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Literature summary extracted from

  • Silva, I.R.; Jers, C.; Meyer, A.S.; Mikkelsen, J.D.
    Rhamnogalacturonan I modifying enzymes an update (2016), New Biotechnol., 33, 41-54 .
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
3.2.1.171 phylogenetic analysis Aspergillus aculeatus
3.2.1.171 phylogenetic analysis Aspergillus niger
3.2.1.172 phylogenetic analysis Bacillus subtilis
3.2.1.173 phylogenetic analysis Aspergillus aculeatus
3.2.1.174 phylogenetic analysis Aspergillus aculeatus

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.2.1.172 0.1
-
 2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose pH 4.0, 30°C Bacillus subtilis
3.2.1.172 0.719
-
 2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose pH 6.0, 30°C Bacillus subtilis
3.2.1.173 0.085
-
 rhamnogalacturonan I pH 5.0, 40°C Aspergillus aculeatus
3.2.1.173 0.23
-
 MHR-S pH 5.0, 40°C Aspergillus aculeatus

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.2.1.171 rhamnogalacturonan I + H2O Aspergillus aculeatus 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 ?
-
 ?
3.2.1.171 rhamnogalacturonan I + H2O Aspergillus niger 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 ?
-
 ?
3.2.1.172 2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + H2O Bacillus subtilis
-
 5-dehydro-4-deoxy-D-glucuronate + L-rhamnopyranose
-
 ?
3.2.1.172 rhamnogalacturonan I + H2O Bacillus subtilis 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 beta-L-rhamnose + ?
-
 ?
3.2.1.173 rhamnogalacturonan I + H2O Aspergillus aculeatus 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 ?
-
 ?
3.2.1.174 rhamnogalacturonan I + H2O Aspergillus aculeatus 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 beta-L-rhamnose + ?
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
3.2.1.171 Aspergillus aculeatus P87161
-
-
3.2.1.171 Aspergillus aculeatus Q00001
-
-
3.2.1.171 Aspergillus niger P87160
-
-
3.2.1.172 Bacillus subtilis O31521
-
-
3.2.1.172 Bacillus subtilis O34559
-
-
3.2.1.173 Aspergillus aculeatus
-
-
-
3.2.1.174 Aspergillus aculeatus
-
-
-

Reaction

EC Number Reaction Comment Organism Reaction ID
3.2.1.171 Endohydrolysis of alpha-D-GalA-(1->2)-alpha-L-Rha glycosidic bond in the rhamnogalacturonan I backbone with initial inversion of anomeric configuration releasing oligosaccharides with beta-D-GalA at the reducing end mode of action and site of action, overview. RGI endo-hydrolases, RGHs, attack the RGI backbone randomly in an endo-fashion and catalyse bond cleavage of alpha-(1->2) glycosidic bonds between D-GalpA and L-Rhap. The mechanism involves an inversion of the anomeric C1 configuration in galacturonic acid releasing oligosaccharides with beta-D-GalpA at the reducing end and L-Rhap at the non-reducing end as products Aspergillus aculeatus
a
3.2.1.171 Endohydrolysis of alpha-D-GalA-(1->2)-alpha-L-Rha glycosidic bond in the rhamnogalacturonan I backbone with initial inversion of anomeric configuration releasing oligosaccharides with beta-D-GalA at the reducing end mode of action and site of action, overview. RGI endo-hydrolases, RGHs, attack the RGI backbone randomly in an endo-fashion and catalyse bond cleavage of alpha-(1->2) glycosidic bonds between D-GalpA and L-Rhap. The mechanism involves an inversion of the anomeric C1 configuration in galacturonic acid releasing oligosaccharides with beta-D-GalpA at the reducing end and L-Rhap at the non-reducing end as products Aspergillus niger
a
3.2.1.172 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 Bacillus subtilis
a
3.2.1.172 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 Bacillus subtilis
a
3.2.1.173 Exohydrolysis of the alpha-D-GalA-(1->2)-alpha-L-Rha bond in rhamnogalacturonan oligosaccharides with initial inversion of configuration releasing D-galacturonic acid from the non-reducing end of rhamnogalacturonan oligosaccharides mode of action and site of action, overview. RGI endo-hydrolases, RGHs, attack the RGI backbone randomly in an endo-fashion and catalyse bond cleavage of alpha-(1->2) glycosidic bonds between D-GalpA and L-Rhap. The mechanism involves an inversion of the anomeric C1 configuration in galacturonic acid releasing oligosaccharides with beta-D-GalpA at the reducing end and L-Rhap at the non-reducing end as products Aspergillus aculeatus
a
3.2.1.174 Exohydrolysis of the alpha-L-Rha-(1->4)-alpha-D-GalA bond in rhamnogalacturonan oligosaccharides with initial inversion of configuration releasing beta-L-rhamnose from the non-reducing end of rhamnogalacturonan oligosaccharides mode of action and site of action, overview Aspergillus aculeatus
a

