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PDBsum entry 1uaq

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1uaq
Jmol
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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q12178  (FCY1_YEAST) -  Cytosine deaminase
Seq:
Struc:
158 a.a.
151 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.5.4.1  - Cytosine deaminase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Cytosine + H2O = uracil + NH3
Cytosine
+ H(2)O
=
uracil
Bound ligand (Het Group name = DUC)
corresponds exactly
+ NH(3)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     UMP salvage   4 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23042606 L.E.Metzger, J.K.Lee, J.S.Finer-Moore, C.R.Raetz, and R.M.Stroud (2012).
LpxI structures reveal how a lipid A precursor is synthesized.
  Nat Struct Mol Biol, 19, 1132-1138.
PDB codes: 4ggi 4ggm 4j6e
20617462 P.Vandeputte, L.Pineau, G.Larcher, T.Noel, D.Brèthes, D.Chabasse, and J.P.Bouchara (2011).
Molecular mechanisms of resistance to 5-fluorocytosine in laboratory mutants of Candida glabrata.
  Mycopathologia, 171, 11-21.  
19704126 B.A.McManus, G.P.Moran, J.A.Higgins, D.J.Sullivan, and D.C.Coleman (2009).
A Ser29Leu substitution in the cytosine deaminase Fca1p is responsible for clade-specific flucytosine resistance in Candida dubliniensis.
  Antimicrob Agents Chemother, 53, 4678-4685.  
19265397 J.I.Park, L.Cao, V.M.Platt, Z.Huang, R.A.Stull, E.E.Dy, J.J.Sperinde, J.S.Yokoyama, and F.C.Szoka (2009).
Antitumor therapy mediated by 5-fluorocytosine and a recombinant fusion protein containing TSG-6 hyaluronan binding domain and yeast cytosine deaminase.
  Mol Pharm, 6, 801-812.  
19414575 M.Florent, T.Noël, G.Ruprich-Robert, B.Da Silva, V.Fitton-Ouhabi, C.Chastin, N.Papon, and F.Chapeland-Leclerc (2009).
Nonsense and missense mutations in FCY2 and FCY1 genes are responsible for flucytosine resistance and flucytosine-fluconazole cross-resistance in clinical isolates of Candida lusitaniae.
  Antimicrob Agents Chemother, 53, 2982-2990.  
19169351 M.Henry, D.Guétard, R.Suspène, C.Rusniok, S.Wain-Hobson, and J.P.Vartanian (2009).
Genetic editing of HBV DNA by monodomain human APOBEC3 cytidine deaminases and the recombinant nature of APOBEC3G.
  PLoS ONE, 4, e4277.  
18973166 A.Liu, J.Wang, Z.Lu, L.Yao, Y.Li, and H.Yan (2008).
Hydrogen-bond detection, configuration assignment and rotamer correction of side-chain amides in large proteins by NMR spectroscopy through protium/deuterium isotope effects.
  Chembiochem, 9, 2860-2871.  
18624631 D.Wolf, and S.P.Goff (2008).
Host restriction factors blocking retroviral replication.
  Annu Rev Genet, 42, 143-163.  
18288108 K.M.Chen, E.Harjes, P.J.Gross, A.Fahmy, Y.Lu, K.Shindo, R.S.Harris, and H.Matsuo (2008).
Structure of the DNA deaminase domain of the HIV-1 restriction factor APOBEC3G.
  Nature, 452, 116-119.
PDB code: 2jyw
17889624 S.S.Brar, E.J.Sacho, I.Tessmer, D.L.Croteau, D.A.Erie, and M.Diaz (2008).
Activation-induced deaminase, AID, is catalytically active as a monomer on single-stranded DNA.
  DNA Repair (Amst), 7, 77-87.  
17663441 T.Matsubara, M.Dupuis, and M.Aida (2008).
An insight into the environmental effects of the pocket of the active site of the enzyme. Ab initio ONIOM-molecular dynamics (MD) study on cytosine deaminase.
  J Comput Chem, 29, 458-465.  
17651436 E.Johansson, M.Thymark, J.H.Bynck, M.Fanø, S.Larsen, and M.Willemoës (2007).
Regulation of dCTP deaminase from Escherichia coli by nonallosteric dTTP binding to an inactive form of the enzyme.
