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Information on EC 4.2.2.23 - rhamnogalacturonan endolyase
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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
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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 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, rgl11y, solyc11g011300, rhamnogalacturonase b, rgl11a, rhamnogalacturonan lyase a, rhamnogalacturonan endolyase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
alpha-L-rhamnopyranosyl-(1->4)-alpha-D-galactopyranosyluronide lyase
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RG-lyase
RGase B
RglA
RglF
rhamnogalacturonan alpha-L-rhamnopyranosyl-(1,4)-alpha-D-galactopyranosyluronide lyase
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-
rhamnogalacturonan lyase A
rhamnogalacturonase B
RhiE
YesW
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REACTION
REACTION DIAGRAM
COMMENTARY
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.
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PATHWAY SOURCE
PATHWAYS
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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.
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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
azurine-crosslinked rhamnogalacturonan
azurine-crosslinked unsaturated rhamnogalacturonan oligosaccharides
-
-
-
?
potato 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
rhamnogalacturonan tetrasaccharide with 4-deoxy-4,5-unsaturated galacturonic acid at the nonreducing end
i.e. soybean rhamnogalacturonan
-
-
?
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
soybean 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
potato pectic galactan
potato pectic galactan oligosaccharides
apple-derived and potato-derived rhamnogalacturonan substrates. The enzyme has a strong preference for rhamnogalacturonans that contain galactose side chains, and which are not esterified. The increase in absorbance at 235 nm indicates that glycosidic bond cleavage is mediated via a beta-elimination mechanism
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-
?
potato pectic galactan
potato pectic galactan oligosaccharides
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beta-eliminative cleavage of the alpha-L-Rhap-(1->4)-alpha-D-GalpA glycosidic bond in the backbone of rhamnogalacturonan I (RGI) via a beta-elimination mechanism. Its specific activity on potato pectic galactan and rhamnogalacturonan is 28 and 3.6 IU/mg, respectively, indicating that Rgl11Y requires galactan decoration of the rhamnogalacturonan backbone
beta-eliminative cleavage of glycosidic bonds with the production of DELTA4,5 unsaturated sugar can be followed spectrophotometrically at 235 nm
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?
potato 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
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-
-
?
potato 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
Acetivibrio thermocellus DSM 1237
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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
RGL4 is involved in the degradation of rhamnogalacturonan-I, an important pectic plant cell wall polysaccharide
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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
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endolyase cleavage of the alpha-L-Rhap-(1->4)-alpha-D-GalpA glycosidic linkage in partially debranched sycamore rhamnogalacturonan I, thereby generating oligosaccharides terminating at the non-reducing end with a hex-4-enopyranosyluronic acid residue
backbone oligosaccharide fragments from partially debranched sycamore rhamnogalacturonan I, recombinant rhamnogalacturonan lyase releases partially galactosylated oligomers with an rhamnogalacturonan backbone of 4, 6, and 8 degree of polymerization from sycamore rhamnogalacturonan I
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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
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RG-lyase is active toward oligomers that contain at least six GalA units, i.e. degree of polymerization 12 with a GalA at the nonreducing and a Rha at the reducing end. The preferential cleavage site is for the smaller oligomers four residues, and for the largest oligomer six residues from the reducing Rha. From the observed cleavage patterns it can be speculated that in hairy regions, the rhamnogalacturonan stretches have to be at least 16 residues long for the RG-lyase in order to produce one tetramer
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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
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rhamnogalacturonan I domains in saponified hairy regions of apple pectin. The enzyme fragments rhamnogalacturonan I by a multiple attack mechanism. The catalytic efficiency of recombinant rhamnogalacturonan lyase increases with decreasing degree of acetylation. Removal of arabinose side chains improves the action of recombinant rhamnogalacturonan lyase. Removal of galactose side chains decreases the catalytic efficiency of recombinant rhamnogalacturonanlyase. The average degree of multiple attack is 2.5 (the degree of multiple attack is defined as the average number of catalytic events, following the first, during the lifetime of an individual enzyme-substrate complex)