Specific Activity [micromol/min/mg]

EC Number Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
3.2.1.171 0.4
-
 substrate MHR-S, pH 4.5, 30°C Aspergillus aculeatus
3.2.1.171 0.9
-
 substrate MHR-S, pH 4.5, 30°C Aspergillus niger
3.2.1.171 2.5
-
 substrate MHR-S, pH 4.5, 30°C Aspergillus aculeatus
3.2.1.173 16
-
 substrate MHR-S, pH 5.0, 40°C Aspergillus aculeatus
3.2.1.173 21
-
 substrate rhamnogalacturonan I, pH 5.0, 40°C Aspergillus aculeatus
3.2.1.174 12.9
-
 substrate MHR-S, pH 5.0, 60°C Aspergillus aculeatus
3.2.1.174 57.6
-
 substrate degalactosylated MHR-S, pH 5.0, 60°C Aspergillus aculeatus

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.2.1.171 MHR-S + H2O i.e. saponified modified hairy regions of rhamnogalacturonan I, from apple pectin, residue remaining after enzymatic liquefaction of pectin Aspergillus aculeatus ?
-
 ?
3.2.1.171 MHR-S + H2O i.e. saponified modified hairy regions of rhamnogalacturonan I, from apple pectin, residue remaining after enzymatic liquefaction of pectin Aspergillus niger ?
-
 ?
3.2.1.171 additional information RGI endo-hydrolases, RGHs, attack the RGI backbone randomly in an endo-fashion and catalyse bond cleavage of alpha-(1->2) glycosidic bonds between D-GalpA and L-Rhap. The mechanism involves an inversion of the anomeric C1 configuration in galacturonic acid releasing oligosaccharides with beta-D-GalpA at the reducing end and L-Rhap at the non-reducing end as products Aspergillus niger ?
-
 ?
3.2.1.171 additional information RGI endo-hydrolases, RGHs, attack the RGI backbone randomly in an endo-fashion and catalyse bond cleavage of alpha-(1->2) glycosidic bonds between D-GalpA and L-Rhap. The mechanism involves an inversion of the anomeric C1 configuration in galacturonic acid releasing oligosaccharides with beta-D-GalpA at the reducing end and L-Rhap at the non-reducing end as products Aspergillus aculeatus ?
-
 ?
3.2.1.171 additional information RGI endo-hydrolases, RGHs, attack the RGI backbone randomly in an endo-fashion and catalyse bond cleavage of alpha-(1->2) glycosidic bonds between D-GalpA and L-Rhap. The mechanism involves an inversion of the anomeric C1 configuration in galacturonic acid releasing oligosaccharides with beta-D-GalpA at the reducing end and L-Rhap at the non-reducing end as products. Aspergillus aculeatus RhgA catalyses the hydrolytic cleavage of the alpha-D-GalpA-(1->2)-alpha-L-Rhap glycosidic linkages thus releasing (oligomeric) products with Rhap at the non-reducing end Aspergillus aculeatus ?
-
 ?
3.2.1.171 rhamnogalacturonan I + H2O
-
 Aspergillus aculeatus ?
-
 ?
3.2.1.171 rhamnogalacturonan I + H2O
-
 Aspergillus niger ?
-
 ?
3.2.1.171 rhamnogalacturonan I + H2O 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 Aspergillus aculeatus ?
-
 ?
3.2.1.171 rhamnogalacturonan I + H2O 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 Aspergillus niger ?
-
 ?
3.2.1.172 2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + H2O
-
 Bacillus subtilis 5-dehydro-4-deoxy-D-glucuronate + L-rhamnopyranose
-
 ?
3.2.1.172 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) Bacillus subtilis ?
-
 ?
3.2.1.172 rhamnogalacturonan I + H2O 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 Bacillus subtilis beta-L-rhamnose + ?
-
 ?
3.2.1.172 rhamnogalacturonan I + H2O
-
 Bacillus subtilis L-rhamnose + ?
-
 ?
3.2.1.173 MHR-S + H2O i.e. saponified modified hairy regions of rhamnogalacturonan I, from apple pectin, residue remaining after enzymatic liquefaction of pectin Aspergillus aculeatus D-galactose + ?
-
 ?
