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PDBsum entry 1uaq
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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 structure of yeast cytosine deaminase. Insights into enzyme mechanism and evolution.
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Authors
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T.P.Ko,
J.J.Lin,
C.Y.Hu,
Y.H.Hsu,
A.H.Wang,
S.H.Liaw.
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Ref.
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J Biol Chem, 2003,
278,
19111-19117.
[DOI no: ]
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PubMed id
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Abstract
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Yeast cytosine deaminase is an attractive candidate for anticancer gene therapy
because it catalyzes the deamination of the prodrug 5-fluorocytosine to form
5-fluorouracil. We report here the crystal structure of the enzyme in complex
with the inhibitor 2-hydroxypyrimidine at 1.6-A resolution. The protein forms a
tightly packed dimer with an extensive interface of 1450 A2 per monomer. The
inhibitor was converted into a hydrated adduct as a transition-state analog. The
essential zinc ion is ligated by the 4-hydroxyl group of the inhibitor together
with His62, Cys91, and Cys94 from the protein. The enzyme shares similar
active-site architecture to cytidine deaminases and an unusually high structural
homology to 5-aminoimidazole-4-carboxamide-ribonucleotide transformylase and
thereby may define a new superfamily. The unique C-terminal tail is involved in
substrate specificity and also functions as a gate controlling access to the
active site. The complex structure reveals a closed conformation, suggesting
that substrate binding seals the active-site entrance so that the catalytic
groups are sequestered from solvent. A comparison of the crystal structures of
the bacterial and fungal cytosine deaminases provides an elegant example of
convergent evolution, where starting from unrelated ancestral proteins, the same
metal-assisted deamination is achieved through opposite chiral intermediates
within distinctly different active sites.
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Figure 1.
FIG. 1. Structure of yeast CD. A, stereo view of the
monomer, which is a three-layered  /  / structure with a
central -sheet sandwiched on
either side by -helices. The tightly
bound zinc ion is shown as a magenta sphere with its ligands and
the inhibitor (3,4-dihydrouracil (DHU)) as ball-and-stick
representations. B, the dimer has one monomer colored in red
(helices) and green (strands), whereas the other is colored in
magenta (helices) and blue (strands). The zinc ions are shown as
yellow spheres.
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Figure 3.
FIG. 3. The active site. A, stereo view of the 2F[o] - F[c]
electron density map of the active site contoured at 1.5  level
and shown in cyan and the difference anomalous map for the zinc
ion contoured at 30 level and shown in
purple. The densities of the inhibitor molecule are highlighted
in green. The active-site residues and the inhibitor
(3,4-dihydrouracil (DHU)) are shown as ball-and-stick
representations, and the zinc ion is shown as a magenta sphere.
B, stereo view of the interaction networks in the active site.
There are six direct hydrogen bonds between the protein molecule
and the inhibitor (see The Active Site Architecture and
Substrate Binding). C, stereo view of a comparison of the active
sites of the yeast (magenta) and E. coli cytosine deaminase
(Protein Data Bank code 1K70 [PDB]
, green) based on superposition of the inhibitor
3,4-dihydrouracil. The residue numbering is labeled in the same
color for each protein. The bacterial enzymes utilize three
histidines and one aspartate for iron ligation (His61, His63,
His214, and Asp313). Asp313 also forms a hydrogen bond with the
attacking water molecule. Glu217 interacts with the N3 atom of
the pyrimidine ring, and Gln156 interacts with the O2 and N1
atoms.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2003,
278,
19111-19117)
copyright 2003.
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Secondary reference #1
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Title
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Crystallization and preliminary crystallographic analysis of yeast cytosine deaminase.
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Authors
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Y.H.Hsu,
C.Y.Hu,
J.J.Lin,
S.H.Liaw.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2003,
59,
950-952.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1 Yeast cytosine deaminase crystals. Two crystal
morphologies were commonly observed: prismatic crystals with
typical dimensions of 0.2 × 0.2 × 0.15 mm and long thin
rod-shaped crystals with dimensions of 0.5 × 0.1 × 0.05 mm. The
rod crystals appeared more often, but diffracted X-rays poorly.
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The above figure is
reproduced from the cited reference
with permission from the IUCr
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