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Information on EC 4.2.2.23 - rhamnogalacturonan endolyase and Organism(s) Aspergillus aculeatus and UniProt Accession Q00019
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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
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beta-elimination
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pectic
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hairy
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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 taxonomic range for the selected organisms is: Aspergillus aculeatus
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, rgl11y, solyc11g011300, rhamnogalacturonase b, rgl11a, rhamnogalacturonan lyase a, rhamnogalacturonan endolyase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
alpha-L-rhamnopyranosyl-(1->4)-alpha-D-galactopyranosyluronide lyase
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rhamnogalacturonan alpha-L-rhamnopyranosyl-(1,4)-alpha-D-galactopyranosyluronide lyase
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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.
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
additional information
?
-
-
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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-
?
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
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
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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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?
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
RGL4 is involved in the degradation of rhamnogalacturonan-I, an important pectic plant cell wall polysaccharide
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?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
rhamnogalacturonan I
Km-value is 1.3 mg/ml or 0.27 mM cleavable bonds, pH 6.0, 30°C
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additional information
rhamnogalacturonan I
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KM-values of recombinant rhamnogalacturonan lyase towards enzyme-treated saponified modified hairy regions of pectin
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
rhamnogalacturonan I
kcat-value is 4.1/s, pH 6.0, 30°C
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
8
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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
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). RGLA_ASPAC
527
0
56190
Swiss-Prot
Secretory Pathway (Reliability: 2)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
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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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
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
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
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
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
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
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
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)
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
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
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)
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