Literature summary extracted from

Nakamura, M.; Yasukawa, Y.; Furusawa, A.; Fuchiwaki, T.; Honda, T.; Okamura, Y.; Fujita, K.; Iwai, H.
Functional characterization of unique enzymes in Xanthomonas euvesicatoria related to degradation of arabinofurano-oligosaccharides on hydroxyproline-rich glycoproteins (2018), PLoS ONE, 13, e0201982 .

Cloned(Commentary)

EC Number	Cloned (Comment)	Organism
3.2.1.B48	gene XCV2728, belongs to operon xehypBA2-AA containing genes XCV2724, XCV2728, and XCV2729, DNA and amino acid sequence determination and analysis, and genetic structure. The promoter region of the operon (xehypBA2 and xehypAA) contains the plant-inducible promoter box for binding the regulator protein HrpX involved in pathogenicity. Recombinant expression of His-tagged wild-type and mutant enzymes without the signal peptide in Brevibacillus choshinensis strain SP3, recombinant expression of the operon in transgenic Solanum lycopersicum strain Micro-Tom	Xanthomonas euvesicatoria
3.2.1.185	gene XCV2724, belongs to operon xehypBA2-AA containing genes XCV2724, XCV2728, and XCV2729, DNA and amino acid sequence determination and analysis, and genetic structure, recombinant expression of wild-type and mutant enzymes without the signal peptide in Escherichia coli strain BL21(DE3), recombinant expression of the operon in transgenic Solanum lycopersicum strain Micro-Tom	Xanthomonas euvesicatoria
3.2.1.187	gene XCV2729, belongs to operon xehypBA2-AA containing genes XCV2724, XCV2728, and XCV2729, DNA and amino acid sequence determination and analysis, and genetic structure. The promoter region of the operon (xehypBA2 and xehypAA) contains the plant-inducible promoter box for binding the regulator protein HrpX involved in pathogenicity, recombinant expression of wild-type and mutant enzymes without the signal peptide and fused with the trigger factor chaperone in Escherichia coli strain BL21(DE3), recombinant expression of the operon in transgenic Solanum lycopersicum strain Micro-Tom	Xanthomonas euvesicatoria

Protein Variants

EC Number	Protein Variants	Comment	Organism
3.2.1.B48	additional information	construction of a single-gene deletion mutant, DELTAxehypAA and a triple-gene deletion mutant DELTAxehypBA1-BA2-AA. The mutants remain pathogenic, and mutations of the operon or the single genes XCV2724, XCV2728, and XCV2729 have no effect on nonhost resistance, either, indicating that these three enzymes are not involved in either pathogenicity or nonhost resistance reactions	Xanthomonas euvesicatoria
3.2.1.185	additional information	construction of a single-gene deletion mutant, DELTAxehypBA1 and a triple-gene deletion mutant DELTAxehypBA1-BA2-AA. The mutants remain pathogenic, and mutations of the operon or the single genes XCV2724, XCV2728, and XCV2729 have no effect on nonhost resistance, either, indicating that these three enzymes are not involved in either pathogenicity or nonhost resistance reactions	Xanthomonas euvesicatoria
3.2.1.187	additional information	construction of a single-gene deletion mutant, DELTAxehypBA2 and a triple-gene deletion mutant DELTAxehypBA1-BA2-AA. The mutants remain pathogenic, and mutations of the operon or the single genes XCV2724, XCV2728, and XCV2729 have no effect on nonhost resistance, either, indicating that these three enzymes are not involved in either pathogenicity or nonhost resistance reactions	Xanthomonas euvesicatoria

Localization

EC Number	Localization	Comment	Organism	GeneOntology No.	Textmining
3.2.1.B48	additional information	the enzyme contains a 24 amino-acid signal peptide	Xanthomonas euvesicatoria	-	-
3.2.1.185	additional information	the enzyme contains a 43 amino-acid signal peptide	Xanthomonas euvesicatoria	-	-
3.2.1.187	additional information	the enzyme contains a 42 amino-acid signal peptide	Xanthomonas euvesicatoria	-	-

Natural Substrates/ Products (Substrates)

