BRENDA - Enzyme Database show
show all sequences of 3.1.1.41

Functional and structural characterization of a thermostable acetyl esterase from Thermotoga maritima

Levisson, M.; Han, G.W.; Deller, M.C.; Xu, Q.; Biely, P.; Hendriks, S.; Ten Eyck, L.F.; Flensburg, C.; Roversi, P.; Miller, M.D.; McMullan, D.; von Delft, F.; Kreusch, A.; Deacon, A.M.; van der Oost, J.; Lesley, S.A.; Elsliger, M.A.; Kengen, S.W.; Wilson, I.A.; Proteins 80, 1545-1559 (2012)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
gene TM0077, expression of N-terminally His-tagged wild-type enzyme in Escherichia coli and selenomethionine-labeled enzyme in Escherichia coli methionine auxotrophic strain DL41
Thermotoga maritima
Crystallization (Commentary)
Crystallization
Organism
purified recombinant selenomethionine-substituted and wild-type enzyme in complex with covalently bound phenylmethylsulfonyl fluoride and paraoxon, hanging drop vapour diffusion method, for selenomethionine-substituted enzyme: mixing of 500 nl of 15 mg/ml protein in 20 mM Tris pH 7.9, 150 mM NaCl, 0.25 mM TCEP, in presence or absence of inhibitors, with 500 nl of reservoir solution containing 20% w/v PEG-3000, 0.1 M HEPES pH 7.5, 0.2 M NaCl, and equilibration against 0.25 ml of reservoir solution, for wild-type enzyme: mixing of 100 nl of 22.8 mg/ml protein in 20 mM Tris pH 7.9, 150 mM NaCl, 0.25 mM TCEP, in presence or absence of inhibitors, with 100 nl of reservoir solution containing 0.2 M calcium acetate hydrate, 20% w/v PEG 3350, pH 7.3, and equilibration against 0.06 ml of reservoir solution, 20°C, X-ray diffraction structure determination and analysis at 2.4 A and 2.1 A resolution, respectively, molecular replacement, structure modeling
Thermotoga maritima
Inhibitors
Inhibitors
Commentary
Organism
Structure
paraoxon
competitive irreversible inhibitors of esterases. Inhibition proceeds by the formation of a reversible Michaelis complex, followed by an irreversible step, the inhibitor binds covalently to the catalytic serine (Ser188), upon binding of inhibitor, the catalytic serine adopts an altered conformation
Thermotoga maritima
phenylmethylsulfonyl fluoride
competitive irreversible inhibitors of esterases. Inhibition proceeds by the formation of a reversible Michaelis complex, followed by an irreversible step, the inhibitor binds covalently to the catalytic serine (Ser188), upon binding of inhibitor, the catalytic serine adopts an altered conformation. In the PMSF-bound structure, the phenyl ring of the inhibitor is located in the small active site groove surrounded by hydrophobic residues Tyr92, Trp124, Pro228, Ile276, and His303. The sulfonyl group of PMSF makes hydrogen bonds with the backbone amides of Tyr92 and Gln189
Thermotoga maritima
Localization
Localization
Commentary
Organism
GeneOntology No.
Textmining
cytosol
the enzyme has no predicted signal sequence
Thermotoga maritima
5829
-
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Ca2+
not required for activity, one calcium ion is located at the N-terminal region of helix alphaA-1, and is coordinated by the backbone carbonyl of Lys22 and the Glu26 carboxylate, Asp25 carboxylate contributes to the calcium binding via one of the coordinating water molecules. Another calcium ion is bound in a crystal packing interface between chain A and chain C' of a crystallographic symmetry-related hexamer and is coordinated by the carboxylates of GluA45 and AspA58 from one chain and the carboxylate from Glu C'45 (bidentate coordination) of the symmetry-related chain with three water molecules completing a capped-octahedral coordination sphere
Thermotoga maritima
additional information
no significant stimulation or reduction of enzyme activity in the presence of divalent metal ions or EDTA. In the paraoxon-bound structure, the diethylphosphate moiety is stabilized by hydrogen-bonding interactions with the oxyanion hole. One of the two ethyl arms of bound paraoxon points toward the larger pocket in the protein, while the other follows the groove of the small pocket. The two ethyl arms are stabilized by packing against Tyr92, Trp124, Pro228, Ile276, and His303
Thermotoga maritima
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
cephalosporin C + H2O
Thermotoga maritima
-
deacetylcephalosporin C + acetate
-
-
?
additional information
Thermotoga maritima
the enzyme is active on a variety of acetylated compounds, including cephalosporin C, its esterase activity is confined to short-chain acyl esters of C2-C3 chain length
?