major oligomeric reaction products contain an alternating rhamnogalacturonan backbone with a degree of polymerization of 4, 6, 8, and 10 and with an alpha-D-(4,5)-unsaturated D-galactopyranosyluronic acid at the nonreducing end and an L-rhamnopyranose at the reducing end
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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
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rhamnogalacturonase B cleaves alpha-L-Rhap-(1->4)-alpha-D-GalpA bond of rhamnogalacturonan I domains (rhamnogalacturonan backbone) in ramified hairy regions of pectin. Pectin consists of three distinct domains: homogalacturonan (smooth region), rhamnogalacturonan I (RG-I, hairy region), and rhamnogalacturonan-II. Rhamnogalacturonan I consists of repeating stretches of (1->4)-alpha-D-galacturonate-(1->2)-alpha-L-rhamnose dimers in which L-arabinose- and D-galactose-rich side chains may be attached to the rhamnose residues
eliminative cleavage alpha-L-Rhap-(1->4)-alpha-D-GalpA bond of rhamnogalacturonan I domains in ramified hairy regions of pectin leaving rhamnose at the nonreducing end and unsaturated galacturonic acid at the nonreducing end
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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 actual size of the average oligosaccharide is a 25-mer to 30-mer (Mr= 4600 Da), indicating that some of the rhamnogalacturonan regions have a structure recalcitrant to degradation. Domain I of RGL4 contributes the catalytic and many substrate binding residues, but domain III contributes two conserved arginines also involved in substrate binding. Domain II mediates the correct respective positioning of domains I and III
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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
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
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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 lyase produced by plant pathogenic and saprophytic microbes plays an important role in degrading plant cell walls
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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 lyases degrades rhamnogalacturonan I, a major component of pectin, through a beta-elimination reaction
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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 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
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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
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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-
?
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
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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 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
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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
apple-derived and potato-derived rhamnogalacturonan substrates. The enzyme has a strong preference for rhamnogalacturonans that contain galactose side chains, and which are not esterified. The increase in absorbance at 235 nm indicates that glycosidic bond cleavage is mediated via a beta-elimination mechanism
-
-
?
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
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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
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(GR)n oligomers, where n = 7, 8 or 9, prelabeled with fluorescent 8-aminopyrene-1,3,6-trisulfonic acid, trisodium salt tags are injected into the intercellular spaces in cotton cotyledons, degradation of the oligomers is observed by capillary zone electrophoresis. Rhamnogalacturonan lyase products are identified as such by co-migration with the digestion products of linear rhamnogalacturonan oligomers when the oligomers are treated with fungal RG lyase but not when treated with fungal rhamnogalacturonan hydrolase
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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
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beta-eliminative cleavage of the alpha-L-Rhap-(1->4)-alpha-D-GalpA glycosidic bond in the backbone of rhamnogalacturonan I (RGI) via a beta-elimination mechanism. Its specific activity on potato pectic galactan and rhamnogalacturonan is 28 and 3.6 IU/mg, respectively, indicating that Rgl11Y requires galactan decoration of the rhamnogalacturonan backbone
beta-eliminative cleavage of glycosidic bonds with the production of DELTA4,5 unsaturated sugar can be followed spectrophotometrically at 235 nm
-
?
soybean 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
-
-
-
?
soybean 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
Acetivibrio thermocellus DSM 1237
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?
additional information
?
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no activity toward polygalacturonic acid at pH 6 or pH 8 either with or without 1 mM Ca2+ in the reaction mixture
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-
?
additional information
?
-
the purified enzyme is not able to provoke maceration of potato tubers or chicory leaves. No activity with polygalacturonate, pectin or arabinogalactan
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?
additional information
?
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the purified enzyme is not able to provoke maceration of potato tubers or chicory leaves. No activity with polygalacturonate, pectin or arabinogalactan
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?
additional information
?