EC Number	Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
3.2.1.B48	4-O-(beta-L-arabinofuranosyl-(1->3)-alpha-L-arabinofuranosyl)(1->2)-beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl-(2S,4S)-4-hydroxyproline + H2O	Xanthomonas euvesicatoria	-	alpha-L-arabinofuranose + 4-O-(beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline	-	?
3.2.1.B48	4-O-(beta-L-arabinofuranosyl-(1->3)-alpha-L-arabinofuranosyl)(1->2)-beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl-(2S,4S)-4-hydroxyproline + H2O	Xanthomonas euvesicatoria 85-10	-	alpha-L-arabinofuranose + 4-O-(beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline	-	?
3.2.1.B48	4-O-(beta-L-arabinofuranosyl-(1->3)-alpha-L-arabinofuranosyl)(1->2)-beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl-(2S,4S)-4-hydroxyproline + H2O	Xanthomonas euvesicatoria UPB139	-	alpha-L-arabinofuranose + 4-O-(beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline	-	?
3.2.1.B48	additional information	Xanthomonas euvesicatoria	enzyme XeHypAA specifically degrades Ara4-Hyp to Ara3-Hyp and L-arabinose. The enzyme does not hydrolyze Ara3-Hyp, Ara2-Hyp, and Ara-Hyp, indicating that XeHypAA is an alpha-1,3-specific alpha-L-arabinofuranosidase, which recognizes the Araf-alpha-1,3-Araf structure of Ara4-Hyp	?	-	?
3.2.1.B48	additional information	Xanthomonas euvesicatoria 85-10	enzyme XeHypAA specifically degrades Ara4-Hyp to Ara3-Hyp and L-arabinose. The enzyme does not hydrolyze Ara3-Hyp, Ara2-Hyp, and Ara-Hyp, indicating that XeHypAA is an alpha-1,3-specific alpha-L-arabinofuranosidase, which recognizes the Araf-alpha-1,3-Araf structure of Ara4-Hyp	?	-	?
3.2.1.B48	additional information	Xanthomonas euvesicatoria UPB139	enzyme XeHypAA specifically degrades Ara4-Hyp to Ara3-Hyp and L-arabinose. The enzyme does not hydrolyze Ara3-Hyp, Ara2-Hyp, and Ara-Hyp, indicating that XeHypAA is an alpha-1,3-specific alpha-L-arabinofuranosidase, which recognizes the Araf-alpha-1,3-Araf structure of Ara4-Hyp	?	-	?
3.2.1.185	beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranose + H2O	Xanthomonas euvesicatoria	-	2 beta-L-arabinofuranose	-	?
3.2.1.185	beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranose + H2O	Xanthomonas euvesicatoria 85-10	-	2 beta-L-arabinofuranose	-	?
3.2.1.185	beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranose + H2O	Xanthomonas euvesicatoria UPB139	-	2 beta-L-arabinofuranose	-	?
3.2.1.185	beta-L-arabinofuranosyl-L-hydroxyproline + H2O	Xanthomonas euvesicatoria	-	beta-L-arabinofuranose + L-hydroxyproline	-	?
3.2.1.185	beta-L-arabinofuranosyl-L-hydroxyproline + H2O	Xanthomonas euvesicatoria 85-10	-	beta-L-arabinofuranose + L-hydroxyproline	-	?
3.2.1.185	beta-L-arabinofuranosyl-L-hydroxyproline + H2O	Xanthomonas euvesicatoria UPB139	-	beta-L-arabinofuranose + L-hydroxyproline	-	?

Organism

EC Number	Organism	UniProt	Comment	Textmining
3.2.1.B48	Xanthomonas euvesicatoria	Q3BS04	-	-
3.2.1.B48	Xanthomonas euvesicatoria 85-10	Q3BS04	-	-
3.2.1.B48	Xanthomonas euvesicatoria UPB139	Q3BS04	-	-
3.2.1.185	Xanthomonas euvesicatoria	Q3BS08	-	-
3.2.1.185	Xanthomonas euvesicatoria 85-10	Q3BS08	-	-
3.2.1.185	Xanthomonas euvesicatoria UPB139	Q3BS08	-	-
3.2.1.187	Xanthomonas euvesicatoria	Q3BS03	-	-
3.2.1.187	Xanthomonas euvesicatoria 85-10	Q3BS03	-	-
3.2.1.187	Xanthomonas euvesicatoria UPB139	Q3BS03	-	-

Substrates and Products (Substrate)

