D00675
type: Enzyme
rlcp: p562
rlcp: p563
cath: Urease, subunit C; domain 1
cath: TIM Barrel
ec: https://purl.uniprot.org/enzyme/3.5.4.1
uniprot: P25524
kegg enzyme: Cytosine deaminase
kegg enzyme: Isocytosine deaminase
kegg pathway: Pyrimidine metabolism
kegg cofactor: Fe2+
kegg substrate: cytosine
kegg substrate: H2O
kegg product: uracil
kegg product: NH3
kegg intermediate: 4-Hydroxy-cytosine
pdb: 1k6wA01
pdb: 1k70A01
pdb: 1r9xA01
pdb: 1r9yA01
pdb: 1r9zA01
pdb: 1ra0A01
pdb: 1ra5A01
pdb: 1rakA01
pdb: 3g77A01
pdb: 3o7uA01
pdb: 3r0dA01
pdb: 3rn6A01
pdb: 1k6wA02
pdb: 1k70A02
pdb: 1r9xA02
pdb: 1r9yA02
pdb: 1r9zA02
pdb: 1ra0A02
pdb: 1ra5A02
pdb: 1rakA02
pdb: 3g77A02
pdb: 3o7uA02
pdb: 3r0dA02
pdb: 3rn6A02
pdb bound state: Unbound
  compound: cytosine
  pdb: 1k6wA01
pdb bound state: Unbound
  compound: cytosine
  pdb: 1k70A01
pdb bound state: Unbound
  compound: cytosine
  pdb: 1r9xA01
pdb bound state: Unbound
  compound: cytosine
  pdb: 1r9yA01
pdb bound state: Unbound
  compound: cytosine
  pdb: 1r9zA01
pdb bound state: Unbound
  compound: cytosine
  pdb: 1ra0A01
pdb bound state: Unbound
  compound: cytosine
  pdb: 1ra5A01
pdb bound state: Unbound
  compound: cytosine
  pdb: 1rakA01
pdb bound state: Unbound
  compound: cytosine
  pdb: 3g77A01
pdb bound state: Unbound
  compound: cytosine
  pdb: 3o7uA01
pdb bound state: Unbound
  compound: cytosine
  pdb: 3r0dA01
pdb bound state: Unbound
  compound: cytosine
  pdb: 3rn6A01
pdb bound state: Unbound
  compound: cytosine
  pdb: 1k6wA02
pdb bound state: Unbound
  compound: cytosine
  pdb: 1k70A02
pdb bound state: Unbound
  compound: cytosine
  pdb: 1r9xA02
pdb bound state: Unbound
  compound: cytosine
  pdb: 1r9yA02
pdb bound state: Unbound
  compound: cytosine
  pdb: 1r9zA02
pdb bound state: Unbound
  compound: cytosine
  pdb: 1ra0A02
pdb bound state: Unbound
  compound: cytosine
  pdb: 1ra5A02
pdb bound state: Unbound
  compound: cytosine
  pdb: 1rakA02
pdb bound state: Unbound
  compound: cytosine
  pdb: 3g77A02
pdb bound state: Unbound
  compound: cytosine
  pdb: 3o7uA02
pdb bound state: Unbound
  compound: cytosine
  pdb: 3r0dA02
active site residues resources: Crystal structure of yeast cytosine deaminase. Insights into enzyme mechanism and evolution.
active site residues resources: 1k6w
active site residues resources: 1k70
references: Atomic structure of adenosine deaminase complexed with a transition-state analog: understanding catalysis and immunodeficiency mutations.
references: A pre-transition-state mimic of an enzyme: X-ray structure of adenosine deaminase with bound 1-deazaadenosine and zinc-activated water.
references: Cytosine deaminase. The roles of divalent metal ions in catalysis.
references: Complexes of adenosine deaminase with two potent inhibitors: X-ray structures in four independent molecules at pH of maximum activity.
references: Escherichia coli cytosine deaminase: the kinetics and thermodynamics for binding of cytosine to the apoenzyme and the Zn(2+) holoenzyme are similar.
references: The structure of Escherichia coli cytosine deaminase.
references: Crystal structure of yeast cytosine deaminase. Insights into enzyme mechanism and evolution.
references: The 1.14 A crystal structure of yeast cytosine deaminase: evolution of nucleotide salvage enzymes and implications for genetic chemotherapy.
references: Metal-mediated deamination of cytosine: experiment and DFT calculations.
references: Alanine-scanning mutagenesis reveals a cytosine deaminase mutant with altered substrate preference.
references: Random mutagenesis and selection of Escherichia coli cytosine deaminase for cancer gene therapy.
references: Three-dimensional structure and catalytic mechanism of cytosine deaminase.
references: Rescue of the orphan enzyme isoguanine deaminase.
comment: This enzyme is homologous to adenosine deaminase (EC 3.5.4.4; S00232 in EzCatDB) and guanine deaminase (EC 3.5.4.3; D00873 in EzCatDB). Although its catalytic site is similar to those of the homologous enzymes, cofactor ion, Fe2+, is different from the cofactor ion, zinc ion, adopted by the homologous enzymes. However, the reaction mechanism seems to be very similar to those homologous enzymes. According to the literature [12] and the reaction mechanism of the homologous enzymes(S00232 and D00873 in EzCatDB), this enzyme catalyzes two successive reactions (rather than hydrolysis) as follows: (A) Addition of water to imine carbon to form a tetrahedral intermediate (I00151). (A1) Asp313 (or Glu217) acts as a general base to deprotonate the Fe2+-bound water. Here, the positive charge of His246 seems to stabilize the activated water. His246 may assist the catalytic function of Glu217 as well (see [12]). (A2) The activated water makes a nucleophilic attack on the C4 atom of cytosine, whilst Glu217 acts as a general acid to protonate the N3 atom (protonation site) of the cytosine. This reaction leads to the formation of tetrahedral intermediate at the C4 atom, transforming N3-C4 bond from a double bond to a single bond (I00151). (B) Elimination of amine group from the intermediate (I00151), forming a carbonyl group. (B1) Asp313 acts as a general acid to protonate the eliminated amine group, releasing the ammonia. (B2) Asp313 acts as a general base to deprotonate the hydroxyl group, bound to the Fe2+ ion and His246. (Here, His246 may assist the catalytic function of Asp313 as well.) This reaction leads to the enol form of the product, cytosine. (This may be an E1-like reaction, as amine elimination occurs prior to deprotonation.)