-
-
-
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Thermotoga maritima
Q9WXT2
gene TM0077
-
Purification (Commentary)
Commentary
Organism
recombinant N-terminally His-tagged wild-type and selenomethionine-labeled enzymes from Escherichia coli by nickel affinity chromatography, anion exchange chromatography, and gel filtration
Thermotoga maritima
Reaction
Reaction
Commentary
Organism
cephalosporin C + H2O = deacetylcephalosporin C + acetate
a catalytic mechanism in which this Ser hydroxyl rotation prevents reversal of the reaction and allows access of a water molecule for completion of the reaction
Thermotoga maritima
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
4-nitrophenyl beta-D-xylopyranoside + H2O
4-nitrophenyl-beta-D-xylopyranoside monoacetates as substrates in a beta-xylosidase-coupled assay, TM0077 hydrolyzes acetate at positions 2, 3 and 4 with equal efficiencyas substrates in a ?-xylosidase-coupled assay
730907
Thermotoga maritima
4-nitrophenol + D-xylopyranose
-
-
-
?
cephalosporin C + H2O
-
730907
Thermotoga maritima
deacetylcephalosporin C + acetate
-
-
-
?
additional information
the enzyme is active on a variety of acetylated compounds, including cephalosporin C, its esterase activity is confined to short-chain acyl esters of C2-C3 chain length
730907
Thermotoga maritima
?
-
-
-
-
additional information
the enzyme is an acetyl esterase and not an acetyl xylan esterase, that shows no activity with xylan or acetylated xylan
730907
Thermotoga maritima
?
-
-
-
-
Subunits
Subunits
Commentary
Organism
hexamer
the relevant physiological oligomeric state of the enzyme is a hexamer, in the crystal structure, two hexamers in the asymmetric unit, that are related by a non-crystallographic two-fold axis, contain each a dimer of trimers with a back-to-back arrangement, enzyme quaternary structure, overview. Two main interfaces play an essential role in complex formation, the first interface between subunit A and B, and he second interface between A and F. The entrance to the internal cavity is blocked by three phenylalanine residues (Phe4), one for each of three monomers that compose half of the hexamer
Thermotoga maritima
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
100
-
-
Thermotoga maritima
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.5
-
-
Thermotoga maritima
Ki Value [mM]
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
additional information
-
additional information
inhibition kinetics
Thermotoga maritima
Cloned(Commentary) (protein specific)
Commentary
Organism
gene TM0077, expression of N-terminally His-tagged wild-type enzyme in Escherichia coli and selenomethionine-labeled enzyme in Escherichia coli methionine auxotrophic strain DL41
Thermotoga maritima
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified recombinant selenomethionine-substituted and wild-type enzyme in complex with covalently bound phenylmethylsulfonyl fluoride and paraoxon, hanging drop vapour diffusion method, for selenomethionine-substituted enzyme: mixing of 500 nl of 15 mg/ml protein in 20 mM Tris pH 7.9, 150 mM NaCl, 0.25 mM TCEP, in presence or absence of inhibitors, with 500 nl of reservoir solution containing 20% w/v PEG-3000, 0.1 M HEPES pH 7.5, 0.2 M NaCl, and equilibration against 0.25 ml of reservoir solution, for wild-type enzyme: mixing of 100 nl of 22.8 mg/ml protein in 20 mM Tris pH 7.9, 150 mM NaCl, 0.25 mM TCEP, in presence or absence of inhibitors, with 100 nl of reservoir solution containing 0.2 M calcium acetate hydrate, 20% w/v PEG 3350, pH 7.3, and equilibration against 0.06 ml of reservoir solution, 20°C, X-ray diffraction structure determination and analysis at 2.4 A and 2.1 A resolution, respectively, molecular replacement, structure modeling
Thermotoga maritima
Inhibitors (protein specific)
Inhibitors
Commentary
Organism
Structure
paraoxon
competitive irreversible inhibitors of esterases. Inhibition proceeds by the formation of a reversible Michaelis complex, followed by an irreversible step, the inhibitor binds covalently to the catalytic serine (Ser188), upon binding of inhibitor, the catalytic serine adopts an altered conformation
Thermotoga maritima
phenylmethylsulfonyl fluoride
competitive irreversible inhibitors of esterases. Inhibition proceeds by the formation of a reversible Michaelis complex, followed by an irreversible step, the inhibitor binds covalently to the catalytic serine (Ser188), upon binding of inhibitor, the catalytic serine adopts an altered conformation. In the PMSF-bound structure, the phenyl ring of the inhibitor is located in the small active site groove surrounded by hydrophobic residues Tyr92, Trp124, Pro228, Ile276, and His303. The sulfonyl group of PMSF makes hydrogen bonds with the backbone amides of Tyr92 and Gln189
Thermotoga maritima
Ki Value [mM] (protein specific)
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
additional information
-
additional information
inhibition kinetics
Thermotoga maritima
Localization (protein specific)
Localization
Commentary
Organism
GeneOntology No.
