BRENDA - Enzyme Database
show all sequences of 4.2.2.6

The active site of oligogalacturonate lyase provides unique insights into cytoplasmic oligogalacturonate beta-elimination

Abbott, D.W.; Gilbert, H.J.; Boraston, A.B.; J. Biol. Chem. 285, 39029-39038 (2010) View publication on PubMedView publication on EuropePMC

Data extracted from this reference:

Cloned(Commentary)
Cloned (Commentary)
Organism
gene ogl, phylogenetic tree of the OGL family, expression of YeOGL containing a thrombin-cleavable N-terminal His6 tag in Escherichia coli BL21-pLysS (DE3) cells
Yersinia enterocolitica
Crystallization (Commentary)
Crystallization (Commentary)
Organism
purified recombinant detagged YeOGL, hanging drop vapor diffusion method, 12.5 mg/ml protein in 20 mM Tris-HCl, precipitation from 0.2 M CaCl2, 0.1 M NaOAc, pH 4.8, 20% PEG 3350, and cryoprotection by 15% ethylene glycol, 18°C, X-ray diffraction structure determination and analysis at 1.65 A resolution
Yersinia enterocolitica
Inhibitors
Inhibitors
Commentary
Organism
Structure
pectate
substrate inhibition at high concentrations
Yersinia enterocolitica
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
additional information
-
additional information
Michaelis-Menten kinetics
Yersinia enterocolitica
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Mn2+
activates, octahedral metal binding site, coordination structure involving N-His287, O-Gln350, N-His353, and His-355, overview
Yersinia enterocolitica
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
4-(4-deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonate
Yersinia enterocolitica
-
2 5-dehydro-4-deoxy-D-glucuronate
-
-
?
4-(4-deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonate
Yersinia enterocolitica 8081
-
2 5-dehydro-4-deoxy-D-glucuronate
-
-
?
Organism
Organism
UniProt
Commentary
Textmining
Yersinia enterocolitica
A1JMA5
subsp. enterocolitica, gene ogl, locus YE1876
-
Yersinia enterocolitica 8081
A1JMA5
subsp. enterocolitica, gene ogl, locus YE1876
-
Purification (Commentary)
Purification (Commentary)
Organism
recombinant N-terminally His-tagged YeOGL from Escherichia coli by nickel affinity chromatography, ultrafiltration, His-tag cleavage through thrombin, and gel filtration
Yersinia enterocolitica
Reaction
Reaction
Commentary
Organism
Reaction ID
4-(4-deoxy-alpha-D-galact-4-enuronosyl)-D-galacturonate = 2 5-dehydro-4-deoxy-D-glucuronate
active site structure modeling and beta-elimination reaction mechanism, overview
Yersinia enterocolitica
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
Substrate Product ID
4-(4-deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonate
-
715562
Yersinia enterocolitica
2 5-dehydro-4-deoxy-D-glucuronate
-
-
-
?
4-(4-deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonate
-
715562
Yersinia enterocolitica 8081
2 5-dehydro-4-deoxy-D-glucuronate
-
-
-
?
Subunits
Subunits
Commentary
Organism
More
YeOGL adopts a seven-bladed beta-propeller fold that has structural similarity to the WD40 family of proteins
Yersinia enterocolitica
Synonyms
Synonyms
Commentary
Organism
oligogalacturonate lyase
-
Yersinia enterocolitica
YeOGL
-
Yersinia enterocolitica
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
25
-
assay at
Yersinia enterocolitica
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7
-
assay at
Yersinia enterocolitica
Cloned(Commentary) (protein specific)
Commentary
Organism
gene ogl, phylogenetic tree of the OGL family, expression of YeOGL containing a thrombin-cleavable N-terminal His6 tag in Escherichia coli BL21-pLysS (DE3) cells
Yersinia enterocolitica
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified recombinant detagged YeOGL, hanging drop vapor diffusion method, 12.5 mg/ml protein in 20 mM Tris-HCl, precipitation from 0.2 M CaCl2, 0.1 M NaOAc, pH 4.8, 20% PEG 3350, and cryoprotection by 15% ethylene glycol, 18°C, X-ray diffraction structure determination and analysis at 1.65 A resolution
Yersinia enterocolitica
Inhibitors (protein specific)
Inhibitors
Commentary
Organism
Structure
pectate
substrate inhibition at high concentrations
Yersinia enterocolitica
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
additional information
-
additional information
Michaelis-Menten kinetics
Yersinia enterocolitica
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Mn2+
activates, octahedral metal binding site, coordination structure involving N-His287, O-Gln350, N-His353, and His-355, overview
Yersinia enterocolitica
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
4-(4-deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonate
Yersinia enterocolitica
-
2 5-dehydro-4-deoxy-D-glucuronate
-
-
?
4-(4-deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonate
Yersinia enterocolitica 8081
-
2 5-dehydro-4-deoxy-D-glucuronate
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant N-terminally His-tagged YeOGL from Escherichia coli by nickel affinity chromatography, ultrafiltration, His-tag cleavage through thrombin, and gel filtration
Yersinia enterocolitica
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ID
4-(4-deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonate
-
715562
Yersinia enterocolitica
2 5-dehydro-4-deoxy-D-glucuronate
-
-
-
?
4-(4-deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonate
-
715562
Yersinia enterocolitica 8081
2 5-dehydro-4-deoxy-D-glucuronate
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
More
YeOGL adopts a seven-bladed beta-propeller fold that has structural similarity to the WD40 family of proteins
Yersinia enterocolitica
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
25
-
assay at
Yersinia enterocolitica
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7
-
assay at
Yersinia enterocolitica
General Information
General Information
Commentary
Organism
metabolism