-
no substrate: homogalacturonan
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?
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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
RGL4 is involved in the degradation of rhamnogalacturonan-I, an important pectic plant cell wall polysaccharide
-
-
?
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
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
-
-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ca2+
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+
Ca2+
3 mM, 1.5fold activation of wild-type, 1.3fold activation of truncated mutant protein of 63900 Da
Ca2+
a calcium ion coordinated by Asp401, Glu422, His363, and His399 may be required for the enzyme activity
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
EDTA
-
completely abolishes activity against potato pectic galactan
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
degalactosylated rhamnogalacturonan
Km value 0.74 mg/ml, pH 7.0, 37°C
-
additional information
degalactosylated rhamnogalacturonan
-
Km value 0.74 mg/ml, pH 7.0, 37°C
-
additional information
pectic galactan
Km value of wild-type 10 mg/ml, of truncated mutant 11.2 mg/ml, respectively, pH 8.5, 70°C
-
additional information
Pectin
Km value of wild-type 8.2 mg/ml, of truncated mutant 7.6 mg/ml, respectively, pH 8.5, 70°C
additional information
potato galactan
Km value of wild-type 4.7 mg/ml, of truncated mutant 6.4 mg/ml, respectively, pH 8.5, 70°C
-
additional information
potato pectic galactan
-
Km-value: 1 g/l, pH 8.5, 37°C
-
additional information
potato pectic galactan
KM-value: 8.5 mg/ml at pH 9.5
-
additional information
potato pectic galactan
-
KM-value: 8.5 mg/ml at pH 9.5
-
additional information
potato rhamnogalacturonan I
Km value of wild-type 4.9 mg/ml, of truncated mutant 6.0 mg/ml, respectively, pH 8.5, 70°C
-
additional information
rhamnogalacturonan
Km value 1.67 mg/ml, pH 7.0, 37°C
-
additional information
rhamnogalacturonan
-
Km value 1.67 mg/ml, pH 7.0, 37°C
-
additional information
rhamnogalacturonan I
KM-value is 0.181 mg/ml, pH 7.5, 30°C
-
additional information
rhamnogalacturonan I
Km-value is 0.35 mg/ml, pH 7.5, 30°C
-
additional information
rhamnogalacturonan I
Km-value is 1.3 mg/ml or 0.27 mM cleavable bonds, pH 6.0, 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
-
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
-
additional information
rhamnogalacturonan I
-
KM-values of recombinant rhamnogalacturonan lyase towards enzyme-treated saponified modified hairy regions of pectin
-
additional information
soybean rhamnogalacturonan I
Km value of wild-type 4.8 mg/ml, of truncated mutant 5.1 mg/ml, respectively, pH 8.5, 70°C
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
6
potato rhamnogalacturonan I
truncated mutant, pH 8.5, 70°C
-
6.9
soybean rhamnogalacturonan I
truncated mutant, pH 8.5, 70°C
-
additional information
potato pectic galactan
kcat-value: 6500/s at pH 9.5
-
additional information
potato pectic galactan
-
kcat-value: 6500/s at pH 9.5
-
additional information
rhamnogalacturonan I
kcat-value is 4.1/s, pH 6.0, 30°C
-
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
pectic galactan
kcat/Km value of wild-type 0.77 ml/mg/s, of truncated mutant 0.43 ml/mg/s, respectively, pH 8.5, 70°C
-
additional information
Pectin
kcat/Km value of wild-type 1.19 ml/mg/s, of truncated mutant 0.3 ml/mg/s, respectively, pH 8.5, 70°C
additional information
potato galactan
kcat/Km value of wild-type 1.36 ml/mg/s, of truncated mutant 0.32 ml/mg/s, respectively, pH 8.5, 70°C
-
additional information
potato rhamnogalacturonan I
kcat/Km value of wild-type 4.28 ml/mg/s, of truncated mutant 1.13 ml/mg/s, respectively, pH 8.5, 70°C
-
additional information
soybean rhamnogalacturonan I
kcat/Km value of wild-type 4.1 ml/mg/s, of truncated mutant 1.35 ml/mg/s, respectively, pH 8.5, 70°C
-
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
4.5
substrate soybean rhamnogalacturonan I, pH 8.5, temperature not specified in the publication
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
8.5
8
-
lyase activity toward saponified modified hairy regions from apple pectin is 20% higher in 20 mM Tris-HCl buffer, pH 8, than in 50 mM NaOAc buffer, pH 6
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
10
-
completely inactive at, substrate: potato pectic galactan
7 - 9
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
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
50
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
40 - 75
40°C: about 45% of maximal activity, 75°C: about 50% of maximal activity
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
RhiE is present in one-third of the strains tested
SwissProt
brenda
RhiE is present in one-third of the strains tested
SwissProt
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
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
brenda
highest expression levels are observed in leaves and roots
brenda
highest expression levels are observed in leaves and roots
