-co-[12%]3-hydroxyvalerate)n
show the reaction diagram
poly(3-hydroxybutyrate-co-[14%]3-hydroxyvalerate)n + H2O
poly(3-hydroxybutyrate-co-[14%]3-hydroxyvalerate)n-x + poly(3-hydroxybutyrate-co-[14%]3-hydroxyvalerate)
show the reaction diagram
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?
poly(3-hydroxybutyrate-co-[22%]3-hydroxyvalerate)n + H2O
poly(3-hydroxybutyrate-co-[22%]3-hydroxyvalerate)n-x + poly(3-hydroxybutyrate-co-[22%]3-hydroxyvalerate)
show the reaction diagram
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best carbon source for enzyme synthesis in strain W6
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?
poly(3-hydroxybutyrate-co-[43%]3-hydroxyvalerate)n + H2O
poly(3-hydroxybutyrate-co-[43%]3-hydroxyvalerate)n-x + poly(3-hydroxybutyrate-co-[43%]3-hydroxyvalerate)
show the reaction diagram
poly(3-hydroxybutyrate-co-[9%]3-hydroxyvalerate)n + H2O
poly(3-hydroxybutyrate-co-[9%]3-hydroxyvalerate)n-x + poly(3-hydroxybutyrate-co-[9%]3-hydroxyvalerate)n
show the reaction diagram
poly(3-hydroxybutyric acid) + H2O
?
show the reaction diagram
poly(3-hydroxypropionate) + H2O
?
show the reaction diagram
poly(3-hydroxypropionate)n + H2O
poly(3-hydroxypropionate)n-x + poly(3-propionate)
show the reaction diagram
poly(3-hydroxyvalerate)n + H2O
poly(3-hydroxyvalerate)n-x + poly(3-hydroxyvalerate)
show the reaction diagram
poly(4-hydroxybutyrate)n + H2O
poly(4-hydroxybutyrate)n-x + poly(4-hydroxybutyrate)
show the reaction diagram
poly(beta-propiolactone) + H2O
?
show the reaction diagram
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?
poly(ethylene adipate)n + H2O
poly(ethylene adipate)n-x + poly(ethylene adipate)
show the reaction diagram
poly(ethylene succinate)n + H2O
poly(ethylene succinate)n-x + poly(ethylene succinate)
show the reaction diagram
poly(L-lactic acid) + H2O
?
show the reaction diagram
poly(lactic acid) + H2O
?
show the reaction diagram
poly(propiolactone)n + H2O
poly(propiolactone)n-x + poly(propiolactone)n
show the reaction diagram
poly(R)-3-hydroxybutyrate + H2O
?
show the reaction diagram
poly-3-hydroxybutyrate + H2O
?
show the reaction diagram
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?
poly-[(R)-3-hydroxybutyrate] + H2O
?
show the reaction diagram
degradation of poly-[(R)-3-hydroxybutyrate] (PHB) films
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?
polyhydroxyalkanoate + H2O
?
show the reaction diagram
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?
polyhydroxybutyrate + H2O
3-hydroxybutyrate + ?
show the reaction diagram
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?
poly[(R)-3-hydroxybutanoate]n + H2O
poly[(R)-3-hydroxybutanoate]n-x + poly[(R)-3-hydroxybutanoate]x
show the reaction diagram
[(R)-3-hydroxybutanoate]n + H2O
[(R)-3-hydroxybutanoate]n-x + poly[(R)-3-hydroxybutanoate]
show the reaction diagram
[(R)-3-hydroxybutanoate]n + H2O
[(R)-3-hydroxybutanoate]n-x + [(R)-3-hydroxybutanoate]x
show the reaction diagram
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
(3-hydroxy-phenylalkanoic acid)n + H2O
(3-hydroxy-phenylalkanoic acid)n-x + 3-hydroxy-phenylalkanoic acid
show the reaction diagram
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novel natural aromatic plastic with an even number of carbon atoms
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?
poly((R)-3-hydroxybutyrate) + H2O
?
show the reaction diagram
P12625
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?
poly(3-hydroxybutyrate) + H2O
?
show the reaction diagram
poly(3-hydroxybutyrate-co-3-hydroxyvalerate) + H2O
?
show the reaction diagram
poly(3-hydroxypropionate) + H2O
?
