PDBsum entry 1uaq

Hydrolase

PDB id: 1uaq

Contents

Protein chains

151 a.a. *

Ligands

DUC ×2

Metals

_ZN ×2

Waters ×484

* Residue conservation analysis

PDB id:

1uaq

Name:

Hydrolase

Title:

The crystal structure of yeast cytosine deaminase

Structure:

Cytosine deaminase. Chain: a, b. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: fcy1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.60Å R-factor: 0.177 R-free: 0.215

Authors:

T.-P.Ko,J.-J.Lin,C.-Y.Hu,Y.-H.Hsu,A.H.-J.Wang,S.-H.Liaw

Key ref:

T.P.Ko et al. (2003). Crystal structure of yeast cytosine deaminase. Insights into enzyme mechanism and evolution. J Biol Chem, 278, 19111-19117. PubMed id: 12637534 DOI: 10.1074/jbc.M300874200

Date:

14-Mar-03 Release date: 29-Apr-03

Protein chains

Q12178  (FCY1_YEAST) -  Cytosine deaminase from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 158 a.a.

Struc: 151 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.4.1 - cytosine deaminase.
• Reaction: cytosine + H2O + H⁺ = uracil + NH4⁺

cytosine + H2O + H(+) = uracil + NH4(+) (Bound ligand (Het Group name = DUC) corresponds exactly)

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

Added reference

DOI no: 10.1074/jbc.M300874200

J Biol Chem 278:19111-19117 (2003)

PubMed id: 12637534

Crystal structure of yeast cytosine deaminase. Insights into enzyme mechanism and evolution.

T.P.Ko, J.J.Lin, C.Y.Hu, Y.H.Hsu, A.H.Wang, S.H.Liaw.

ABSTRACT

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.

Selected figure(s)

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.

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.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 19111-19117) copyright 2003.

Figures were selected by an automated process.