Literature summary for 4.2.2.3 extracted from

Ogura, K.; Yamasaki, M.; Mikami, B.; Hashimoto, W.; Murata, K.
Substrate recognition by family 7 alginate lyase from Sphingomonas sp. A1 (2008), J. Mol. Biol., 380, 373-385.

Search for more literature for 4.2.2.3

Cloned(Commentary)

Cloned (Comment)	Organism
expressed as a His-tagged fusion protein	Sphingomonas sp.

Protein Variants

Protein Variants	Comment	Organism
H191N/Y284F	crystal structure of mutant H191N/Y284F complexed with a tetrasaccharide bound at subsites -1 to +3 suggests that Gln189 functions as a neutralizer for the substrate carboxyl group, His191 as a general base, and Tyr284 as a general acid	Sphingomonas sp.
N141C/N199C	almost all molecules of N141C/N199C form a disulfide bond between Cys141 and Cys199. Crystal structure of N141C/N199C is determined at 2.1 A resolution by X-ray crystallography. Mutant has a glove-like beta- sandwich structure composed of four short alpha-helices and two beta-sheets. Two sulfate ions derived from the crystallization solution are accommodated at subsites +1 and +3. The loops of the mutant adopt the closed form. A disulfide bond between Cys141 and Cys199 forms in the absence of reducing agents	Sphingomonas sp.
N141C/N199C	Km (mg/ml) (alginate): 0.32 (N141C/N199C + 0.5 mM DTT), 0.14 (N141C/N199C), Vmax (U/mg) (alginate): 7.1 (N141C/N199C + 0.5 mM DTT), 0.63 (N141C/N199C)	Sphingomonas sp.
Y284F	molecular activity is significantly lower than that of wild-type enzyme. GGG- and MMG bound Y284F crystal structure are refined at 1.65 A and 1.55 A resolution. Mutant enzyme interacts appropriately with substrate hydroxyl groups at subsites +1 and +2 and accommodates alpha-L-guluronate or beta-D-mannuronate, while substrate carboxyl groups are strictly recognized by specific residues	Sphingomonas sp.

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
additional information	-	additional information	Km (mg/ml) (alginate): 0.018 (wild-type), 0.32 (mutant N141C/N199C + 0.5 mM DTT), 0.14 (mutant N141C/N199C)	Sphingomonas sp.
additional information	-	additional information	Vmax (U/mg) (alginate): 42.9 (wild-type), 7.1 (mutant N141C/N199C + 0.5 mM DTT), 0.63 (mutant N141C/N199C)	Sphingomonas sp.

Organism

Organism	UniProt	Comment	Textmining
Sphingomonas sp.	-	-	-

Purification (Commentary)

Purification (Comment)	Organism
using Ni-NTA chromatography	Sphingomonas sp.

Reaction

Reaction	Comment	Organism	Reaction ID
R2-beta-D-mannuronic acid-R1 = R2-OH + 4-deoxy-alpha-L-erythro-hex-4-enopyranuronosyl-R1	A1-II with a glove-like beta-sandwich as a basic scaffold forms a cleft covered with two lid loops (L1/L2). Loop flexibility for substrate binding and structural determinants for broad substrate recognition and catalytic reaction is shown. The two loops associate mutually over the cleft through the formation of a hydrogen bond between their edges (Asn141 and Asn199)	Sphingomonas sp.	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
alginate	-	Sphingomonas sp.	unsaturated algino-oligosaccharides	-	?

Synonyms

Synonyms	Comment	Organism
A1 alginate lyase	-	Sphingomonas sp.
A1-II	-	Sphingomonas sp.

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
37	-	assay at	Sphingomonas sp.

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.5	-	assay at	Sphingomonas sp.

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Release 2023.1 (January 2023)