brenda
additional information
additional information
highest expression levels are observed at 10 and 20 days after anthesis
brenda
additional information
-
highest expression levels are observed at 10 and 20 days after anthesis
brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
Rgl11Y is incorporated in the Clostridium cellulolyticum cellulosome through a typical cohesin-dockerin interaction
brenda
RhiE is secreted through the type II Out secretion pathway. RhiE has no disulfide bond. The absence of RhiE secretion in a dsb mutant indicates that disulfide bond formation is required for the biogenesis of the secretion apparatus
-
brenda
-
RhiE is secreted through the type II Out secretion pathway. RhiE has no disulfide bond. The absence of RhiE secretion in a dsb mutant indicates that disulfide bond formation is required for the biogenesis of the secretion apparatus
-
-
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
physiological function
malfunction
reduced virulence of the rhiE mutant indicates that degradation of the RG-I region of pectin is important for full virulence of Erwinia chrysanthemi
malfunction
-
reduced virulence of the rhiE mutant indicates that degradation of the RG-I region of pectin is important for full virulence of Erwinia chrysanthemi
-
physiological function
reduced virulence of the rhiE mutant indicates that degradation of the RG-I region of pectin is important for full virulence of Erwinia chrysanthemi
physiological function
both the full-length Rgl protein (80000 Da) and its truncated derivative (63900 Da) display maximum activity against rhamnogalacturonan I
physiological function
expression of the Solyc11g011300 gene under a constitutive promoter in tomato cv. Ohio 8245. Transgenic lines exhibit lower rhamnogalacturonan lyase activity in leaves and roots and during fruit ripening, but higher activity is observed at 10, 20, and 30 days after anthesis than in the isogenic line and positive control. Transgenic lines show a lower number of seeds and fruits, higher root length, and less pollen germination percentage and viability. In red ripe tomatoes, transgenic fruits show greater firmness, longer shelf life, and reduced shriveling than wild-type. Additionally, a delay of one week in fruit ripening in transgenic fruits is also recorded
physiological function
hot buffer-soluble solids from cell wall material of transgenic Solanum tuberosum lines expressing rhamno-galacturonan lyase mutant contain 27% more galacturonic acid and 55% less galactose on fresh potato weight basis, due to the removal of galactan-rich rhamnogalacturonan I segments. All pectin populations of the transgenic strain show consistently low levels of rhamnogalacturonan I segments
physiological function
Acetivibrio thermocellus DSM 1237
-
both the full-length Rgl protein (80000 Da) and its truncated derivative (63900 Da) display maximum activity against rhamnogalacturonan I
-
physiological function
-
reduced virulence of the rhiE mutant indicates that degradation of the RG-I region of pectin is important for full virulence of Erwinia chrysanthemi
-
Show AA Sequence and Transmembrane Helices (4419 entries)
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
55000
64444
64444
1 * 64444, mature form of YesW including the C-terminal 8His-tag
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
monomer
1 * 64444, mature form of YesW including the C-terminal 8His-tag
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POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
no glycoprotein
protein does not contain N-linked carbohydrates
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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
-
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
rhamnogalacturonan lyase reveals a unique three-domain modular structure for polysaccharide lyase family 4
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
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
expression of a protein derivative without the N-terminal Dockerin I. Truncated protein has a molecular mass of 63900 Da
additional information
Acetivibrio thermocellus DSM 1237
-
expression of a protein derivative without the N-terminal Dockerin I. Truncated protein has a molecular mass of 63900 Da
-
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
40
60
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Aspergillus oryzae
expression in Escherichia coli
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
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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
-
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
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
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
-
-
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
food industry
-
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
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Kadirvelraj, R.; Harris, P.; Poulsen, J.C.; Kauppinen, S.; Larsen, S.
