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Literature summary 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.
    View publication on PubMed

Cloned(Commentary)

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

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
4.2.2.2 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

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

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
4.2.2.2 0.19
-
 tetragalacturonate at pH8.5 and in the presence of 5mMCa2+ Bacillus subtilis
4.2.2.2 1.2
-
 trigalacturonate at pH8.5 and in the presence of 5mMCa2+ Bacillus subtilis

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
4.2.2.2 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

EC Number Organism UniProt Comment Textmining
4.2.2.2 Bacillus subtilis P39116
-
-

Purification (Commentary)

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

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4.2.2.2 additional information digalacturonate is not cleaved at an appreciable rate Bacillus subtilis ?
-
 ?
4.2.2.2 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 ?
-
 ?
4.2.2.2 polygalacturonate
-
 Bacillus subtilis unsaturated oligogalacturonides
-
 ?
4.2.2.2 tetragalacturonate
-
 Bacillus subtilis ?
-
 ?
4.2.2.2 trigalacturonate
-
 Bacillus subtilis ?
-
 ?

Synonyms

EC Number Synonyms Comment Organism
4.2.2.2 Pel
-
 Bacillus subtilis

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
4.2.2.2 340
-
 trigalacturonate at pH8.5 and in the presence of 5mMCa2+ Bacillus subtilis
4.2.2.2 1000
-
 tetragalacturonate at pH8.5 and in the presence of 5mMCa2+ Bacillus subtilis
4.2.2.2 1200
-
 Polygalacturonate at pH8.5 and in the presence of 5mMCa2+ Bacillus subtilis