Textmining
cytosol
the enzyme has no predicted signal sequence
Thermotoga maritima
5829
-
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Ca2+
not required for activity, one calcium ion is located at the N-terminal region of helix alphaA-1, and is coordinated by the backbone carbonyl of Lys22 and the Glu26 carboxylate, Asp25 carboxylate contributes to the calcium binding via one of the coordinating water molecules. Another calcium ion is bound in a crystal packing interface between chain A and chain C' of a crystallographic symmetry-related hexamer and is coordinated by the carboxylates of GluA45 and AspA58 from one chain and the carboxylate from Glu C'45 (bidentate coordination) of the symmetry-related chain with three water molecules completing a capped-octahedral coordination sphere
Thermotoga maritima
additional information
no significant stimulation or reduction of enzyme activity in the presence of divalent metal ions or EDTA. In the paraoxon-bound structure, the diethylphosphate moiety is stabilized by hydrogen-bonding interactions with the oxyanion hole. One of the two ethyl arms of bound paraoxon points toward the larger pocket in the protein, while the other follows the groove of the small pocket. The two ethyl arms are stabilized by packing against Tyr92, Trp124, Pro228, Ile276, and His303
Thermotoga maritima
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
cephalosporin C + H2O
Thermotoga maritima
-
deacetylcephalosporin C + acetate
-
-
?
additional information
Thermotoga maritima
the enzyme is active on a variety of acetylated compounds, including cephalosporin C, its esterase activity is confined to short-chain acyl esters of C2-C3 chain length
?
-
-
-
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant N-terminally His-tagged wild-type and selenomethionine-labeled enzymes from Escherichia coli by nickel affinity chromatography, anion exchange chromatography, and gel filtration
Thermotoga maritima
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
4-nitrophenyl beta-D-xylopyranoside + H2O
4-nitrophenyl-beta-D-xylopyranoside monoacetates as substrates in a beta-xylosidase-coupled assay, TM0077 hydrolyzes acetate at positions 2, 3 and 4 with equal efficiencyas substrates in a ?-xylosidase-coupled assay
730907
Thermotoga maritima
4-nitrophenol + D-xylopyranose
-
-
-
?
cephalosporin C + H2O
-
730907
Thermotoga maritima
deacetylcephalosporin C + acetate
-
-
-
?
additional information
the enzyme is active on a variety of acetylated compounds, including cephalosporin C, its esterase activity is confined to short-chain acyl esters of C2-C3 chain length
730907
Thermotoga maritima
?
-
-
-
-
additional information
the enzyme is an acetyl esterase and not an acetyl xylan esterase, that shows no activity with xylan or acetylated xylan
730907
Thermotoga maritima
?
-
-
-
-
Subunits (protein specific)
Subunits
Commentary
Organism
hexamer
the relevant physiological oligomeric state of the enzyme is a hexamer, in the crystal structure, two hexamers in the asymmetric unit, that are related by a non-crystallographic two-fold axis, contain each a dimer of trimers with a back-to-back arrangement, enzyme quaternary structure, overview. Two main interfaces play an essential role in complex formation, the first interface between subunit A and B, and he second interface between A and F. The entrance to the internal cavity is blocked by three phenylalanine residues (Phe4), one for each of three monomers that compose half of the hexamer
Thermotoga maritima
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
100
-
-
Thermotoga maritima
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.5
-
-
Thermotoga maritima
General Information
General Information
Commentary
Organism
evolution
the enzyme is a member of the carbohydrate esterase family 7, CE7 family, showing a classic alpha/beta-hydrolase fold
Thermotoga maritima
additional information
the active site has a classic catalytic triad, consisting of Ser188 as the nucleophile, His303 as the proton acceptor/donor, and Asp274 as the acidic residue stabilizing the histidine. The catalytic serine Ser188 is located within a conserved pentapeptide sequence, Gly-X-Ser-X-Gly (GGSQG), characteristic of esterases and lipases, overview
Thermotoga maritima
General Information (protein specific)
General Information
Commentary
Organism
evolution
the enzyme is a member of the carbohydrate esterase family 7, CE7 family, showing a classic alpha/beta-hydrolase fold
Thermotoga maritima
additional information
the active site has a classic catalytic triad, consisting of Ser188 as the nucleophile, His303 as the proton acceptor/donor, and Asp274 as the acidic residue stabilizing the histidine. The catalytic serine Ser188 is located within a conserved pentapeptide sequence, Gly-X-Ser-X-Gly (GGSQG), characteristic of esterases and lipases, overview
Thermotoga maritima
Other publictions for EC 3.1.1.41
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
749261
Singh
Structural role of a conserve ...
