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Literature summary for 4.2.2.6 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
Search for more literature for 4.2.2.6

Cloned(Commentary)

Cloned (Comment) Organism
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)

Crystallization (Comment) Organism
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

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

KM Value [mM]

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

Metals/Ions

Metals/Ions Comment Organism Structure
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)

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

Organism

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

Purification (Commentary)

Purification (Comment) Organism
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

Reaction Comment Organism Reaction ID
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)

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

Subunits

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

Synonyms

Synonyms Comment Organism
oligogalacturonate lyase
-
 Yersinia enterocolitica
YeOGL
-
 Yersinia enterocolitica

Temperature Optimum [°C]

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

pH Optimum

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

General Information

General Information Comment Organism
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