EC Number	Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
3.2.1.B48	4-O-(beta-L-arabinofuranosyl-(1->3)-alpha-L-arabinofuranosyl)(1->2)-beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl-(2S,4S)-4-hydroxyproline + H2O	-	Xanthomonas euvesicatoria	alpha-L-arabinofuranose + 4-O-(beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline	-	?
3.2.1.B48	4-O-(beta-L-arabinofuranosyl-(1->3)-alpha-L-arabinofuranosyl)(1->2)-beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl-(2S,4S)-4-hydroxyproline + H2O	-	Xanthomonas euvesicatoria 85-10	alpha-L-arabinofuranose + 4-O-(beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline	-	?
3.2.1.B48	4-O-(beta-L-arabinofuranosyl-(1->3)-alpha-L-arabinofuranosyl)(1->2)-beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl-(2S,4S)-4-hydroxyproline + H2O	-	Xanthomonas euvesicatoria UPB139	alpha-L-arabinofuranose + 4-O-(beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline	-	?
3.2.1.B48	additional information	enzyme XeHypAA specifically degrades Ara4-Hyp to Ara3-Hyp and L-arabinose. The enzyme does not hydrolyze Ara3-Hyp, Ara2-Hyp, and Ara-Hyp, indicating that XeHypAA is an alpha-1,3-specific alpha-L-arabinofuranosidase, which recognizes the Araf-alpha-1,3-Araf structure of Ara4-Hyp	Xanthomonas euvesicatoria	?	-	?
3.2.1.B48	additional information	substrate specificity, overview. Enzyme XeHypAA (XCV2728) releases L-arabinose from L-arabinofuranose (Araf)-alpha1,3-Araf-beta1,2-Araf-beta1,2-Araf-beta-Hyp (Ara4-Hyp), cleaving its alpha-1,3 bond	Xanthomonas euvesicatoria	?	-	?
3.2.1.B48	additional information	enzyme XeHypAA specifically degrades Ara4-Hyp to Ara3-Hyp and L-arabinose. The enzyme does not hydrolyze Ara3-Hyp, Ara2-Hyp, and Ara-Hyp, indicating that XeHypAA is an alpha-1,3-specific alpha-L-arabinofuranosidase, which recognizes the Araf-alpha-1,3-Araf structure of Ara4-Hyp	Xanthomonas euvesicatoria 85-10	?	-	?
3.2.1.B48	additional information	substrate specificity, overview. Enzyme XeHypAA (XCV2728) releases L-arabinose from L-arabinofuranose (Araf)-alpha1,3-Araf-beta1,2-Araf-beta1,2-Araf-beta-Hyp (Ara4-Hyp), cleaving its alpha-1,3 bond	Xanthomonas euvesicatoria 85-10	?	-	?
3.2.1.B48	additional information	enzyme XeHypAA specifically degrades Ara4-Hyp to Ara3-Hyp and L-arabinose. The enzyme does not hydrolyze Ara3-Hyp, Ara2-Hyp, and Ara-Hyp, indicating that XeHypAA is an alpha-1,3-specific alpha-L-arabinofuranosidase, which recognizes the Araf-alpha-1,3-Araf structure of Ara4-Hyp	Xanthomonas euvesicatoria UPB139	?	-	?
3.2.1.B48	additional information	substrate specificity, overview. Enzyme XeHypAA (XCV2728) releases L-arabinose from L-arabinofuranose (Araf)-alpha1,3-Araf-beta1,2-Araf-beta1,2-Araf-beta-Hyp (Ara4-Hyp), cleaving its alpha-1,3 bond	Xanthomonas euvesicatoria UPB139	?	-	?
3.2.1.185	beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranose + H2O	-	Xanthomonas euvesicatoria	2 beta-L-arabinofuranose	-	?
3.2.1.185	beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranose + H2O	-	Xanthomonas euvesicatoria 85-10	2 beta-L-arabinofuranose	-	?
3.2.1.185	beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranose + H2O	-	Xanthomonas euvesicatoria UPB139	2 beta-L-arabinofuranose	-	?
3.2.1.185	beta-L-arabinofuranosyl-L-hydroxyproline + H2O	-	Xanthomonas euvesicatoria	beta-L-arabinofuranose + L-hydroxyproline	-	?
3.2.1.185	beta-L-arabinofuranosyl-L-hydroxyproline + H2O	-	Xanthomonas euvesicatoria 85-10	beta-L-arabinofuranose + L-hydroxyproline	-	?
3.2.1.185	beta-L-arabinofuranosyl-L-hydroxyproline + H2O	-	Xanthomonas euvesicatoria UPB139	beta-L-arabinofuranose + L-hydroxyproline	-	?
3.2.1.185	additional information	substrate specificity, overview. Enzyme XeHypBA1 prefers Ara-Hyp as a substrate and liberates L-arabinose and is only slightly active on beta-Ara2, but does not use Ara4-Hyp and Ara3-Hyp at all. Ara2-Hyp is completely degraded in its dansylated form, but only partially when unmodified	Xanthomonas euvesicatoria	?	-	?
3.2.1.185	additional information	substrate specificity, overview. Enzyme XeHypBA1 prefers Ara-Hyp as a substrate and liberates L-arabinose and is only slightly active on beta-Ara2, but does not use Ara4-Hyp and Ara3-Hyp at all. Ara2-Hyp is completely degraded in its dansylated form, but only partially when unmodified	Xanthomonas euvesicatoria 85-10	?	-	?
3.2.1.185	additional information	substrate specificity, overview. Enzyme XeHypBA1 prefers Ara-Hyp as a substrate and liberates L-arabinose and is only slightly active on beta-Ara2, but does not use Ara4-Hyp and Ara3-Hyp at all. Ara2-Hyp is completely degraded in its dansylated form, but only partially when unmodified	Xanthomonas euvesicatoria UPB139	?	-	?
3.2.1.187	4-O-(beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline + H2O	-	Xanthomonas euvesicatoria	4-O-(beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline + beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranose	-	?
3.2.1.187	4-O-(beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline + H2O	-	Xanthomonas euvesicatoria 85-10	4-O-(beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline + beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranose	-	?
3.2.1.187	4-O-(beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline + H2O	-	Xanthomonas euvesicatoria UPB139	4-O-(beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline + beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranose	-	?
3.2.1.187	additional information	substrate specificity, overview. Enzyme XeHypBA2 releases the disaccharide Araf-beta1,2-Araf from Araf-beta1,2-Araf-beta1,2-Araf-beta-Hyp (Ara3-Hyp)	Xanthomonas euvesicatoria	?	-	?
3.2.1.187	additional information	substrate specificity, overview. Enzyme XeHypBA2 releases the disaccharide Araf-beta1,2-Araf from Araf-beta1,2-Araf-beta1,2-Araf-beta-Hyp (Ara3-Hyp)	Xanthomonas euvesicatoria 85-10	?	-	?
3.2.1.187	additional information	substrate specificity, overview. Enzyme XeHypBA2 releases the disaccharide Araf-beta1,2-Araf from Araf-beta1,2-Araf-beta1,2-Araf-beta-Hyp (Ara3-Hyp)	Xanthomonas euvesicatoria UPB139	?	-	?

