Literature summary for 4.2.2.2 extracted from

Seyedarabi, A.; To, T.T.; Ali, S.; Hussain, S.; Fries, M.; Madsen, R.; Clausen, M.H.; Teixteira, S.; Brocklehurst, K.; Pickersgill, R.W.
Structural insights into substrate specificity and the anti beta-elimination mechanism of pectate lyase (2010), Biochemistry, 49, 539-546.

Search for more literature for 4.2.2.2

Cloned(Commentary)

Cloned (Comment)	Organism
expressed in Escherichia coli BL21(DE3) cells	Bacillus subtilis

Crystallization (Commentary)

Crystallization (Comment)	Organism
R279A mutant, streak seeding pre-equilibrated protein drops, using 0.1 M sodium acetate (pH 4.6), 0.2 M ammonium acetate, and 18% (w/v) PEG 4000, supplemented with 20 mM trigalacturonate, 7 mM calcium chloride, and 15% glycerol as a cryoprotectant	Bacillus subtilis

Protein Variants

Protein Variants	Comment	Organism
D173A	the mutation results in approximately 40% of wild type activity	Bacillus subtilis
D173A/N180A/K247A	the mutation results in approximately 0.2% of wild type activity	Bacillus subtilis
D173A/N180N	the mutation results in approximately 5% of wild type activity	Bacillus subtilis
N180A	the mutation results in approximately 30% of wild type activity	Bacillus subtilis
R279A	inactive	Bacillus subtilis

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
0.19	-	tetragalacturonate	at pH8.5 and in the presence of 5mMCa2+	Bacillus subtilis
1.2	-	trigalacturonate	at pH8.5 and in the presence of 5mMCa2+	Bacillus subtilis

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Ca2+	the enzyme in the absence of substrate binds a single calcium ion, two additional calcium ions bind between enzyme and substrate carboxylates occupying the +1 subsite in the Michaelis complex	Bacillus subtilis

Organism

Organism	UniProt	Comment	Textmining
Bacillus subtilis	P39116	-	-

Purification (Commentary)

Purification (Comment)	Organism
ion exchange chromatography and gel filtration	Bacillus subtilis

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
additional information	digalacturonate is not cleaved at an appreciable rate	Bacillus subtilis	?	-	?
pectin	pectate lyases harness anti beta-elimination chemistry to cleave the alpha-1,4 linkage in the homogalacturonan region of plant cell wall pectin	Bacillus subtilis	?	-	?
polygalacturonate	-	Bacillus subtilis	unsaturated oligogalacturonides	-	?
tetragalacturonate	-	Bacillus subtilis	?	-	?
trigalacturonate	-	Bacillus subtilis	?	-	?

Synonyms

Synonyms	Comment	Organism
Pel	-	Bacillus subtilis

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism	Structure
340	-	trigalacturonate	at pH8.5 and in the presence of 5mMCa2+	Bacillus subtilis
1000	-	tetragalacturonate	at pH8.5 and in the presence of 5mMCa2+	Bacillus subtilis
1200	-	Polygalacturonate	at pH8.5 and in the presence of 5mMCa2+	Bacillus subtilis

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Release 2023.1 (January 2023)