3.2.1.173 additional information RGI endo-hydrolases, RGHs, attack the RGI backbone randomly in an endo-fashion and catalyse bond cleavage of alpha-(1->2) glycosidic bonds between D-GalpA and L-Rhap. The mechanism involves an inversion of the anomeric C1 configuration in galacturonic acid releasing oligosaccharides with beta-D-GalpA at the reducing end and L-Rhap at the non-reducing end as products. The RGGH type of exo-enzyme cleaves off the terminal nonreducing galacturonosyl residue by catalysing cleavage of alpha-(1->2) glycosidic bonds between D-GalpA and L-Rhap in the non-reducing terminus, releasing single beta-D-GalpA. The RGGH from Aspergillus aculeatus is active towards different types of rhamnogalacturonan I (RGI), for example, pectin or pure RGI, except for the ones with unsaturated GalpA at the nonreducing end. The enzyme displays preference for smaller RGI substrates since it has higher activities towards RGI fragment DP6 than saponified modified hairy regions of rhamnogalacturonan I (MHR-S). Aspergillus aculeatus RGGH shows no activity towards HG sub-strates, for example, polygalacturonic acid or small size GalpA acid oligomers Aspergillus aculeatus ?
-
 ?
3.2.1.173 rhamnogalacturonan I + H2O 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 Aspergillus aculeatus ?
-
 ?
3.2.1.173 rhamnogalacturonan I + H2O RGI DP 6 Aspergillus aculeatus D-galactose + ?
-
 ?
3.2.1.174 degalactosylated MHR-S + H2O degalactosylated saponified modified hairy regions of xylogalacturonan, from apple pectin, residue remaining after enzymatic liquefaction of pectin, galactosyl residues removed. The activity increases 78% when tested with MHR-S without galactose substitutions, and in essence the activity of this enzyme is thus hindered by galactose substitutions Aspergillus aculeatus beta-L-rhamnose + ?
-
 ?
3.2.1.174 MHR + H2O i.e. modified hairy regions of xylogalacturonan, from apple pectin, residue remaining after enzymatic liquefaction of pectin, the enzyme is active towards MHR-S as well as unsaponified MHR Aspergillus aculeatus beta-L-rhamnose + ?
-
 ?
3.2.1.174 MHR-S + H2O i.e. saponified modified hairy regions of xylogalacturonan, from apple pectin, residue remaining after enzymatic liquefaction of pectin, the enzyme is active towards MHR-S as well as unsaponified MHR Aspergillus aculeatus beta-L-rhamnose + ?
-
 ?
3.2.1.174 additional information RGRH exo-enzyme catalyses the cleavage of the alpha-(1->4) glycosidic bonds between L-Rhap and D-GalpA in the non-reducing terminus, releasing single beta-L-Rhap. Enzyme RGRH requires Rhap at the non-reducing end for action Aspergillus aculeatus ?
-
 ?
3.2.1.174 rhamnogalacturonan I + H2O 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 Aspergillus aculeatus beta-L-rhamnose + ?
-
 ?
3.2.1.174 rhamnogalacturonan I + H2O Aspergillus aculeatus RGRH is active on the nonreducing end Rhap-linkage in RGI fragments Aspergillus aculeatus L-rhamnose + ?
-
 ?

Subunits

EC Number Subunits Comment Organism
3.2.1.171 ? x * 47000 Aspergillus niger
3.2.1.171 ? x * 46000 Aspergillus aculeatus
3.2.1.171 ? x * 58000 Aspergillus aculeatus
3.2.1.171 More structure analysis, overview Aspergillus aculeatus
3.2.1.172 ? x * 43000 Bacillus subtilis
3.2.1.172 ? x * 39000 Bacillus subtilis
3.2.1.172 More enzyme URGH from GH105 has a alpha/alpha double toroid structure with six-a-hairpins arranged in a double helical barrel Bacillus subtilis
3.2.1.172 More enzyme URGH from GH105 has a alpha/alpha double toroid structure with six-alpha-hairpins arranged in a double helical barrel, overview Bacillus subtilis
3.2.1.173 ? x * 66000 Aspergillus aculeatus
3.2.1.174 ? x * 84000 Aspergillus aculeatus