Subunits

EC Number	Subunits	Comment	Organism
3.2.1.B48	?	x * 55300, recombinant His-tagged enzyme, SDS-PAGE	Xanthomonas euvesicatoria
3.2.1.187	?	x * 152000, recombinant untagged enzyme, SDS-PAGE	Xanthomonas euvesicatoria

Synonyms

EC Number	Synonyms	Comment	Organism
3.2.1.B48	GH43 alpha-L-arabinofuranosidase	-	Xanthomonas euvesicatoria
3.2.1.B48	xcv2728	-	Xanthomonas euvesicatoria
3.2.1.B48	XeHypAA	-	Xanthomonas euvesicatoria
3.2.1.185	GH 127 beta-L-arabinofuranosidase	-	Xanthomonas euvesicatoria
3.2.1.185	GH127 beta-L-arabinofuranosidase	-	Xanthomonas euvesicatoria
3.2.1.185	xcv2724	-	Xanthomonas euvesicatoria
3.2.1.185	XeHypBA1	-	Xanthomonas euvesicatoria
3.2.1.187	GH 121 beta-L-arabinofuranosidase	-	Xanthomonas euvesicatoria
3.2.1.187	GH121 beta-L-arabinobiosidase	-	Xanthomonas euvesicatoria
3.2.1.187	xcv2729	-	Xanthomonas euvesicatoria
3.2.1.187	XeHypBA2	-	Xanthomonas euvesicatoria

Temperature Optimum [°C]

EC Number	Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
3.2.1.B48	30	-	assay at	Xanthomonas euvesicatoria
3.2.1.185	30	-	assay at	Xanthomonas euvesicatoria
3.2.1.187	30	-	assay at	Xanthomonas euvesicatoria

pH Optimum

EC Number	pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
3.2.1.B48	4.5	-	assay at	Xanthomonas euvesicatoria
3.2.1.185	4.5	-	assay at	Xanthomonas euvesicatoria
3.2.1.187	4.5	-	assay at	Xanthomonas euvesicatoria