A stepwise optimization of crystals of rhamnogalacturonan lyase from Aspergillus aculeatus
Acta Crystallogr. Sect. D
58
1346-1349
2002
Aspergillus aculeatus
brenda
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)
brenda
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)
brenda
McKie, V.A.; Vincken, J.P.; Voragen, A.G.; van den Broek, L.A.; Stimson, E.; Gilbert, H.J.
A new family of rhamnogalacturonan lyases contains an enzyme that binds to cellulose
Biochem. J.
355
167-177
2001
Cellvibrio japonicus (Q9AF09), Cellvibrio japonicus
brenda
Mutter, M.; Renard, C.M.; Beldman, G.; Schols, H.A.; Voragen, A.G.
Mode of action of RG-hydrolase and RG-lyase toward rhamnogalacturonan oligomers. Characterization of degradation products using RG-rhamnohydrolase and RG-galacturonohydrolase
Carbohydr. Res.
311
155-164
1998
Aspergillus aculeatus
brenda
McDonough, M.A.; Kadirvelraj, R.; Harris, P.; Poulsen, J.C.; Larsen, S.
Rhamnogalacturonan lyase reveals a unique three-domain modular structure for polysaccharide lyase family 4
FEBS Lett.
565
188-194
2004
Aspergillus aculeatus (Q00019), Aspergillus aculeatus
brenda
Azadi, P.; O'Neill, M.A.; Bergmann, C.; Darvill, A.G.; Albersheim, P.
The backbone of the pectic polysaccharide rhamnogalacturonan I is cleaved by an endohydrolase and an endolyase
Glycobiology
5
783-789
1995
Aspergillus aculeatus
brenda
Laatu, M.; Condemine, G.
Rhamnogalacturonate lyase RhiE is secreted by the out system in Erwinia chrysanthemi
J. Bacteriol.
185
1642-1649
2003
Dickeya chrysanthemi (Q8RJP2), Dickeya chrysanthemi 3937 (Q8RJP2)
brenda
Pages, S.; Valette, O.; Abdou, L.; Belaich, A.; Belaich, J.P.
A rhamnogalacturonan lyase in the Clostridium cellulolyticum cellulosome
J. Bacteriol.
185
4727-4733
2003
Ruminiclostridium cellulolyticum
brenda
Kofod, L.V.
Kauppinen, S.; Christgau, S.; Andersen, L.N.; Heldt-Hansen, H.P.; Drreich, K.; Dalboge, H.: Cloning and characterization of two structurally and functionally divergent rhamnogalacturonases from Aspergillus aculeatus
J. Biol. Chem.
269
29182-29189
1994
Aspergillus aculeatus (Q00019), Aspergillus aculeatus
brenda
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
brenda
Ochiai, A.; Itoh, T.; Mikami, B.; Hashimoto, W.; Murata, K.
Structural determinants responsible for substrate recognition and mode of action in family 11 polysaccharide lyases
J. Biol. Chem.
284
10181-10189
2009
Bacillus subtilis (O31526)
brenda
Jensen, M.H.; Otten, H.; Christensen, U.; Borchert, T.V.; Christensen, L.L.; Larsen, S.; Leggio, L.L.