Thermotoga maritima, Thermotoga maritima ATCC 43589, Thermotoga maritima DSM 3109
Proteins
85
694-708
2017
-
-
1
1
2
-
-
18
-
-
2
-
-
6
-
-
1
-
-
-
13
-
23
-
3
-
1
20
1
1
-
-
-
-
-
-
-
1
-
1
2
-
-
-
-
18
-
-
2
-
-
-
-
1
-
-
13
-
23
-
3
-
1
20
1
1
-
-
-
-
-
-
19
19
746975
Singh
Crystal structure of Thermoto ...
Thermotoga maritima, Thermotoga maritima ATCC 43589, Thermotoga maritima DSM 3109
Biochem. Biophys. Res. Commun.
476
63-68
2016
-
-
-
1
-
-
-
-
-
-
-
-
-
8
-
-
1
-
-
-
-
-
16
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
16
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
749834
Ma
-
High-level expression of Ceph ...
Bacillus subtilis, Bacillus subtilis SIL3
Biochem. Eng. J.
114
183-190
2016
-
1
-
-
-
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
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-
-
1
-
-
-
-
-
-
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-
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-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
749837
Ma
-
One-pot enzymatic production ...
Pseudomonas sp. SE83
Biochem. Eng. J.
95
1-8
2015
-
1
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
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-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
752071
Tao
-
Efficient production of perac ...
Bacillus subtilis
Process Biochem.
50
2121-2127
2015
-
-
1
-
1
-
1
5
-
-
-
-
-
1
-
-
-
-
-
-
-
-
2
1
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
1
-
-
1
-
5
-
-
-
-
-
-
-
-
-
-
-
-
2
1
-
-
-
-
-
-
-
-
-
-
-
-
5
5
729073
Tian
A novel cephalosporin deacetyl ...
Bacillus subtilis, Bacillus subtilis CICC 20034
Appl. Microbiol. Biotechnol.
98
2081-2089
2014
-
-
1
-
-
-
15
-
-
-
2
2
-
2
-
-
1
-
-
-
6
-
13
1
1
1
3
-
1
1
1
-
-
-
-
-
-
1
-
-
-
-
-
15
-
-
-
-
2
2
-
-
-
1
-
-
6
-
13
1
1
1
3
-
1
1
1
-
-
1
1
-
-
-
730072
Wang
Double knockout of beta-lactam ...
Escherichia coli, Escherichia coli JM105
J. Biosci. Bioeng.
113
737-741
2012
-
-
-
-
1
-
-
-
-
-
-
2
-
7
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
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1
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-
-
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2
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
730907
Levisson
Functional and structural char ...
Thermotoga maritima
Proteins
80
1545-1559
2012
-
-
1
1
-
-
2
-
1
2
-
2
-
1
-
-
1
1
-
-
-
-
4
1
1
-
-
-
1
-
-
-
1
-
-
-
-
1
-
1
-
-
-
2
1
-
1
2
-
2
-
-
-
1
-
-
-
-
4
1
1
-
-
-
1
-
-
-
-
2
2
-
-
-
747164
Hedge
The structural basis for the ...
Thermotoga maritima, Thermotoga maritima DSM 3109
Biochim. Biophys. Acta
1824
1024-1030
2012
-
-
1
-
1
-
-
10
-
-
-
-
-
4
-
-
1
-
-
-
-
-
15
-
1
-
-
-
1
-
-
-
-
-
-
-
-
1
-
-
1
-
-
-
-
10
-
-
-
-
-
-
-
1
-
-
-
-
15
-
1
-
-
-
1
-
-
-
-
-
-
-
10
10
677538
Martinez-Martinez
A colorimetric assay for the d ...
Bacillus pumilus, Bacillus pumilus CECT 5072
Anal. Biochem.
369
210-217
2007
-
1
1
-
-
-
-
2
-
-
-
-
-
4
-
-
1
-
-
-
-
-
4
-
1
-
-
-
1
-
-
-
-
-
-
-
1
1
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
1
-
-
-
-
4
-
1
-
-
-
1
-
-
-
-
-
-
-
-
-
671502
Takimoto
Batch production of deacetyl 7 ...
Bacillus subtilis, Bacillus subtilis SHS0133
Appl. Microbiol. Biotechnol.
65
263-267
2004
-
1
1
-
-
1
1
-
-
-
-
2
-
5
-
-
1
-
-
-
-
1
4
-
-
-
1
-
-
-
2
-
-
-
-
-
1
1
-
-
-
1
-
1
-
-
-
-
-
2
-
-
-
1
-
-
-
1
4
-
-
-
1
-
-
-
2
-
-
-
-
-
-
-
675216
Basch
Expression of a cephalosporin ...
Rhodotorula toruloides
J. Ind. Microbiol. Biotechnol.
31
531-539
2004
-
1
1
-
-
-
-
-
-
-
-
1
-
4
-
-
-
-
-
-
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Abbott
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Hinnem
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Fujisawa
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