Urease, subunit C; domain 1
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/2.30.40.10

TIM Barrel
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.20.20.140
catalytic domain: index.html

Pyrimidine metabolism
type: KeggPathway
references: KEGG:MAP00240

Fe2+
type: KeggCofactor
references: KEGG:C14818
compound type: heavy metal
references: CHEBI:29033
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

cytosine
type: KeggSubstrate
references: KEGG:C00380
compound type: amide group
compound type: amine group
compound type: aromatic ring (with nitrogen atoms)
references: CHEBI:16040
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

H2O
type: KeggSubstrate
references: KEGG:C00001
compound type: H2O
references: CHEBI:15377
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

uracil
type: KeggProduct
references: KEGG:C00106
compound type: amide group
compound type: aromatic ring (with nitrogen atoms)
references: CHEBI:17568
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

NH3
type: KeggProduct
references: KEGG:C00014
compound type: amine group
compound type: organic ion
references: CHEBI:16134
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

4-Hydroxy-cytosine
type: KeggIntermediate
references: KEGG:I00151

1k6wA02
type: Pdb
references: 1k6w
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1k6w
catalytic residue: GLU 217;HIS 246;ASP 313
cofactor binding residue: HIS 61;HIS 63;HIS 214;ASP 313(Fe2+ binding)

1k70A02
type: Pdb
references: 1k70
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1k70
catalytic residue: GLU 217;HIS 246;ASP 313
cofactor binding residue: HIS 61;HIS 63;HIS 214;ASP 313(Fe2+ binding)

