Information on EC 4.2.2.24 - rhamnogalacturonan exolyase

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The expected taxonomic range for this enzyme is: Bacillus subtilis

EC NUMBER
COMMENTARY hide
4.2.2.24
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RECOMMENDED NAME
GeneOntology No.
rhamnogalacturonan exolyase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
Exotype eliminative cleavage of alpha-L-rhamnopyranosyl-(1->4)-alpha-D-galactopyranosyluronic acid bonds of rhamnogalacturonan I oligosacharides containing alpha-L-rhamnopyranose at the reducing end and 4-deoxy-4,5-unsaturated D-galactopyranosyluronic acid at the non-reducing end. The products are the disaccharide 2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose and the shortened rhamnogalacturonan oligosaccharide containing one 4-deoxy-4,5-unsaturated D-galactopyranosyluronic acid at the non-reducing end.
show the reaction diagram
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
rhamnogalacturonan type I degradation II (bacteria)
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SYSTEMATIC NAME
IUBMB Comments
alpha-L-rhamnopyranosyl-(1->4)-alpha-D-galactopyranosyluronate exolyase
The enzyme is part of the degradation system for rhamnogalacturonan I in Bacillus subtilis strain 168.
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain 168
SwissProt
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
rhamnogalacturonan I
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + shortened rhamnogalacturonan oligosaccharide containing one 4,5-deoxy-4,5-unsaturated D-galactopyranosyluronic acid at the non-reducing end
show the reaction diagram
responsible for an initial cleavage of the rhamnogalacturonan I region of plant cell wall pectin. Bacillus subtilis strain 168 secretes two rhamnogalacturonan lyases, YesW and YesX, extracellularly. YesW cleaves the glycoside bond of the rhamnogalacturonan chain endolytically, and the resultant oligosaccharides are subsequently converted to disaccharides, unsaturated galacturonyl rhamnose, through the exotype reaction of YesX
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?
rhamnogalacturonan I oligosaccharide
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + shortened rhamnogalacturonan oligosaccharide containing one 4,5-deoxy-4,5-unsaturated D-galactopyranosyluronic acid at the non-reducing end
show the reaction diagram
exotype eliminative cleavage of alpha-L-rhamnopyranosyl-(1->4)-alpha-D-GalA bonds of rhamnogalacturonan I oligosacharides containing L-rhamnopyranose at the reducing end and 4,5-deoxy-4,5-unsaturated D-galactopyranosyluronic acid at the nonreducing end. The products are the disaccharide 2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose and the shortened rhamnogalacturonan oligosaccharide containing one 4,5-deoxy-4,5-unsaturated D-galactopyranosyluronic acid at the non-reducing end
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-
?
rhamnogalacturonan I oligosaccharide
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + shortened rhamnogalacturonan oligosaccharide containing one 4-deoxy-4,5-unsaturated D-galactopyranosyluronic acid at the non-reducing end
show the reaction diagram
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
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + shortened rhamnogalacturonan oligosaccharide containing one 4,5-deoxy-4,5-unsaturated D-galactopyranosyluronic acid at the non-reducing end
show the reaction diagram
O31527
responsible for an initial cleavage of the rhamnogalacturonan I region of plant cell wall pectin. Bacillus subtilis strain 168 secretes two rhamnogalacturonan lyases, YesW and YesX, extracellularly. YesW cleaves the glycoside bond of the rhamnogalacturonan chain endolytically, and the resultant oligosaccharides are subsequently converted to disaccharides, unsaturated galacturonyl rhamnose, through the exotype reaction of YesX
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-
?
rhamnogalacturonan I oligosaccharide
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + shortened rhamnogalacturonan oligosaccharide containing one 4-deoxy-4,5-unsaturated D-galactopyranosyluronic acid at the non-reducing end
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
1 mM, addition the chelator-treated enzyme partly restores activity
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
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
D-galacturonic acid
5 mM, 41% loss of activity
EDTA
10 mM, complete loss of activity
EGTA
10 mM, complete loss of activity
iodoacetic acid
1 mM, 45% loss of activity
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
D-glucose
5 mM, 1.2fold activation
D-glucuronic acid
5 mM, 1.25fold activation
D-sucrose
5 mM, 1.2fold activation
D-xylose
5 mM, 1.37fold activation
L-rhamnose
5 mM, 1.24fold activation
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
rhamnogalacturonan I
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5 - 10
pH 7.5: about 40% of maximal activity, pH 10.0: about 40% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
45 - 75
40C: about 40% of maximal activity, 75C: about 50% of maximal activity
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
68000
1 * 68000, SDS-PAGE
68754
x * 68754, calculated from sequence
70000
gel filtration
687544
1 * 687544, mature form of YesX including the C-terminal 8His-tag
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 68754, calculated from sequence
monomer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
sitting drop vapor diffusion method, structure determined at 1.32 A and 1.65 resolution, respectively. YesX crystal belongs to space group P2(1)2(1)2(1) with unit cell parameters of a = 72.9 A, b = 88.1 A, and c = 99.3 A. One molecule is present in an asymmetric unit
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50
5 min, stable below
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
native YesX and YesX del_loop mutant
recombinant enzyme from Escherichia coli cells
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
expression in Escherichia coli and Bacillus subtilis strain natto
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
YesX del_loop
the mutant enzyme shows an endolytic reaction profile. Vmax/Km-value for the mutant enzyme is 275fold lower than the Vmax/KM-value for the wild-type enzyme