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Literature summary extracted from

  • Abbott, D.W.; Gilbert, H.J.; Boraston, A.B.
    The active site of oligogalacturonate lyase provides unique insights into cytoplasmic oligogalacturonate beta-elimination (2010), J. Biol. Chem., 285, 39029-39038.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
4.2.2.6 gene ogl, phylogenetic tree of the OGL family, expression of YeOGL containing a thrombin-cleavable N-terminal His6 tag in Escherichia coli BL21-pLysS (DE3) cells Yersinia enterocolitica

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
4.2.2.6 purified recombinant detagged YeOGL, hanging drop vapor diffusion method, 12.5 mg/ml protein in 20 mM Tris-HCl, precipitation from 0.2 M CaCl2, 0.1 M NaOAc, pH 4.8, 20% PEG 3350, and cryoprotection by 15% ethylene glycol, 18°C, X-ray diffraction structure determination and analysis at 1.65 A resolution Yersinia enterocolitica

Inhibitors

EC Number Inhibitors Comment Organism Structure
4.2.2.6 pectate substrate inhibition at high concentrations Yersinia enterocolitica

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
4.2.2.6 additional information
-
 additional information Michaelis-Menten kinetics Yersinia enterocolitica

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
4.2.2.6 Mn2+ activates, octahedral metal binding site, coordination structure involving N-His287, O-Gln350, N-His353, and His-355, overview Yersinia enterocolitica

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
4.2.2.6 4-(4-deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonate Yersinia enterocolitica
-
 2 5-dehydro-4-deoxy-D-glucuronate
-
 ?
4.2.2.6 4-(4-deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonate Yersinia enterocolitica 8081
-
 2 5-dehydro-4-deoxy-D-glucuronate
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
4.2.2.6 Yersinia enterocolitica A1JMA5 subsp. enterocolitica, gene ogl, locus YE1876
-
4.2.2.6 Yersinia enterocolitica 8081 A1JMA5 subsp. enterocolitica, gene ogl, locus YE1876
-

Purification (Commentary)

EC Number Purification (Comment) Organism
4.2.2.6 recombinant N-terminally His-tagged YeOGL from Escherichia coli by nickel affinity chromatography, ultrafiltration, His-tag cleavage through thrombin, and gel filtration Yersinia enterocolitica

Reaction

EC Number Reaction Comment Organism Reaction ID
4.2.2.6 4-(4-deoxy-alpha-D-galact-4-enuronosyl)-D-galacturonate = 2 5-dehydro-4-deoxy-D-glucuronate active site structure modeling and beta-elimination reaction mechanism, overview Yersinia enterocolitica
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4.2.2.6 4-(4-deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonate
-
 Yersinia enterocolitica 2 5-dehydro-4-deoxy-D-glucuronate
-
 ?
4.2.2.6 4-(4-deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonate
-
 Yersinia enterocolitica 8081 2 5-dehydro-4-deoxy-D-glucuronate
-
 ?

Subunits

EC Number Subunits Comment Organism
4.2.2.6 More YeOGL adopts a seven-bladed beta-propeller fold that has structural similarity to the WD40 family of proteins Yersinia enterocolitica

Synonyms

EC Number Synonyms Comment Organism
4.2.2.6 oligogalacturonate lyase
-
 Yersinia enterocolitica
4.2.2.6 YeOGL
-
 Yersinia enterocolitica

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
4.2.2.6 25
-
 assay at Yersinia enterocolitica

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
4.2.2.6 7
-
 assay at Yersinia enterocolitica

General Information

EC Number General Information Comment Organism
4.2.2.6 metabolism OGL is involved in the pectin degradation pathway performing extracellular pectin depolymerization, overview. In the initial stages, intracellular di- and trigalacturonides are processed into saturated monogalacturonate, GalA, and a 4,5-unsaturated GalA-like monosaccharide, 5-keto-4-deoxyuronate, by the combined activities of an exo-acting family 2 pectate lyase,YePL2B, and oligogalacturonate lyase, YeOGL/YePL22, a lyase family preferentially active on digalacturonides Yersinia enterocolitica