OGL is involved in the pectin degradation pathway performing extracellular pectin depolymerization, overview. In the initial stages, intracellular di- and trigalacturonides are processed into saturated monogalacturonate, GalA, and a 4,5-unsaturated GalA-like monosaccharide, 5-keto-4-deoxyuronate, by the combined activities of an exo-acting family 2 pectate lyase,YePL2B, and oligogalacturonate lyase, YeOGL/YePL22, a lyase family preferentially active on digalacturonides
Yersinia enterocolitica
General Information (protein specific)
General Information
Commentary
Organism
metabolism
OGL is involved in the pectin degradation pathway performing extracellular pectin depolymerization, overview. In the initial stages, intracellular di- and trigalacturonides are processed into saturated monogalacturonate, GalA, and a 4,5-unsaturated GalA-like monosaccharide, 5-keto-4-deoxyuronate, by the combined activities of an exo-acting family 2 pectate lyase,YePL2B, and oligogalacturonate lyase, YeOGL/YePL22, a lyase family preferentially active on digalacturonides
Yersinia enterocolitica
Other publictions for EC 4.2.2.6
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
Synonyms
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)
715562
Abbott
The active site of oligogalact ...
Yersinia enterocolitica, Yersinia enterocolitica 8081
J. Biol. Chem.
285
39029-39038
2010
-
-
1
1
-
-
1
1
-
1
-
2
-
5
-
-
1
1
-
-
-
-
2
1
2
1
-
-
-
1
-
-
-
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1
-
1
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-
1
-
1
-
1
-
2
-
-
-
1
-
-
-
-
2
1
1
-
-
-
1
-
-
-
-
1
1
-
-
-
677684
Yang
Global effect of indole-3-acet ...
Dickeya chrysanthemi
Appl. Environ. Microbiol.
73
1079-1088
2007
-
-
-
-
-
-
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-
-
-
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-
4
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-
34108
Shevchik
The exopolygalacturonate lyase ...
Dickeya chrysanthemi, Dickeya chrysanthemi 3937
J. Bacteriol.
181
3912-3919
1999
-
-
1
-
-
-
1
2
2
4
1
-
-
14
-
-
-
-
-
-
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6
1
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-
1
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-
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-
1
-
-
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-
1
-
2
2
4
1
-
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-
-
-
6
1
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-
1
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-
-
-
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-
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-
651970
Kester
Performance of selected microb ...
Dickeya chrysanthemi
J. Biol. Chem.
274
37053-37059
1999
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-
-
-
-
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7
-
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1
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1
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8
-
2
1
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1
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1
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8
-
1
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1
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-
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-
34109
Reverchon
Nucleotide sequences of the Er ...
Dickeya chrysanthemi, Dickeya chrysanthemi 3937
Gene
85
125-134
1989
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-
-
-
-
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10
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34107
Reverchon
Molecular cloning of an Erwini ...
Dickeya chrysanthemi, Dickeya chrysanthemi 3937
Gene
55
125-133
1987
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1
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16
-
-
-
-
-
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1
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-
-
-
-
-
-
-
-
34106
Hatanaka
-
Pectolytic enzymes of exo-type ...
Pseudomonas sp.
Agric. Biol. Chem.
35
1617-1624
1971
1
-
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1
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1
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1
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6
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1
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1
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1
-
6
-
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-
-
-
-
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-
-
-
-
-
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-
34104
Hatanaka
-
An oligogalacturonate transeli ...
Erwinia aroidea
Agric. Biol. Chem.
34
1618-1624
1970
-
-
-
-
-
-
1
-
-
-
-
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1
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1
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1
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7
-
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1
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1
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1
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1
-
7
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
34105
Moran
Oligogalacturonide trans-elimi ...
Erwinia aroidea
Arch. Biochem. Biophys.
125
734-741
1968
-
-
-
-
-
-
-
2
-
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1
-
3
-
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1
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1
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4
-
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1
1
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2
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1
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1
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1
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4
-
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1
1
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