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Information on EC 3.2.1.172 - unsaturated rhamnogalacturonyl hydrolase and Organism(s) Bacillus subtilis and UniProt Accession O34559
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3.2.1.172 unsaturated rhamnogalacturonyl hydrolaseIUBMB Comments
The enzyme is part of the degradation system for rhamnogalacturonan I in Bacillus subtilis strain 168.
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The taxonomic range for the selected organisms is: Bacillus subtilis
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Reaction Schemes
Synonyms
ca_c0359, unsaturated rhamnogalacturonyl hydrolase, 
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topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + H2O = 5-dehydro-4-deoxy-D-glucuronate + L-rhamnopyranose
mode of action and site of action, overview. In the active site of YteR Asp143 is most likely functioning as proton donor
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + H2O = 5-dehydro-4-deoxy-D-glucuronate + L-rhamnopyranose
mode of action and site of action, overview. In the active site of YesR Asp135 is most likely functioning as proton donor
PATHWAY SOURCE
PATHWAYS
-
-
SYSTEMATIC NAME
IUBMB Comments
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose hydrolase
The enzyme is part of the degradation system for rhamnogalacturonan I in Bacillus subtilis strain 168.
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
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + H2O
4-deoxy-alpha-L-threo-hex-4-enopyranuronate + alpha-L-rhamnopyranose
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + H2O
4-deoxy-alpha-L-threo-hex-4-enopyranuronate + L-rhamnopyranose
the enzyme is involved in the degradation of the rhamnogalacturonan I main chain in Bacillus subtilis
-
-
?
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + H2O
5-dehydro-4-deoxy-D-glucuronate + L-rhamnopyranose
-
-
-
?
rhamnogalacturonan I + H2O
beta-L-rhamnose + ?
RGI, degrading enzymes are active on the RGI backbone of pectin and are thus strictly specific for cleaving bonds in the repetitive [(1->2)-alpha-L-Rhap-(1->4)-alpha-D-GalpA-(1->2)] structure
-
-
?
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + H2O
4-deoxy-alpha-L-threo-hex-4-enopyranuronate + L-rhamnopyranose
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + H2O
5-dehydro-4-deoxy-D-glucuronate + L-rhamnopyranose
-
-
-
?
rhamnogalacturonan I + H2O
beta-L-rhamnose + ?
RGI, degrading enzymes are active on the RGI backbone of pectin and are thus strictly specific for cleaving bonds in the repetitive [(1->2)-alpha-L-Rhap-(1->4)-alpha-D-GalpA-(1->2)] structure
-
-
?
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + H2O
4-deoxy-alpha-L-threo-hex-4-enopyranuronate + alpha-L-rhamnopyranose
-
-
-
?
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + H2O
4-deoxy-alpha-L-threo-hex-4-enopyranuronate + alpha-L-rhamnopyranose
postulation of the enzyme reaction mechanism: YteR triggers the hydration of vinyl ether group in 4-deoxy-beta-L-threo-hex-4-enopyranuronose (DELTAGalA), but not of glycoside bond, by using Asp143 as a general acid and base catalyst. Asp143 donates proton to the double bond of 4-deoxy-beta-L-threo-hex-4-enopyranuronose as an acid catalyst and also deprotonates a water molecule as a base catalyst. Deprotonated water molecule attacks the C5 atom of 4-deoxy-beta-L-threo-hex-4-enopyranuronose
-
-
?
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + H2O
4-deoxy-alpha-L-threo-hex-4-enopyranuronate + L-rhamnopyranose
-
-
-
?
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + H2O
4-deoxy-alpha-L-threo-hex-4-enopyranuronate + L-rhamnopyranose
the enzyme is involved in the degradation of the rhamnogalacturonan I main chain in Bacillus subtilis
-
-
?
additional information
?
-
no activity with: DELTAGlcA-GalNAc, DELTAGlcA-GlcNAc, and DELTAGalA-(GalA)n
-
-
?
additional information
?
-
no activity with: DELTAGlcA-GalNAc, DELTAGlcA-GlcNAc, and DELTAGalA-(GalA)n
-
-
?
additional information
?
