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Literature summary for 2.4.2.3 extracted from

  • Eistrikh-Heller, P.; Rubinsky, S.; Prokofev, I.; Gabdulkhakov, A.; Mironov, A.; Lashkov, A.
    X-ray structure and molecular dynamics study of uridine phosphorylase from Vibrio cholerae in complex with 2,2-anhydrouridine (2020), Crystallogr. Rep., 65, 269-277 .
No PubMed abstract available

Crystallization (Commentary)

Crystallization (Comment) Organism
purified enzyme in complex with 2,2-anhydrouridine, X-ray diffraction structure determination and analysis at 1.34 A resolution, molecular replacement method using the structure of VchUPh in complex with 6-methyluracil (PDB ID 4K6O) as the starting model, from which all ligands, including enzyme-bound water molecules, are removed. The inhibitor molecules are located in all six active sites of the hexameric UPh molecule Vibrio cholerae

Inhibitors

Inhibitors Comment Organism Structure
2,2'-anhydrouridine high-resolution three-dimensional structure of uridine phosphorylase from in complex with the competitive inhibitor determined by X-ray diffraction (PDB ID 6RCA), detailed binding structure analysis, overview. The binding of the inhibitor at the active site of the protein is energetically more favorable than the binding of the native substrate uridine. The inhibitor molecules are located in all six active sites of the hexameric UPh molecule. Effect of 2,2'-anhydrouridine binding on the conformation of structurally functional elements of VchUPh Vibrio cholerae

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
uridine + phosphate Vibrio cholerae
-
uracil + alpha-D-ribose 1-phosphate
-
r

Organism

Organism UniProt Comment Textmining
Vibrio cholerae
-
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
uridine + phosphate
-
Vibrio cholerae uracil + alpha-D-ribose 1-phosphate
-
r

Synonyms

Synonyms Comment Organism
VchUPh
-
Vibrio cholerae

General Information

General Information Comment Organism
additional information enzyme structure modeling, molecular dynamics simulation, overview. Calculation of the protein-ligand binding free energy Vibrio cholerae