Information on EC 4.2.2.23 - rhamnogalacturonan endolyase

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

EC NUMBER
COMMENTARY hide
4.2.2.23
-
RECOMMENDED NAME
GeneOntology No.
rhamnogalacturonan endolyase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
Endotype eliminative cleavage of L-alpha-rhamnopyranosyl-(1->4)-alpha-D-galactopyranosyluronic acid bonds of rhamnogalacturonan I domains in ramified hairy regions of pectin leaving L-rhamnopyranose at the reducing end and 4-deoxy-4,5-unsaturated D-galactopyranosyluronic acid at the non-reducing end.
show the reaction diagram
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-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
rhamnogalacturonan type I degradation I (fungi)
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rhamnogalacturonan type I degradation II (bacteria)
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SYSTEMATIC NAME
IUBMB Comments
alpha-L-rhamnopyranosyl-(1->4)-alpha-D-galactopyranosyluronate endolyase
The enzyme is part of the degradation system for rhamnogalacturonan I in Bacillus subtilis strain 168 and Aspergillus aculeatus.
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
UniProt
Manually annotated by BRENDA team
strain 168
SwissProt
Manually annotated by BRENDA team
strain 3937. RhiE is present in one-third of the strains tested
SwissProt
Manually annotated by BRENDA team
strain 3937. RhiE is present in one-third of the strains tested
SwissProt
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
potato pectic galactan
potato pectic galactan oligosaccharides
show the reaction diagram
rhamnogalacturonan I
rhamnogalacturonan I oligosaccharides with alpha-L-rhamnopyranose at the reducing end and 4-deoxy-4,5-unsaturated D-galactopyranosyluronic acid at the nonreducing end
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
rhamnogalacturonan I
rhamnogalacturonan I oligosaccharides with alpha-L-rhamnopyranose at the reducing end and 4-deoxy-4,5-unsaturated D-galactopyranosyluronic acid at the nonreducing end
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
-
1 mM, addition the chelator-treated enzyme restores activity
Mn2+
-
1 mM, addition the chelator-treated enzyme restores activity
Zn2+
-
1 mM, addition the chelator-treated enzyme restores activity
additional information
the enzyme does not require a divalent cation for its activity. RhiE activity is not increased by the addition of 0.2 mM Ca2+, Mn2+, Co2+, Cu2+, or Zn2+
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
EDTA
-
completely abolishes activity against potato pectic galactan
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
potato pectic galactan
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
34
potato pectic galactan
Clostridium cellulolyticum
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pH 8.5, 37C
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additional information
potato pectic galactan
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8.5
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substrate: potato pectic galactan
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 9
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pH 7.0: about 40% of maximal activity, pH 9.0: about 50% of maximal activity
8.5 - 10.5
pH 8.5: about 60% of maximal activity, pH 10.5: about about 40% of maximal activity
10
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completely inactive at, substrate: potato pectic galactan
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
40 - 75
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40C: about 45% of maximal activity, 75C: about 50% of maximal activity
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.1 - 5.3
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zymography
5.2
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isoelectric focusing
5.5
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calculated from sequence
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
rhamnogalacturonan lyase activity is the highest in rapidly expanding 3- to 4-day-old cotyledons and gradually decreases during the slow-down in expansion over the next 23 days
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
-
Rgl11Y is incorporated in the Clostridium cellulolyticum cellulosome through a typical cohesin-dockerin interaction
Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
54200
-
x * 54200, calculated from sequence
57000
-
gel filtration
61940
x * 61940, calculated from sequence
62000
x * 62000, SDS-PAGE
64000
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x * 64000, SDS-PAGE
65000
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gel filtration
68000
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1 * 68000, SDS-PAGE
75000
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x * 75000, SDS-PAGE
93415
x * 93415, calculated from sequence
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystals are grown using hanging-drop vapour-diffusion and microseeding techniques. Crystallization conditions: 20% PEG 4000, 9% PEG 400, 0.1 M (NH4)2SO4 and 0.1 M sodium acetate pH 4.4. These crystals diffract to a resolution of 1.5 A. The unit-cell parameters are a = b = 77.0, c = 170.8 A with the possible space group P4(3)2(1)2 or P4(1)2(1)2
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hanging-drop vapor diffusion, structure determination of the RGL4_K150A and RGL4_H210A enzyme variants. determination of the 2.4 A crystal structure of the RGL4 mutant RGL4_K150A with an rhamnogalacturonan I hexasaccharide. Crystals of the RGL4_K150A variant soaked with a rhamnogalacturonan digest gave a clear picture of substrate bound in the -3/+3 subsites
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rhamnogalacturonan lyase reveals a unique three-domain modular structure for polysaccharide lyase family 4
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crystallization of YesW in complex with rhamnose, sitting drop vapor diffusion method, structure determined at 1.32 A and 1.65 resolution, respectively
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sitting-drop vapor diffusion method, crystal structures of YesW and its complex with galacturonan disaccharide, a reaction product analogue, are determined at 1.4 and 2.5 A resolutions with final R-factors of 16.4% and 16.6%, respectively. The enzyme is composed of an eight-bladed beta-propeller with a deep cleft in the center as a basic scaffold
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sitting-drop vapour-diffusion method with 2-methyl-2,4-pentanediol as a precipitant
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 8
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40C, stable
710298
6
-
unstable below
708968
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
40
-
pH 5.0, 4.5 h, stable
55
10 min, about 5% loss of activity
65
10 min, about 65% loss of activity
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
completely resistant to proteinase attack
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
native and recombinant enzyme
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recombinant enzyme
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recombinant enzyme from Escherichia coli cells
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Aspergillus oryzae
expression in Escherichia coli
expression in Escherichia coli and Bacillus subtilis strain natto
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expression in Escherichia coli. Expression of the three modules of the Pseudomonas protein in Escherichia coli shows that its C-terminal module is a functional cellulose-binding domain, and the N-terminal module consists of a catalytic domain that hydrolyzes rhamnogalacturonan-containing substrates
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
rhamnogalacturonan lyase activity is the highest in rapidly expanding 3- to 4-day-old cotyledons and gradually decreases during the slow-down in expansion over the next 23 days
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rhiE expression is strongly induced in the presence of rhamnose but is also regulated by PecT and Crp, two regulators of the transcription of pectinolytic enzyme genes
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
H210A
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relative activity is 0.001% of wild-type activity
K150A
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relative activity is 0.04% of wild-type activity
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
food industry
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rhamnogalacturonan lyase is useful in the processing of fruit, where it is important that the commercial pectolytic enzyme preparations solubilize and hydrolyze the branched RG structures, which otherwise remain as colloidally dissolved polymers in the juice and lead to problems during filtration and clarification