  FEBS J, 274, 4188-4198.
PDB codes: 2j4h 2j4q
17267497 H.Huthoff, and M.H.Malim (2007).
Identification of amino acid residues in APOBEC3G required for regulation by human immunodeficiency virus type 1 Vif and Virion encapsidation.
  J Virol, 81, 3807-3815.  
17766382 J.Dechancie, F.R.Clemente, A.J.Smith, H.Gunaydin, Y.L.Zhao, X.Zhang, and K.N.Houk (2007).
How similar are enzyme active site geometries derived from quantum mechanical theozymes to crystal structures of enzyme-inhibitor complexes? Implications for enzyme design.
  Protein Sci, 16, 1851-1866.  
17218460 L.Yao, H.Yan, and R.I.Cukier (2007).
A molecular dynamics study of the ligand release path in yeast cytosine deaminase.
  Biophys J, 92, 2301-2310.  
17091334 A.Liu, Y.Li, L.Yao, and H.Yan (2006).
Simultaneous NMR assignment of backbone and side chain amides in large proteins with IS-TROSY.
  J Biomol NMR, 36, 205-214.  
17124494 M.Kato, R.M.Wynn, J.L.Chuang, C.A.Brautigam, M.Custorio, and D.T.Chuang (2006).
A synchronized substrate-gating mechanism revealed by cubic-core structure of the bovine branched-chain alpha-ketoacid dehydrogenase complex.
  EMBO J, 25, 5983-5994.
PDB codes: 2ihw 2ii3 2ii4 2ii5
16498617 Y.Kim, N.Maltseva, I.Dementieva, F.Collart, D.Holzle, and A.Joachimiak (2006).
Crystal structure of hypothetical protein YfiH from Shigella flexneri at 2 A resolution.
  Proteins, 63, 1097-1101.
PDB code: 1xaf
15858841 M.P.Xiong, and G.S.Kwon (2005).
PEGylation of yeast cytosine deaminase for pretargeting.
  J Pharm Sci, 94, 1249-1258.  
15651027 Q.Xu, R.Schwarzenbacher, D.McMullan, P.Abdubek, E.Ambing, T.Biorac, J.M.Canaves, H.J.Chiu, X.Dai, A.M.Deacon, M.DiDonato, M.A.Elsliger, A.Godzik, C.Grittini, S.K.Grzechnik, E.Hampton, M.Hornsby, L.Jaroszewski, H.E.Klock, E.Koesema, A.Kreusch, P.Kuhn, S.A.Lesley, I.Levin, M.D.Miller, A.Morse, K.Moy, J.Ouyang, R.Page, K.Quijano, R.Reyes, A.Robb, E.Sims, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, J.Vincent, F.von Delft, X.Wang, B.West, A.White, G.Wolf, O.Zagnitko, K.O.Hodgson, J.Wooley, and I.A.Wilson (2005).
Crystal structure of a formiminotetrahydrofolate cyclodeaminase (TM1560) from Thermotoga maritima at 2.80 A resolution reveals a new fold.
  Proteins, 58, 976-981.
PDB code: 1o5h
15719022 Y.Shen, N.L.Zhukovskaya, Q.Guo, J.Florián, and W.J.Tang (2005).
Calcium-independent calmodulin binding and two-metal-ion catalytic mechanism of anthrax edema factor.
  EMBO J, 24, 929-941.
PDB codes: 1xfu 1xfv 1xfw 1xfx 1xfy 1xfz 1y0v
15148397 K.Xie, M.P.Sowden, G.S.Dance, A.T.Torelli, H.C.Smith, and J.E.Wedekind (2004).
The structure of a yeast RNA-editing deaminase provides insight into the fold and function of activation-induced deaminase and APOBEC-1.
  Proc Natl Acad Sci U S A, 101, 8114-8119.
PDB code: 1r5t
15516966 R.S.Harris, and M.T.Liddament (2004).
Retroviral restriction by APOBEC proteins.
  Nat Rev Immunol, 4, 868-877.  
15159585 Y.J.Chang, C.H.Huang, C.Y.Hu, and S.H.Liaw (2004).
Crystallization and preliminary crystallographic analysis of Bacillus subtilis guanine deaminase.
  Acta Crystallogr D Biol Crystallogr, 60, 1152-1154.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.