BRENDA - Enzyme Database
show all sequences of 4.4.1.3

Structural and molecular basis for the novel catalytic mechanism and evolution of DddP, an abundant peptidase-like bacterial dimethylsulfoniopropionate lyase a new enzyme from an old fold

Wang, P.; Chen, X.L.; Li, C.Y.; Gao, X.; Zhu, D.Y.; Xie, B.B.; Qin, Q.L.; Zhang, X.Y.; Su, H.N.; Zhou, B.C.; Xun, L.Y.; Zhang, Y.Z.; Mol. Microbiol. 98, 289-301 (2015)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
expression in Escherichia coli
Ruegeria lacuscaerulensis
Crystallization (Commentary)
Crystallization
Organism
wild-type in complex with inhibitor 2-(N-morpholino)ethanesulfonic acid or PO43-, to 2.1 A resolution, and mutants Y366A and D377N bound to acrylate
Ruegeria lacuscaerulensis
Engineering
Amino acid exchange
Commentary
Organism
D377A
complete loss of activity
Ruegeria lacuscaerulensis
D377N
about 10% residual activity
Ruegeria lacuscaerulensis
Y366A
20% residual activity
Ruegeria lacuscaerulensis
Inhibitors
Inhibitors
Commentary
Organism
Structure
1,10-phenanthroline
10 mM, almost complete inhibition
Ruegeria lacuscaerulensis
2-(N-morpholino)ethanesulfonic acid
-
Ruegeria lacuscaerulensis
bipyridyl
10 mM, 50% inhibition
Ruegeria lacuscaerulensis
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
17.1
-
beta-dimethylsulfoniopropanoate
pH 6.0, 60°C
Ruegeria lacuscaerulensis
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Ruegeria lacuscaerulensis
D0CY07
-
-
Ruegeria lacuscaerulensis DSM 11314
D0CY07
-
-
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
beta-dimethylsulfoniopropanoate
-
748685
Ruegeria lacuscaerulensis
dimethylsulfide + acrylate
-
-
-
?
beta-dimethylsulfoniopropanoate
-
748685
Ruegeria lacuscaerulensis DSM 11314
dimethylsulfide + acrylate
-
-
-
?
additional information
enzyme shows no detectable activity toward the typical substrate (Val-Pro) of M24 peptidases
748685
Ruegeria lacuscaerulensis
?
-
-
-
-
additional information
enzyme shows no detectable activity toward the typical substrate (Val-Pro) of M24 peptidases
748685
Ruegeria lacuscaerulensis DSM 11314
?
-
-
-
-
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
60
-
-
Ruegeria lacuscaerulensis
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
6
-
-
Ruegeria lacuscaerulensis
Cloned(Commentary) (protein specific)
Commentary
Organism
expression in Escherichia coli
Ruegeria lacuscaerulensis
Crystallization (Commentary) (protein specific)
Crystallization
Organism
wild-type in complex with inhibitor 2-(N-morpholino)ethanesulfonic acid or PO43-, to 2.1 A resolution, and mutants Y366A and D377N bound to acrylate
Ruegeria lacuscaerulensis
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
D377A
complete loss of activity
Ruegeria lacuscaerulensis
D377N
about 10% residual activity
Ruegeria lacuscaerulensis
Y366A
20% residual activity
Ruegeria lacuscaerulensis
Inhibitors (protein specific)
Inhibitors
Commentary
Organism
Structure
1,10-phenanthroline
10 mM, almost complete inhibition
Ruegeria lacuscaerulensis
2-(N-morpholino)ethanesulfonic acid
-
Ruegeria lacuscaerulensis
bipyridyl
10 mM, 50% inhibition
Ruegeria lacuscaerulensis
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
17.1
-
beta-dimethylsulfoniopropanoate
pH 6.0, 60°C
Ruegeria lacuscaerulensis
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
beta-dimethylsulfoniopropanoate
-
748685
Ruegeria lacuscaerulensis
dimethylsulfide + acrylate
-
-
-
?
beta-dimethylsulfoniopropanoate
-
748685
Ruegeria lacuscaerulensis DSM 11314
dimethylsulfide + acrylate
-
-
-
?
additional information
enzyme shows no detectable activity toward the typical substrate (Val-Pro) of M24 peptidases
748685
Ruegeria lacuscaerulensis
?
-
-
-
-
additional information
enzyme shows no detectable activity toward the typical substrate (Val-Pro) of M24 peptidases
748685
Ruegeria lacuscaerulensis DSM 11314
?
-
-
-
-
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
60
-
-
Ruegeria lacuscaerulensis
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
6
-
-
Ruegeria lacuscaerulensis
Expression
Organism
Commentary
Expression
Ruegeria lacuscaerulensis
the expression of the dddP gene is significantly induced by DMSP but not by peptide Val-Pro or casein
up
Expression (protein specific)
Organism
Commentary
Expression
Ruegeria lacuscaerulensis
the expression of the dddP gene is significantly induced by DMSP but not by peptide Val-Pro or casein
up
Other publictions for EC 4.4.1.3
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)
747144
Lei
The dimethylsulfoniopropionat ...