Structural and biochemical studies elucidate the mechanism of rhamnogalacturonan lyase from Aspergillus aculeatus
J. Mol. Biol.
404
100-111
2010
Aspergillus aculeatus (Q00019)
brenda
Naran, R.; Pierce, M.L.; Mort, A.J.
Detection and identification of rhamnogalacturonan lyase activity in intercellular spaces of expanding cotton cotyledons
Plant J.
50
95-107
2007
Gossypium hirsutum
brenda
Mutter, M.; Colquhoun, I.J.
Schols, H.A.; Beldman, G.; Voragen, A.G.: Rhamnogalacturonase B from Aspergillus aculeatus is a rhamnogalacturonan alpha-L-rhamnopyranosyl-(1->4)-alpha-D-galactopyranosyluronide lyase
Plant Physiol.
110
73-77
1996
Aspergillus aculeatus
brenda
Mutter, M.; Colquhoun, I.J.; Beldman, G.; Schols, H.A.; Bakx, E.J.; Voragen, A.G.
Characterization of recombinant rhamnogalacturonan alpha-L-rhamnopyranosyl-(1,4)-alpha-D-galactopyranosyluronide lyase from Aspergillus aculeatus. An enzyme that fragments rhamnogalacturonan I regions of pectin
Plant Physiol.
117
141-152
1998
Aspergillus aculeatus
brenda
Yoshino-Yasuda, S.; Karita, S.; Kato, M.; Kitamoto, N.
Sequence analysis and heterologous expression of rhamnogalacturonan lyase a gene (AsrglA) from Shoyu Koji mold, Aspergillus sojae KBN1340
Food Sci. Technol. Res.
18
901-909
2012
Aspergillus sojae (I2FIL2), Aspergillus sojae KBN1340 (I2FIL2)
-
brenda
Huang, J.H.; Kortstee, A.; Dees, D.C.; Trindade, L.M.; Schols, H.A.; Gruppen, H.
Modification of potato cell wall pectin by the introduction of rhamnogalacturonan lyase and beta-galactosidase transgenes and their side effects
Carbohydr. Polym.
144
9-16
2016
Aspergillus aculeatus (Q00019)
brenda
Ochoa-Jimenez, V.A.; Berumen-Varela, G.; Burgara-Estrella, A.; Orozco-Avitia, J.A.; Ojeda-Contreras, A.J.; Trillo-Hernandez, E.A.; Rivera-Dominguez, M.; Troncoso-Rojas, R.; Baez-Sanudo, R.; Datsenka, T.; Handa, A.K.; Tiznado-Hernandez, M.E.
Functional analysis of tomato rhamnogalacturonan lyase gene Solyc11g011300 during fruit development and ripening
J. Plant Physiol.
231
31-40
2018
Solanum lycopersicum (A0A3Q7IRE2), Solanum lycopersicum
brenda
Iwai, M.; Yamada, H.; Ikemoto, T.; Matsumoto, S.; Fujiwara, D.; Takenaka, S.; Sakamoto, T.
Biochemical characterization and overexpression of an endo-rhamnogalacturonan lyase from Penicillium chrysogenum
Mol. Biotechnol.
57
539-548
2015
Penicillium chrysogenum (W8VJU1), Penicillium chrysogenum
brenda
Dhillon, A.; Fernandes, V.O.; Dias, F.M.; Prates, J.A.; Ferreira, L.M.; Fontes, C.M.; Centeno, M.S.; Goyal, A.
A New member of family 11 polysaccharide lyase, rhamnogalacturonan lyase (CtRGLf) from Clostridium thermocellum
Mol. Biotechnol.
58
232-240
2016
Acetivibrio thermocellus (A3DC06), Acetivibrio thermocellus DSM 1237 (A3DC06)
brenda
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