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PDBsum entry 1upf
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Crystal structures of toxoplasma gondii uracil phosphoribosyltransferase reveal the atomic basis of pyrimidine discrimination and prodrug binding.
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Authors
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M.A.Schumacher,
D.Carter,
D.M.Scott,
D.S.Roos,
B.Ullman,
R.G.Brennan.
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Ref.
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EMBO J, 1998,
17,
3219-3232.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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.
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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).
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(1998,
17,
3219-3232)
copyright 1998.
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