1r9xA02
type: Pdb
references: 1r9x
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1r9x
catalytic residue: GLU 217;HIS 246;ASP 313
cofactor binding residue: HIS 61;HIS 63;HIS 214;ASP 313(Fe2+ binding)
comment: mutant D314G

1r9yA02
type: Pdb
references: 1r9y
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1r9y
catalytic residue: GLU 217;HIS 246;ASP 313
cofactor binding residue: HIS 61;HIS 63;HIS 214;ASP 313(Fe2+ binding)
comment: mutant D314A

1r9zA02
type: Pdb
references: 1r9z
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1r9z
catalytic residue: GLU 217;HIS 246;ASP 313
cofactor binding residue: HIS 61;HIS 63;HIS 214;ASP 313(Fe2+ binding)
comment: mutant D314S

1ra0A02
type: Pdb
references: 1ra0
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ra0
catalytic residue: GLU 217;HIS 246;ASP 313
cofactor binding residue: HIS 61;HIS 63;HIS 214;ASP 313(Fe2+ binding)
comment: mutant D314G

1ra5A02
type: Pdb
references: 1ra5
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ra5
catalytic residue: GLU 217;HIS 246;ASP 313
cofactor binding residue: HIS 61;HIS 63;HIS 214;ASP 313(Fe2+ binding)
comment: mutant D314A

1rakA02
type: Pdb
references: 1rak
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1rak
catalytic residue: GLU 217;HIS 246;ASP 313
cofactor binding residue: HIS 61;HIS 63;HIS 214;ASP 313(Fe2+ binding)
comment: mutant D314S

3g77A02
type: Pdb
references: 3g77
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:3g77
catalytic residue: GLU 217;HIS 246;ASP 313
cofactor binding residue: HIS 61;HIS 63;HIS 214;ASP 313(Fe2+ binding)
comment: mutant V152A, F316C, D317G

3o7uA02
type: Pdb
references: 3o7u
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:3o7u
catalytic residue: GLU 217;HIS 246;ASP 313
cofactor binding residue: HIS 61;HIS 63;HIS 214;ASP 313(Fe2+ binding)

3r0dA02
type: Pdb
references: 3r0d
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:3r0d
catalytic residue: GLU 217;HIS 246;ASP 313
cofactor binding residue: HIS 61;HIS 63;HIS 214;ASP 313(Fe2+ binding)

3rn6A02
type: Pdb
references: 3rn6
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:3rn6
catalytic residue: GLU 217;HIS 246;ASP 313
cofactor binding residue: HIS 61;HIS 63;HIS 214;ASP 313(Fe2+ binding)

Atomic structure of adenosine deaminase complexed with a transition-state analog: understanding catalysis and immunodeficiency mutations.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/1925539
journal: Science
volume: 252
pages: 1278-84
published year: 1991
authors:
  item: Wilson DK
  item: Rudolph FB
  item: Quiocho FA

A pre-transition-state mimic of an enzyme: X-ray structure of adenosine deaminase with bound 1-deazaadenosine and zinc-activated water.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8439534
journal: Biochemistry
volume: 32
pages: 1689-94
published year: 1993
authors:
  item: Wilson DK
  item: Quiocho FA

Cytosine deaminase. The roles of divalent metal ions in catalysis.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8226944
journal: J Biol Chem
volume: 268
pages: 24005-11
published year: 1993
authors:
  item: Porter DJ
  item: Austin EA

Complexes of adenosine deaminase with two potent inhibitors: X-ray structures in four independent molecules at pH of maximum activity.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9622483
journal: Biochemistry
volume: 37
pages: 8314-24
published year: 1998
authors:
  item: Wang Z
  item: Quiocho FA

Escherichia coli cytosine deaminase: the kinetics and thermodynamics for binding of cytosine to the apoenzyme and the Zn(2+) holoenzyme are similar.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10669789
journal: Biochim Biophys Acta
volume: 1476
pages: 239-52
published year: 2000
authors:
  item: Porter DJ