Alcaligenes faecalis, Halodesulfovibrio aestuarii
Biochemistry
57
3364-3377
2018
-
-
2
-
-
-
2
2
-
4
-
-
-
3
-
-
-
-
-
-
2
-
2
-
-
-
-
2
-
-
-
-
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-
2
-
-
-
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2
-
2
-
4
-
-
-
-
-
-
-
-
2
-
2
-
-
-
-
2
-
-
-
-
-
2
2
-
2
2
748278
Wang
-
How is DMSP decomposed when c ...
Ruegeria lacuscaerulensis, Ruegeria lacuscaerulensis DSM 11314
J. Catal.
360
1-8
2018
-
-
-
-
-
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
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-
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-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
1
-
-
-
748399
Li
Mechanistic insights into dim ...
Acinetobacter bereziniae, Acinetobacter bereziniae NIPH 3
J. Mol. Biol.
429
3850-3862
2017
-
-
1
1
-
-
-
1
-
1
-
-
-
4
-
-
-
-
-
-
-
-
2
-
1
-
-
1
1
-
-
-
-
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-
-
-
1
-
1
-
-
-
-
-
1
-
1
-
-
-
-
-
-
-
-
-
-
2
-
1
-
-
1
1
-
-
-
-
-
-
-
-
-
748814
Burkhardt
Chemical differentiation of t ...
Phaeobacter inhibens, Phaeobacter inhibens DSM 17395, Ruegeria pomeroyi, Ruegeria pomeroyi DSM 15171
Org. Biomol. Chem.
15
4432-4439
2017
-
-
-
-
-
-
-
18
-
-
-
-
-
8
-
-
-
-
-
-
-
-
33
-
-
-
-
18
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
18
-
-
-
-
-
-
-
-
-
-
-
-
33
-
-
-
-
18
-
-
-
-
-
-
-
-
18
18
747110
Brummett
New mechanistic insight from ...
Ruegeria lacuscaerulensis, Ruegeria lacuscaerulensis DSM 11314
Biochemistry
55
6162-6174
2016
-
-
-
1
-
-
-
-
-
1
-
-
-
2
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
1
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
748685
Wang
Structural and molecular basi ...
Ruegeria lacuscaerulensis, Ruegeria lacuscaerulensis DSM 11314
Mol. Microbiol.
98
289-301
2015
-
-
1
1
3
-
3
1
-
-
-
-
-
5
-
-
-
-
-
-
-
-
4
-
1
-
-
-
1
-
-
-
-
-
-
-
-
1
-
1
3
-
-
3
-
1
-
-
-
-
-
-
-
-
-
-
-
-
4
-
1
-
-
-
1
-
-
-
1
-
-
1
-
-
749057
Brummett
Biochemical, kinetic, and spe ...
Ruegeria pomeroyi, Ruegeria pomeroyi DSM 15171
PLoS ONE
10
e0127288
2015
-
-
1
-
-
-
-
2
-
5
2
-
-
9
-
-
1
-
-
-
2
-
2
1
-
-
-
2
1
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
2
-
5
2
-
-
-
-
1
-
-
2
-
2
1
-
-
-
2
1
-
-
-
-
-
-
-
2
2
730958
Conway
Co-cultures of Pseudomonas aer ...
Roseobacter denitrificans, Roseobacter denitrificans Och114
ScientificWorldJournal
2012
120108
2012
-
-
1
-
-
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
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-
1
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-
-
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-
-
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-
-
-
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-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
1
-
-
716093
Franklin
-
Dimethylsulphoniopropionate (D ...
Emiliania huxleyi, Gephyrocapsa oceanica
Mar. Ecol. Prog. Ser.
410
13-23
2010
-
-
-
-
2
-
-
-
-
-
-
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2
-
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-
-
-
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-
-
-
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-
1
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-
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-
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-
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2
-
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-
-
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-
-
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-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
716137
Kirkwood
The dddP gene of Roseovarius n ...
Roseovarius nubinhibens
Microbiology
156
1900-1906
2010
-
-
1
-
6
-
1
1
-
1
3
-
-
4
-
-
1
-
-
-
-
1
2
1
2
-
1
-
1
1
-
-
-
-
-
-
-
1
-
-
6
-
-
1
-
1
-
1
3
-
-
-
-
1
-
-
-
1
2
1
2
-
1
-
1
1
-
-
-
-
-
-
-
-
692099
Curson
Molecular genetic analysis of ...
Fulvimarina pelagi HTCC2506, Pseudooceanicola batsensis HTCC2597, Rhodobacter sphaeroides, Stappia sp., Stappia sp. KB902, Sulfitobacter sp. EE-36, Yoonia vestfoldensis
Environ. Microbiol.
