ISDA: 4E1V

Deposition Date 2012-03-07

Release Date 2013-03-06

Last Version Date 2023-09-13

Entry Detail

PDB ID:

4E1V

Keywords:

TRANSFERASE

Title:

X-RAY Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution

Biological Source:

Source Organism:

Salmonella enterica subsp. enterica serovar Typhimurium (Taxon ID: 99287)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.15 Å

R-Value Free:

0.23

R-Value Work:

0.19

R-Value Observed:

0.19

Space Group:

C 1 2 1

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Uridine phosphorylase
Gene (Uniprot):udp
Chain IDs:A, B (auth: E), C (auth: F), D, E (auth: C), F (auth: B), G (auth: H), H (auth: I), I (auth: G)
Chain Length:253
Number of Molecules:9
Biological Source:Salmonella enterica subsp. enterica serovar Typhimurium

UniProt ID:P0A1F6 Pfam ID:PF01048 EC:2.4.2.3

Ligand Molecules

EDO

GOL

URF

Primary Citation

X-ray structure of Salmonella typhimurium uridine phosphorylase complexed with 5-fluorouracil and molecular modelling of the complex of 5-fluorouracil with uridine phosphorylase from Vibrio cholerae.

Lashkov, A.A, Sotnichenko, S.E, Prokofiev, I.I, Gabdulkhakov, A.G, Agapov, I.I, Shtil, A.A, Betzel, C, Mironov, A.S, Mikhailov, A.M, Lashkov, A.A, Gabdoulkhakov, A.G, Shtil, A.A, Mikhailov, A.M.Show

Acta Crystallogr.,Sect.D 68 968 974 (2012)

PMID: 22868762 DOI: 10.1107/S090744491201815X

Abstact

Uridine phosphorylase (UPh), which is a key enzyme in the reutilization pathway of pyrimidine nucleoside metabolism, is a validated target for the treatment of infectious diseases and cancer. A detailed analysis of the interactions of UPh with the therapeutic ligand 5-fluorouracil (5-FUra) is important for the rational design of pharmacological inhibitors of these enzymes in prokaryotes and eukaryotes. Expanding on the preliminary analysis of the spatial organization of the active centre of UPh from the pathogenic bacterium Salmonella typhimurium (StUPh) in complex with 5-FUra [Lashkov et al. (2009), Acta Cryst. F65, 601-603], the X-ray structure of the StUPh-5-FUra complex was analysed at atomic resolution and an in silico model of the complex formed by the drug with UPh from Vibrio cholerae (VchUPh) was generated. These results should be considered in the design of selective inhibitors of UPhs from various species.

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