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Literature summary for 5.1.3.20 extracted from

  • Kim, M.; Lim, A.; Yang, S.; Park, J.; Lee, D.; Shin, D.
    Structure and in silico substrate-binding mode of ADP-L-glycero-D-manno-heptose 6-epimerase from Burkholderia thailandensis (2013), Acta Crystallogr. Sect. D, 69, 658-668.
    View publication on PubMed

Cloned(Commentary)

Cloned (Comment) Organism
gene rfaD, sequence compariosns, expression of N-terminally His6-tagged enzyme in Escherichia coli strain BL21(DE3) Burkholderia thailandensis

Crystallization (Commentary)

Crystallization (Comment) Organism
purified recombinant His-tagged enzyme, hanging drop vapour diffusion method, mixing of 200 nl of 8.8 mg/ml protein in 0.43 M NaCl, 20 mM Tris-HCl, pH 8.0, with 200 nl of reservoir solution containing 35% PEG 200, 0.1 M bis-tris-HCl, pH 5.5, and equilibration against 0.05 ml of reservori solution, method optimization, X-ray diffraction structure determination and analysis at 2.6 A resolution, molecular replacement Burkholderia thailandensis

Protein Variants

Protein Variants Comment Organism
E210G site-directed mutagenesis, structure compared to the wild-type enzyme Burkholderia thailandensis
K178M site-directed mutagenesis, structure compared to the wild-type enzyme Burkholderia thailandensis

Molecular Weight [Da]

Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
38000
-
x * 38000, recombinant His6-tagged enzyme, SDS-PAGE Burkholderia thailandensis

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
ADP-D-glycero-D-manno-heptose Burkholderia thailandensis
-
ADP-L-glycero-D-manno-heptose
-
r
ADP-D-glycero-D-manno-heptose Burkholderia thailandensis E444
-
ADP-L-glycero-D-manno-heptose
-
r

Organism

Organism UniProt Comment Textmining
Burkholderia thailandensis Q2SY18 gene rfaD
-
Burkholderia thailandensis E444 Q2SY18 gene rfaD
-

Purification (Commentary)

Purification (Comment) Organism
recombinant N-terminally His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity and anion exchange chromatography Burkholderia thailandensis

Reaction

Reaction Comment Organism Reaction ID
ADP-D-glycero-D-manno-heptose = ADP-L-glycero-D-manno-heptose catalytic one-base reaction mechanism from docking study, overview. The key point in the catalytic process of AGME is the inversion at the C6'' stereocentre of ADP-D,D-Hep mediated by the reversible redox reactions of NADP+/NADPH Burkholderia thailandensis

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
ADP-D-glycero-D-manno-heptose
-
Burkholderia thailandensis ADP-L-glycero-D-manno-heptose
-
r
ADP-D-glycero-D-manno-heptose
-
Burkholderia thailandensis E444 ADP-L-glycero-D-manno-heptose
-
r

Subunits

Subunits Comment Organism
? x * 38000, recombinant His6-tagged enzyme, SDS-PAGE Burkholderia thailandensis
More enzyme structure comparisons, detailed overview Burkholderia thailandensis

Synonyms

Synonyms Comment Organism
ADP-L-glycero-D-manno-heptose 6-epimerase
-
Burkholderia thailandensis
AGME
-
Burkholderia thailandensis

Cofactor

Cofactor Comment Organism Structure
NADP+ the enzyme contains a catalytic triad involved in catalyzing hydride transfer with the aid of NADP+ Burkholderia thailandensis
NADPH
-
Burkholderia thailandensis

General Information

General Information Comment Organism
additional information the enzyme contains a catalytic triad involved in catalyzing hydride transfer with the aid of NADP+. The enzyme may recognize their substrate in a lock-and-key fashion, binding analysis, docking study, enzyme structure comparisons, detailed overview Burkholderia thailandensis