PDBsum entry 1upf

Transferase

PDB id: 1upf

Contents

Protein chains

224 a.a. *

Ligands

SO4 ×12

URF ×4

Waters ×207

* Residue conservation analysis

PDB id:

1upf

Name:

Transferase

Title:

Structure of the uracil phosphoribosyltransferase, mutant c128v bound to the drug 5-fluorouracil

Structure:

Uracil phosphoribosyltransferase. Chain: d, c, b, a. Synonym: uprtase. Engineered: yes. Mutation: yes

Source:

Toxoplasma gondii. Organism_taxid: 5811. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Homo-Dimer (from PDB file)

Resolution:

2.30Å R-factor: 0.166

Authors:

M.A.Schumacher,D.Carter,D.Scott,D.Roos,B.Ullman,R.G.Brennan

Key ref:

M.A.Schumacher et al. (1998). Crystal structures of Toxoplasma gondii uracil phosphoribosyltransferase reveal the atomic basis of pyrimidine discrimination and prodrug binding. EMBO J, 17, 3219-3232. PubMed id: 9628859 DOI: 10.1093/emboj/17.12.3219

Date:

17-Jun-98 Release date: 22-Jun-99

Protein chains

Q26998  (UPP_TOXGO) -  Uracil phosphoribosyltransferase from Toxoplasma gondii

Seq: 244 a.a.

Struc: 224 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.4.2.9 - uracil phosphoribosyltransferase.
• Reaction: UMP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + uracil

UMP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + uracil (Bound ligand (Het Group name = URF) matches with 88.89% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1093/emboj/17.12.3219

EMBO J 17:3219-3232 (1998)

PubMed id: 9628859

Crystal structures of Toxoplasma gondii uracil phosphoribosyltransferase reveal the atomic basis of pyrimidine discrimination and prodrug binding.

M.A.Schumacher, D.Carter, D.M.Scott, D.S.Roos, B.Ullman, R.G.Brennan.

ABSTRACT

Uracil phosphoribosyltransferase (UPRTase) catalyzes the transfer of a ribosyl phosphate group from alpha-D-5-phosphoribosyl-1-pyrophosphate to the N1 nitrogen of uracil. The UPRTase from the opportunistic pathogen Toxoplasma gondii is a rational target for antiparasitic drug design. To aid in structure-based drug design studies against toxoplasmosis, the crystal structures of the T.gondii apo UPRTase (1.93 A resolution), the UPRTase bound to its substrate, uracil (2.2 A resolution), its product, UMP (2.5 A resolution), and the prodrug, 5-fluorouracil (2.3 A resolution), have been determined. These structures reveal that UPRTase recognizes uracil through polypeptide backbone hydrogen bonds to the uracil exocyclic O2 and endocyclic N3 atoms and a backbone-water-exocyclic O4 oxygen hydrogen bond. This stereochemical arrangement and the architecture of the uracil-binding pocket reveal why cytosine and pyrimidines with exocyclic substituents at ring position 5 larger than fluorine, including thymine, cannot bind to the enzyme. Strikingly, the T. gondii UPRTase contains a 22 residue insertion within the conserved PRTase fold that forms an extended antiparallel beta-arm. Leu92, at the tip of this arm, functions to cap the active site of its dimer mate, thereby inhibiting the escape of the substrate-binding water molecule.

Selected figure(s)

Figure 3.
Figure 3 Dimerization interface involving the -arm. Shown are the contacts made by the -arm (colored yellow) from one subunit to its dimer pair (colored blue). Only part of the -arm is shown for clarity. Labeled are those residues making dimer contacts, and these include Phe83 and Phe101, which stack against the N-terminus of A2', Tyr96 which is sandwiched between Arg46' and Arg53', and Thr90 which makes hydrogen bonds to the carbonyls of Pro231' and Gly232'. Also shown is Leu92, which encloses the active site of the other monomer. Enzyme-bound uracil and phosphate are displayed and colored by atom type, whereby red is oxygen, blue is nitrogen, gray is carbon, and magenta is phosphorous.

Figure 5.
Figure 5 Stereo view of the superimposition of UMP-bound UPRTase (red) and 5-fluorouracil-bound UPRTase (green) onto the uracil-bound UPRTase (blue). Note the rotation of the 5-fluorouracil ring that occurs to prevent steric clash between the fluorine atom and the C[ ]atom of Ala168. Also, the slightly 'pulled out' position of the uracil ring of the UMP moiety, compared with uracil, is revealed. Labeled are residues Ala168, Tyr228, which stacks over the uracil ring, and Asp235 which hydrogen bonds with the Tyr228. Wat1 of each complex is shown as an appropriately colored sphere. The double-headed arrow highlights the proximity of the fluorine atom of 5-fluorouracil to the C[ ]atom of Ala168. This figure was generated using O (Jones et al., 1991).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1998, 17, 3219-3232) copyright 1998.

Figures were selected by an automated process.