Synonyms

EC Number Synonyms Comment Organism
3.2.1.171 RGH
-
 Aspergillus aculeatus
3.2.1.171 RGH
-
 Aspergillus niger
3.2.1.171 RGI endo-hydrolase
-
 Aspergillus aculeatus
3.2.1.171 RGI endo-hydrolase
-
 Aspergillus niger
3.2.1.171 RGI hydrolase
-
 Aspergillus aculeatus
3.2.1.171 RGI hydrolase
-
 Aspergillus niger
3.2.1.171 RhgA
-
 Aspergillus aculeatus
3.2.1.171 RhgA
-
 Aspergillus niger
3.2.1.171 RhgA_An
-
 Aspergillus niger
3.2.1.171 RhgB
-
 Aspergillus aculeatus
3.2.1.171 RhgB_An
-
 Aspergillus aculeatus
3.2.1.172 RGI hydrolase
-
 Bacillus subtilis
3.2.1.172 URGH
-
 Bacillus subtilis
3.2.1.172 YesR
-
 Bacillus subtilis
3.2.1.172 YteR
-
 Bacillus subtilis
3.2.1.173 RGGH
-
 Aspergillus aculeatus
3.2.1.173 RGI exo-hydrolase
-
 Aspergillus aculeatus
3.2.1.173 RGI galacturonohydrolase
-
 Aspergillus aculeatus
3.2.1.173 RGI hydrolase
-
 Aspergillus aculeatus
3.2.1.174 RGI exo-hydrolase
-
 Aspergillus aculeatus
3.2.1.174 RGI hydrolase
-
 Aspergillus aculeatus
3.2.1.174 RGI rhamnohydrolase
-
 Aspergillus aculeatus
3.2.1.174 RGRH
-
 Aspergillus aculeatus

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
3.2.1.171 30 50
-
 Aspergillus aculeatus
3.2.1.172 50
-
-
 Bacillus subtilis
3.2.1.173 50
-
-
 Aspergillus aculeatus
3.2.1.174 60
-
-
 Aspergillus aculeatus

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
3.2.1.173 60
-
 completely stable at for 3 h Aspergillus aculeatus
3.2.1.174 60
-
 pH 5.0, 1 h, stable Aspergillus aculeatus

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.2.1.171 3.5
-
-
 Aspergillus aculeatus
3.2.1.171 3.6
-
-
 Aspergillus niger
3.2.1.171 4.1
-
-
 Aspergillus aculeatus
3.2.1.172 additional information
-
 residues Asp88 and Tyr41 may modulate the pKa of Asp143 in YteR thereby inducing the lower pH optimum of this enzyme Bacillus subtilis
3.2.1.172 4
-
-
 Bacillus subtilis
3.2.1.172 6
-
-
 Bacillus subtilis
3.2.1.173 4
-
-
 Aspergillus aculeatus
3.2.1.174 4
-
-
 Aspergillus aculeatus

pH Stability

EC Number pH Stability pH Stability Maximum Comment Organism
3.2.1.173 6
-
 stable up to, unstable above Aspergillus aculeatus
3.2.1.174 3 5 stable at, unstable below and above that range Aspergillus aculeatus

pI Value

EC Number Organism Comment pI Value Maximum pI Value
3.2.1.171 Aspergillus niger
-
-
 4
3.2.1.171 Aspergillus aculeatus
-
-
 4.2
3.2.1.171 Aspergillus aculeatus
-
-
 4.6
3.2.1.172 Bacillus subtilis
-
-
 4.9
3.2.1.172 Bacillus subtilis
-
-
 5.9
3.2.1.173 Aspergillus aculeatus
-
-
 5.1
3.2.1.174 Aspergillus aculeatus
-
 5.4 4.9

General Information

EC Number General Information Comment Organism
3.2.1.171 evolution phylogenetic and structural traits of RGI hydrolases, overview Aspergillus aculeatus
3.2.1.171 evolution phylogenetic and structural traits of RGI hydrolases, overview Aspergillus niger
3.2.1.172 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 Bacillus subtilis
3.2.1.172 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 Bacillus subtilis
3.2.1.172 additional information in the active site of YesR Asp135 is most likely functioning as proton donor Bacillus subtilis
3.2.1.172 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 Bacillus subtilis
3.2.1.173 evolution phylogenetic and structural traits of RGI hydrolases, overview. The enzyme belongs to the glycosyl hydrolase family 28, GH28 Aspergillus aculeatus
3.2.1.174 evolution phylogenetic and structural traits of RGI hydrolases, overview. The enzyme belongs to the glycosyl hydrolase family 28, GH28 Aspergillus aculeatus