show the reaction diagram
poly[(R)-3-hydroxybutanoate]n + H2O
poly[(R)-3-hydroxybutanoate]n-x + poly[(R)-3-hydroxybutanoate]x
show the reaction diagram
[(R)-3-hydroxybutanoate]n + H2O
[(R)-3-hydroxybutanoate]n-x + [(R)-3-hydroxybutanoate]x
show the reaction diagram
additional information
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
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10 mM, 1.29fold stimulation
Cu2+
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10 mM, 1.65fold stimulation
Na2SO4
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200 mM required for maximal stimulation
NaCl
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stimulation due to NaCl in seawater
SrCl2
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10 mM required for maximal stimulation
Zn2+
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10 mM, 1.19fold stimulation
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1,2-epoxy-3-(p-nitrophenoxy)propane
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complete inactivation at 100 mM, slow inactivation process
2-Hydroxy-5-nitrobenzyl bromide
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complete inactivation
2-mercaptoethanol
2-propanol
3-hydroxybutyrate
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cyclic trimers, reversible inhibition
acetone
82% inhibition at 10% (vol/vol)
acetonitrile
70% inhibition at 10% (vol/vol)
Aprotinin
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10 mM, 26% inhibition
Ba(CH3COO)2
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complete inhibition at 10 mM
Ba2+
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5 mM, 32% loss of activity
CaCl2
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at 10 mM 39% inhibition
citrate
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depressed activity
diazo-DL-norleucine methyl ester
diethyldicarbonate
40% inhibition at 5 mM, 90% at 20 mM
diethylene glycol
71% inhibition at 10% (vol/vol)
diisopropyl fluorophosphate
diisopropylfluorophosphate
dithioerythritol
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complete inhibition of P(3HV) depolymerase at 4 mM, reversible by dithionitrobenzene
dithiothreitol
DMF
84% inhibition at 10% (vol/vol)
DMSO
85% inhibition at 10% (vol/vol)
ethanol
ethyldicarbonate/glycinamide
33% inhibition at 5 mM
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ethylene glycol
28% inhibition at 10% (vol/vol)
Fe3+
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5 mM, 38% loss of activity
KCl
100 mM, 75% inhibition
mercaptoethanol
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0.5%, 47% loss of activity
Mercuric chloride
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complete inhibition at 10 mM
methanol
91% inhibition at 10% (vol/vol)
MgCl2
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slight inhibition 1 mM, 57% inhibition at 10 mM
N-bromosuccinimide
NaN3
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1 mM: 86%, 10 mM: 84% activity, compared to no addition
Ni2+
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10 mM, 28% inhibition
p-(chloromercuri)benzoic acid
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no inhibition below 1 mM
p-chloromercuribenzoic acid
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complete inhibition at 0.1 mM
Pb2+
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marked inhibition at 0.1 mM
phenylmethanesulfonyl fluoride
Phenylmethylsulfonylfluoride
10% inhibition at 1 mM and 70% inhibition at 10 mM
Plysurf A210G
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100 mg/l, 48% inhibition
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tetrahydrofuran
51% inhibition at 10% (vol/vol)
triethylene glycol
73% inhibition at 10% (vol/vol)
Triton X-100
Tween 20
Tween 80
tyrosine
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depressed activity
additional information
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
acetone
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10% (v/v): 102% activity compared to no addition
ApdA
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without only reduced hydrolysis varying between 5 to 20% of the rate with activation
ethanol
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10% (v/v): 100% activity compared to no addition
methanol
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10% (v/v): 137% activity compared to no addition
methyl-beta-cyclodextrin
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nitrogen
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increase in phaZ transcription can be detected when the cells are cultured under polyhydroxyalkanoate production conditions in the presence of octanoate and a limited content of nitrogen
Octanoate
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increase in phaZ transcription can be detected when the cells are cultured under polyhydroxyalkanoate production conditions in the presence of octanoate and a limited content of nitrogen
seawater
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highest activity by use of 30-100% seawater
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Triton X-100
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at 0.001% (w/v) 120% activity
Trypsin
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without only reduced hydrolysis varying between 5 to 20% of the rate with activation
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.24 - 2.43
4-nitrophenyl acetate
0.16 - 1.25
4-nitrophenyl butyrate
0.05 - 0.45
4-nitrophenyl hexanoate
0.05 - 0.89
4-nitrophenyl pentanoate
0.27 - 2.7
4-nitrophenyl propionate
0.84
cyclic [(R)-3-hydroxybutanoate]3
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cyclic 3-hydroxybutyrate oligomer
0.34 - 4.6
cyclic [(R)-3-hydroxybutanoate]5
0.79
p-nitrophenyl butyrate
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0.67
poly(3-hydroxybutyrate-co-3-hydroxyvalerate)
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pH 8.0, 30C
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4.1 - 9.7
[(R)-3-hydroxybutanoate]3
0.67 - 3.1
[(R)-3-hydroxybutanoate]4
0.56 - 1.3
[(R)-3-hydroxybutanoate]5
0.36
[(R)-3-hydroxybutanoate]6
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cyclic 3-hydroxybutyrate oligomer
additional information
additional information
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
56.3
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purification step: affinity binding to polyhydroxybutyrate
74
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74000 U/mg, 1 U is defined as the release of 1 nmol p-nitrophenol from p-nitrophenyl phosphate per minute
12030
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purified native enzyme, substrate poly(3-hydroxybutyrate-co-3-hydroxyvalerate), pH 8.0, 30C
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 8
substrate p-nitrophenyl butyrate with optimal activity at 50-55C and pH 7-8
7.9
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isoform E2
8.1
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isoform E1
8.5 - 9
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in Tris-HCl buffer