-
-
no activity with: DELTAGlcA-GalNAc, DELTAGlcA-GlcNAc, and DELTAGalA-(GalA)n
-
-
?
additional information
?
-
URGH is active only on RGI oligomers with alpha-DELTA4,5-unsaturated-GalpA (i.e. 2-O-(4-deoxy-beta-L-threo-hex-4-enopyra-nuronosyl)) at the non-reducing end. The URGH activity catalyses the cleavage of the alpha-(1->2) glycosidic bond between the DELTA4,5-unsaturated-GalpA and L-Rhap releasing single unsaturated DELTAGalpA (5-dehydro-4-deoxy-D-galacturonate)
-
-
?
additional information
?
-
URGH is active only on RGI oligomers with alpha-DELTA4,5-unsaturated-GalpA (i.e. 2-O-(4-deoxy-beta-L-threo-hex-4-enopyra-nuronosyl)) at the non-reducing end. The URGH activity catalyses the cleavage of the alpha-(1->2) glycosidic bond between the DELTA4,5-unsaturated-GalpA and L-Rhap releasing single unsaturated DELTAGalpA (5-dehydro-4-deoxy-D-galacturonate)
-
-
?
additional information
?
-
no activity with: DELTAGlcA-GalNAc, DELTAGlcA-GlcNAc, and DELTAGalA-(GalA)n
-
-
?
additional information
?
-
no activity with: DELTAGlcA-GalNAc, DELTAGlcA-GlcNAc, and DELTAGalA-(GalA)n
-
-
?
additional information
?
-
-
no activity with: DELTAGlcA-GalNAc, DELTAGlcA-GlcNAc, and DELTAGalA-(GalA)n
-
-
?
additional information
?
-
URGH is active only on RGI oligomers with alpha-DELTA4,5-unsaturated-GalpA (i.e. 2-O-(4-deoxy-beta-L-threo-hex-4-enopyra-nuronosyl)) at the non-reducing end. The URGH activity catalyses the cleavage of the alpha-(1->2) glycosidic bond between the DELTA4,5-unsaturated-GalpA and L-Rhap releasing single unsaturated DELTAGalpA (5-dehydro-4-deoxy-D-galacturonate)
-
-
?
additional information
?
-
URGH is active only on RGI oligomers with alpha-DELTA4,5-unsaturated-GalpA (i.e. 2-O-(4-deoxy-beta-L-threo-hex-4-enopyra-nuronosyl)) at the non-reducing end. The URGH activity catalyses the cleavage of the alpha-(1->2) glycosidic bond between the DELTA4,5-unsaturated-GalpA and L-Rhap releasing single unsaturated DELTAGalpA (5-dehydro-4-deoxy-D-galacturonate)
-
-
?
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
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + H2O
4-deoxy-alpha-L-threo-hex-4-enopyranuronate + L-rhamnopyranose
the enzyme is involved in the degradation of the rhamnogalacturonan I main chain in Bacillus subtilis
-
-
?
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + H2O
5-dehydro-4-deoxy-D-glucuronate + L-rhamnopyranose
-
-
-
?
rhamnogalacturonan I + H2O
beta-L-rhamnose + ?
RGI, degrading enzymes are active on the RGI backbone of pectin and are thus strictly specific for cleaving bonds in the repetitive [(1->2)-alpha-L-Rhap-(1->4)-alpha-D-GalpA-(1->2)] structure
-
-
?
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + H2O
4-deoxy-alpha-L-threo-hex-4-enopyranuronate + L-rhamnopyranose
the enzyme is involved in the degradation of the rhamnogalacturonan I main chain in Bacillus subtilis
-
-
?
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + H2O
5-dehydro-4-deoxy-D-glucuronate + L-rhamnopyranose
-
-
-
?
rhamnogalacturonan I + H2O
beta-L-rhamnose + ?
RGI, degrading enzymes are active on the RGI backbone of pectin and are thus strictly specific for cleaving bonds in the repetitive [(1->2)-alpha-L-Rhap-(1->4)-alpha-D-GalpA-(1->2)] structure
-
-
?
