Literature summary for 4.2.2.23 extracted from

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 (2007), J. Biol. Chem., 282, 37134-37145.

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Crystallization (Commentary)

Crystallization (Comment)	Organism
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	Bacillus subtilis

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
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	Bacillus subtilis

Localization

Localization	Comment	Organism	GeneOntology No.	Textmining
extracellular	-	Bacillus subtilis	-	-

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Ca2+	a calcium ion coordinated by Asp401, Glu422, His363, and His399 may be required for the enzyme activity	Bacillus subtilis

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
rhamnogalacturonan I	Bacillus subtilis	rhamnogalacturonan lyase produced by plant pathogenic and saprophytic microbes plays an important role in degrading plant cell walls	rhamnogalacturonan I oligosaccharides with alpha-L-rhamnopyranose at the reducing end and 4-deoxy-4,5-unsaturated D-galactopyranosyluronic acid at the nonreducing end	-	?

Organism

Organism	UniProt	Comment	Textmining
Bacillus subtilis	O31526	-	-

Purification (Commentary)

Purification (Comment)	Organism
-	Bacillus subtilis

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
rhamnogalacturonan I	rhamnogalacturonan lyase produced by plant pathogenic and saprophytic microbes plays an important role in degrading plant cell walls	Bacillus subtilis	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	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	Bacillus subtilis	rhamnogalacturonan I oligosaccharides with alpha-L-rhamnopyranose at the reducing end and 4-deoxy-4,5-unsaturated D-galactopyranosyluronic acid at the nonreducing end	-	?

Synonyms

Synonyms	Comment	Organism
RG lyase	-	Bacillus subtilis
YesW	-	Bacillus subtilis

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
30	-	assay at	Bacillus subtilis

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.5	-	assay at	Bacillus subtilis

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Release 2023.1 (January 2023)