10
1099
2008
-
-
6
-
-
-
-
-
-
-
-
7
-
8
-
-
-
-
-
-
-
-
14
-
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-
-
-
-
-
-
-
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-
-
6
-
-
-
-
-
-
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7
-
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-
-
-
14
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
697645
Curson
Molecular genetic analysis of ...
Fulvimarina pelagi, Labrenzia aggregata IAM 12614, Pseudooceanicola batsensis, Rhodobacter sphaeroides 2.4.1, Rhodobacter sphaeroides ATCC 17025, Rhodobacter sphaeroides ATCC 17029, Sulfitobacter sp. EE-36, Yoonia vestfoldensis
Environ. Microbiol.
10
757-767
2008
-
-
1
-
1
-
-
-
-
-
-
-
-
17
-
-
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-
-
-
-
-
8
-
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-
-
-
-
-
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-
-
1
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
8
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
653010
Wolfe
-
Dimethylsulfoniopropionate cle ...
Alexandrium ssp., Alexandrium ssp. Halim, Emiliania huxleyi
J. Phycol.
38
948-960
2002
4
-
-
-
-
-
-
-
-
-
-
-
-
3
-
-
-
-
-
-
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4
-
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-
649363
Ansede
Nuclear magnetic resonance ana ...
unidentified proteobacterium
Appl. Environ. Microbiol.
67
3134-3139
2001
-
-
-
-
-
-
-
-
-
-
-
-
-
2
-
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1
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-
653049
Steinke
-
Determinations of dimethylsulf ...
Emiliania huxleyi
J. Sea Res.
43
233-244
2000
-
-
-
-
-
-
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1
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1
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1
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1
-
1
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-
-
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-
-
653106
Niki
-
DMSP lyase activity in five ma ...
Heterocapsa triquetra, no activity in Gephyrocapsa oceanica, no activity in Heterosigma akashiwo, no activity in Isochrysis galbana, Scrippsiella trochoidea
Mar. Biol.
136
759-764
2000
-
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5
-
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2
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-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
649351
Ansede
Metabolism of acrylate to beta ...
Alcaligenes faecalis
Appl. Environ. Microbiol.
65
5075-5081
1999
-
-
-
-
-
-
-
-
-
-
-
-
-
4
-
-
-
1
-
-
-
-
1
-
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-
-
-
-
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-
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-
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-
-
-
-
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-
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-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
34603
Bacic
In vivo characterization of di ...
Fusarium lateritium
Appl. Environ. Microbiol.
64
106-111
1998
-
-
-
-
-
-
2
1
1
-
-
1
-
4
-
-
-
-
-
-
-
-
2
-
1
-
-
-
1
1
-
-
-
-
-
-
-
-
-
-
-
-
-
2
-
1
1
-
-
1
-
-
-
-
-
-
-
-
2
-
1
-
-
-
1
1
-
-
-
-
-
-
-
-
34602
Ansede
-
Comparison of selenium and sul ...
Alcaligenes sp., Alcaligenes sp. M3A, Oceanimonas doudoroffii
FEMS Microbiol. Ecol.
23
315-324
1997
-
-
-
-
-
-
2
-
-
-
-
3
-
6
-
-
-
-
-
-
-
-
9
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
2
-
-
-
-
-
3
-
-
-
-
-
-
-
-
9
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
34604
Yoch
Evidence for intracellular and ...
Alcaligenes sp., Alcaligenes sp. M3A, Oceanimonas doudoroffii
Appl. Environ. Microbiol.
63
3182-3188
1997
-
-
-
-
-
-
3
-
2
-
-
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10
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-
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-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
3
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
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-
34607
De Souza
-
Dimethylsulfoniopropionate lya ...
Ulva curvata
Planta
199
433-438
1996
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-
-
-
-
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1
-
-
1
-
-
1
-
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1
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-
-
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1
-
-
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-
1
1
-
-
-
-
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-
-
-
-
-
-
-
-
-
-
1
-
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1
-
-
-
-
1
-
-
-
-
-
1
-
-
-
-
1
1
-
-
-
-
-
-
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-
34605
De Souza
Purification and characterizat ...
Alcaligenes sp., Alcaligenes sp. M3A
Appl. Environ. Microbiol.
61
21-26
1995
-
-
-
-
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1
-
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1
2
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7
-
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1
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-
1
-
4
1
1
-
-
-
1
-
-
-
-
-
-
-
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-
-
-
-
-
-
-
-
1
-
-
1
2
-
-
-
1
-
-
1
-
4
1
1
-
-
-
1
-
-
-
-
-
-
-
-
-
34606
De Souza
Comparative physiology of dime ...
Alcaligenes sp., Alcaligenes sp. M3A, Oceanimonas doudoroffii
Appl. Environ. Microbiol.
61
3986-3991
1995
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-
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6
2
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4
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9
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7
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-
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6
-
2
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4
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7
-
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-
34601
Cantoni
Enzymatic cleavage of dimethyl ...
Vertebrata lanosa
J. Biol. Chem.
222
171-177
1956
1
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1
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1
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1
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1
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1
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1
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