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.1
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose
30°C, pH 4.0
0.1
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose
pH 4.0, 30°C
0.719
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose
pH 6.0, 30°C
0.719
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose
30°C, pH 6.0
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.28
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose
30°C, pH 4.0
13.9
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose
30°C, pH 6.0
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2.8
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose
30°C, pH 4.0
19.3
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose
30°C, pH 6.0
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
residues Asp88 and Tyr41 may modulate the pKa of Asp143 in YteR thereby inducing the lower pH optimum of this enzyme
additional information
residues Asp88 and Tyr41 may modulate the pKa of Asp143 in YteR thereby inducing the lower pH optimum of this enzyme
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
4.8 - 7.2
pH 4.8: about 40% of maximal activity, pH 7.2: about 55% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
phylogenetic and structural traits of RGI hydrolases, overview. The enzyme belongs to the glycosyl hydrolase family 105, GH105. The URGH from GH105 has a alpha/alpha double toroid structure with six-a-hairpins arranged in a double helical barrel
evolution
phylogenetic and structural traits of RGI hydrolases, overview. The enzyme belongs to the glycosyl hydrolase family 105, GH105. Enzyme URGH from GH105 has a alpha/alpha double toroid structure with six-a-hairpins arranged in a double helical barrel
additional information
additional information
in the active site of YteR Asp143 is most likely functioning as proton donor. Residues Asp88 and Tyr41 may modulate the pKa of Asp143 in YteR thereby inducing the lower pH optimum of this enzyme
additional information
in the active site of YteR Asp143 is most likely functioning as proton donor. Residues Asp88 and Tyr41 may modulate the pKa of Asp143 in YteR thereby inducing the lower pH optimum of this enzyme
additional information
in the active site of YesR Asp135 is most likely functioning as proton donor
additional information
in the active site of YesR Asp135 is most likely functioning as proton donor
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
enzyme URGH from GH105 has a alpha/alpha double toroid structure with six-alpha-hairpins arranged in a double helical barrel, overview
additional information
enzyme URGH from GH105 has a alpha/alpha double toroid structure with six-alpha-hairpins arranged in a double helical barrel, overview
additional information
enzyme URGH from GH105 has a alpha/alpha double toroid structure with six-a-hairpins arranged in a double helical barrel
additional information
enzyme URGH from GH105 has a alpha/alpha double toroid structure with six-a-hairpins arranged in a double helical barrel
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion method, crystal structure of YteR complexed with unsaturated chondroitin disaccharide (substrate of bacterial unsaturated glucuronyl hydrolase). The substrate is sterically hindered with the active pocket of YteR. The protruding loop of YteR prevents the UGL substrate from being bound effectively
hanging drop vapor diffusion method, structure of D143N in complex with unsaturated rhamnogalacturonan disaccharide substrate 2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose is determined at 1.9 A resolution by X-ray crystallography
vapor diffusion hanging drop method, crystal structure is determined at 1.60 A by the multiwavelength anomalous dispersion method
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Itoh, T.; Ochiai, A.; Mikami, B.; Hashimoto, W.; Murata, K.
Structure of unsaturated rhamnogalacturonyl hydrolase complexed with substrate
Biochem. Biophys. Res. Commun.
347
1021-1029
2006
Bacillus subtilis (O34559), Bacillus subtilis 168 (O34559)
Itoh, T.; Ochiai, A.; Mikami, B.; Hashimoto, W.; Murata, K.
A novel glycoside hydrolase family 105: the structure of family 105 unsaturated rhamnogalacturonyl hydrolase complexed with a disaccharide in comparison with family 88 enzyme complexed with the disaccharide
J. Mol. Biol.
360
573-585
2006
Bacillus subtilis (O31521), Bacillus subtilis (O34559), Bacillus subtilis, Bacillus subtilis 168 (O31521), Bacillus subtilis 168 (O34559)
Zhang, R.; Minh, T.; Lezondra, L.; Korolev, S.; Moy, S.F.; Collart, F.; Joachimiak, A.
1.6 A crystal structure of YteR protein from Bacillus subtilis, a predicted lyase
Proteins
60
561-565
2005
Bacillus subtilis (O34559)
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