The structure of Escherichia coli cytosine deaminase.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS).
references: http://www.ncbi.nlm.nih.gov/pubmed/11812140
journal: J Mol Biol
volume: 315
pages: 687-97
published year: 2002
authors:
  item: Ireton GC
  item: McDermott G
  item: Black ME
  item: Stoddard BL
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P25524

Crystal structure of yeast cytosine deaminase. Insights into enzyme mechanism and evolution.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
references: http://www.ncbi.nlm.nih.gov/pubmed/12637534
journal: J Biol Chem
volume: 278
pages: 19111-7
published year: 2003
authors:
  item: Ko TP
  item: Lin JJ
  item: Hu CY
  item: Hsu YH
  item: Wang AH
  item: Liaw SH

The 1.14 A crystal structure of yeast cytosine deaminase: evolution of nucleotide salvage enzymes and implications for genetic chemotherapy.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.14 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG AND ZINC IONS, AND SUBUNIT.
references: http://www.ncbi.nlm.nih.gov/pubmed/12906827
journal: Structure
volume: 11
pages: 961-72
published year: 2003
authors:
  item: Ireton GC
  item: Black ME
  item: Stoddard BL

Metal-mediated deamination of cytosine: experiment and DFT calculations.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/15468078
journal: Angew Chem Int Ed Engl
volume: 43
pages: 5396-9
published year: 2004
authors:
  item: Sponer JE
  item: Sanz Miguel PJ
  item: Rodriguez-Santiago L
  item: Erxleben A
  item: Krumm M
  item: Sodupe M
  item: Sponer J
  item: Lippert B

Alanine-scanning mutagenesis reveals a cytosine deaminase mutant with altered substrate preference.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/15248753
journal: Biochemistry
volume: 43
pages: 8957-64
published year: 2004
authors:
  item: Mahan SD
  item: Ireton GC
  item: Stoddard BL
  item: Black ME

Random mutagenesis and selection of Escherichia coli cytosine deaminase for cancer gene therapy.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY.
references: http://www.ncbi.nlm.nih.gov/pubmed/15381761
journal: Protein Eng Des Sel
volume: 17
pages: 625-33
published year: 2004
authors:
  item: Mahan SD
  item: Ireton GC
  item: Knoeber C
  item: Stoddard BL
  item: Black ME
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Three-dimensional structure and catalytic mechanism of cytosine deaminase.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/21545144
journal: Biochemistry
volume: 50
pages: 5077-85
published year: 2011
authors:
  item: Hall RS
  item: Fedorov AA
  item: Xu C
  item: Fedorov EV
  item: Almo SC
  item: Raushel FM
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Rescue of the orphan enzyme isoguanine deaminase.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/21604715
journal: Biochemistry
volume: 50
pages: 5555-7
published year: 2011
authors:
  item: Hitchcock DS
  item: Fedorov AA
  item: Fedorov EV
  item: Dangott LJ
  item: Almo SC
  item: Raushel FM
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Analogue
compound: cytosine
pdb: 3rn6A02
ligand het code: IGA

Analogue
compound: Fe2+
pdb: 3o7uA02
ligand het code: _ZN

Analogue
compound: Fe2+
pdb: 3r0dA02
ligand het code: _ZN

Analogue
compound: Fe2+
pdb: 3rn6A02
ligand het code: _ZN

IntermediateAnalogue
compound: 4-Hydroxy-cytosine
pdb: 1k70A02
ligand het code: HPY

IntermediateAnalogue
compound: 4-Hydroxy-cytosine
pdb: 1ra0A02
ligand het code: FPY

IntermediateAnalogue
compound: 4-Hydroxy-cytosine
pdb: 1ra5A02
ligand het code: FPY

IntermediateAnalogue
compound: 4-Hydroxy-cytosine
pdb: 1rakA02
ligand het code: FPY

IntermediateAnalogue
compound: 4-Hydroxy-cytosine
pdb: 3o7uA02
ligand het code: O7U

ReferenceForCatalyticMechanism
reference index: 6
reference section: p. 693-694

ReferenceForCatalyticMechanism
reference index: 12
reference section: Scheme 4