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Information on EC 4.2.2.23 - rhamnogalacturonan endolyase and Organism(s) Bacillus subtilis and UniProt Accession O31526
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4.2.2.23 rhamnogalacturonan endolyaseIUBMB Comments
The enzyme is part of the degradation system for rhamnogalacturonan I in Bacillus subtilis strain 168 and Aspergillus aculeatus.
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Word Map
- 4.2.2.23
- polysaccharide
- aculeatus
- lyases
- homogalacturonans
-
beta-elimination
-
pectic
-
hairy
-
nonreducing
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rhamnogalacturonan-i
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mucilage
-
d-galacturonic
- galactan
- arabinofuranosidase
- chrysogenum
- pectate
- l-rhamnose
- acetylesterase
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endo-acting
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reaction-generated
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camv35s
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ramified
- pectinases
- food industry
The taxonomic range for the selected organisms is: Bacillus subtilis
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
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.
Synonyms
rg-lyase, rg lyase, solyc11g011300, rgl11y, rhamnogalacturonase b, rgl11a, rhamnogalacturonan lyase a, rhamnogalacturonan endolyase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
PATHWAY SOURCE
PATHWAYS
-
-
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.
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
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
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
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 YesX reaction
-
-
?
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
rhamnogalacturonan lyase produced by plant pathogenic and saprophytic microbes plays an important role in degrading plant cell walls
-
-
?
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
rhamnogalacturonan lyases degrades rhamnogalacturonan I, a major component of pectin, through a beta-elimination reaction
-
-
?
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
the enzyme is part of the degradation system of rhamnogalacturonan type I. YesW catalyzes the initial cleavage of the rhamnogalacturonan I main chain, and the resultant oligosaccharides are converted to disaccharides through the extracellular exotype YesX reaction. The disaccharide is finally degraded into its constituent monosaccharides through the reaction of intracellular unsaturated galacturonyl hydrolases YesR and YteR
-
-
?
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
endotype eliminative cleavage, the YesW amino acid residues Asn152, Asp172, Asn532, Gly533, Thr534, and Tyr595 in the active cleft bind to rhamnose molecules through hydrogen bonds and van der Waals contacts
YesW releases a tetrasaccharide and larger saccharides as a major product
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?
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
rhamnogalacturonan I from potatoes. YesW acts on the substrate endolytically and releases both disaccharide and larger saccharides. The enzyme mainly acts on rhamnogalacturonan I backbone, slight activity on polygalacturonan
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-
?
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
the substrate-binding site is located in the deep cleft at the center of the beta-propeller, where positively charged (Lys535 and Arg452) and aromatic (Tyr595) amino acid residues are crucial for binding to the substrate through hydrogen bond formation and stacking interaction
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-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
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
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
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 YesX reaction
-
-
?
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
rhamnogalacturonan lyase produced by plant pathogenic and saprophytic microbes plays an important role in degrading plant cell walls
-
-
?
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
rhamnogalacturonan lyases degrades rhamnogalacturonan I, a major component of pectin, through a beta-elimination reaction
-
-
?
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
the enzyme is part of the degradation system of rhamnogalacturonan type I. YesW catalyzes the initial cleavage of the rhamnogalacturonan I main chain, and the resultant oligosaccharides are converted to disaccharides through the extracellular exotype YesX reaction. The disaccharide is finally degraded into its constituent monosaccharides through the reaction of intracellular unsaturated galacturonyl hydrolases YesR and YteR
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ca2+
Ca2+
a calcium ion coordinated by Asp401, Glu422, His363, and His399 may be required for the enzyme activity
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
rhamnogalacturonan I
KM-value is 0.181 mg/ml, pH 7.5, 30°C
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additional information
rhamnogalacturonan I
Km-value is 0.35 mg/ml, pH 7.5, 30°C
-
additional information
rhamnogalacturonan I
KM-value: 0.13 mg/ml for wild-type enzyme, 1.9 mg/ml for mutant enzyme K535A, 2.5 mg/ml for mutant enzyme R452A, 0.033 mg/ml for mutant enzyme Y595F, 0.1 mg/ml for mutant enzymes D401N and H363A, 0.12 mg/mL for mutant enzyme H399A, pH 7.5, 30°C
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additional information
rhamnogalacturonan I
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KM-value: 0.13 mg/ml for wild-type enzyme, 1.9 mg/ml for mutant enzyme K535A, 2.5 mg/ml for mutant enzyme R452A, 0.033 mg/ml for mutant enzyme Y595F, 0.1 mg/ml for mutant enzymes D401N and H363A, 0.12 mg/mL for mutant enzyme H399A, pH 7.5, 30°C
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7 - 9
pH 7.0: about 40% of maximal activity, pH 9.0: about 50% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
40 - 75
40°C: about 45% of maximal activity, 75°C: about 50% of maximal activity
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
64444
64444
1 * 64444, mature form of YesW including the C-terminal 8His-tag
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
monomer
1 * 64444, mature form of YesW including the C-terminal 8His-tag
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystallization of YesW in complex with rhamnose, sitting drop vapor diffusion method, structure determined at 1.32 A and 1.65 resolution, respectively
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
sitting-drop vapour-diffusion method with 2-methyl-2,4-pentanediol as a precipitant
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Ochiai, A.; Yamasaki, M.; Itoh, T.; Mikami, B.; Hashimoto, W.; Murata, K.
Crystallization and preliminary X-ray analysis of the rhamnogalacturonan lyase YesW from Bacillus subtilis strain 168, a member of polysaccharide lyase family 11
Acta Crystallogr. Sect. F
62
438-440
2006
Bacillus subtilis (O31526), Bacillus subtilis 168 (O31526)
Ochiai, A.; Itoh, T.; Kawamata, A.; Hashimoto, W.; Murata, K.
Plant cell wall degradation by saprophytic Bacillus subtilis strains: gene clusters responsible for rhamnogalacturonan depolymerization
Appl. Environ. Microbiol.
73
3803-3813
2007
Bacillus subtilis (O31526), Bacillus subtilis 168 (O31526)
Ochiai, A.; Itoh, T.; Maruyama, Y.; Kawamata, A.; Mikami, B.; Hashimoto, W.; Murata, K.
A novel structural fold in polysaccharide lyases: Bacillus subtilis family 11 rhamnogalacturonan lyase YesW with an eight-bladed beta-propeller
J. Biol. Chem.
282
37134-37145
2007
Bacillus subtilis (O31526), Bacillus subtilis
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