Expression

EC Number	Organism	Comment	Expression
3.2.1.B48	Xanthomonas euvesicatoria	the operon is upregulated by transcription factor HrpX	up
3.2.1.185	Xanthomonas euvesicatoria	the operon is upregulated by transcription factor HrpX	up
3.2.1.187	Xanthomonas euvesicatoria	the operon is upregulated by transcription factor HrpX	up

General Information

EC Number	General Information	Comment	Organism
3.2.1.B48	evolution	the enzyme belongs to the glycosyl hydrolase family 43, GH43	Xanthomonas euvesicatoria
3.2.1.B48	malfunction	single deletion mutants of genes XCV2724, XCV2728, and XCV2729 and the triple deletion mutant remain pathogenic, and mutations of the operon or the single genes have no effect on nonhost resistance, indicating that the enzyme is not involved in either pathogenicity or nonhost resistance reactions	Xanthomonas euvesicatoria
3.2.1.B48	physiological function	enzymes XCV2724, XCV2728, and XCV2729 in Xanthomonas euvesicatoria degrade the arabinofuranooligosaccharides present on hydroxyproline (Hyp)-rich glycoproteins (HRGPs) such as extensin and solanaceous lectins in plant cell walls. These enzymes work coordinately to degrade the oligosaccharides. The main oligosaccharide structure of Ara4-Hyp on the HRGPs is degraded to Ara3-Hyp, then to Ara-Hyp, and finally to Ara monosaccharides by the action of these three enzymes. Structure of arabino-oligosaccharides on extensin and solanaceous lectins in plant cell walls, overview. HRGPs containing oligosaccharide substrates have been reported to contribute to plant defense. The enzyme are not involved in either pathogenicity or nonhost resistance reactions	Xanthomonas euvesicatoria
3.2.1.185	evolution	the enzyme belongs to the glycosyl hydrolase family 127, GH127	Xanthomonas euvesicatoria
3.2.1.185	malfunction	single deletion mutants of genes XCV2724, XCV2728, and XCV2729 and the triple deletion mutant remain pathogenic, and mutations of the operon or the single genes have no effect on nonhost resistance, either, indicating that these three enzymes are not involved in either pathogenicity or nonhost resistance reactions	Xanthomonas euvesicatoria
3.2.1.185	physiological function	enzymes XCV2724, XCV2728, and XCV2729 in Xanthomonas euvesicatoria degrade the arabinofuranooligosaccharides present on hydroxyproline (Hyp)-rich glycoproteins (HRGPs) such as extensin and solanaceous lectins in plant cell walls. These enzymes work coordinately to degrade the oligosaccharides. The main oligosaccharide structure of Ara4-Hyp on the HRGPs is degraded to Ara3-Hyp, then to Ara-Hyp, and finally to Ara monosaccharides by the action of these three enzymes. Structure of arabino-oligosaccharides on extensin and solanaceous lectins in plant cell walls, overview. HRGPs containing oligosaccharide substrates have been reported to contribute to plant defense. The enzyme is not involved in either pathogenicity or nonhost resistance reactions	Xanthomonas euvesicatoria
3.2.1.187	evolution	the enzyme belongs to the glycosyl hydrolase family 121, GH121	Xanthomonas euvesicatoria
3.2.1.187	malfunction	single deletion mutants of genes XCV2724, XCV2728, and XCV2729 and the triple deletion mutant remain pathogenic, and mutations of the operon or the single genes have no effect on nonhost resistance, indicating that the enzyme is not involved in either pathogenicity or nonhost resistance reactions	Xanthomonas euvesicatoria
3.2.1.187	physiological function	enzymes XCV2724, XCV2728, and XCV2729 in Xanthomonas euvesicatoria degrade the arabinofuranooligosaccharides present on hydroxyproline (Hyp)-rich glycoproteins (HRGPs) such as extensin and solanaceous lectins in plant cell walls. These enzymes work coordinately to degrade the oligosaccharides. The main oligosaccharide structure of Ara4-Hyp on the HRGPs is degraded to Ara3-Hyp, then to Ara-Hyp, and finally to Ara monosaccharides by the action of these three enzymes. Structure of arabino-oligosaccharides on extensin and solanaceous lectins in plant cell walls, overview. HRGPs containing oligosaccharide substrates have been reported to contribute to plant defense. The enzyme are not involved in either pathogenicity or nonhost resistance reactions	Xanthomonas euvesicatoria