DB code: D00406

RLCP classification 5.201.1660000.464 : Elimination
4.12.642300.465 : Addition
CATH domain 3.40.140.10 : Cytidine Deaminase; domain 2 Catalytic domain
3.40.140.10 : Cytidine Deaminase; domain 2
E.C. 3.5.4.5
CSA 1ctt
M-CSA 1ctt
MACiE M0097

CATH domain Related DB codes (homologues)
3.40.140.10 : Cytidine Deaminase; domain 2 S00808 S00810

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P0ABF6 Cytidine deaminase
EC 3.5.4.5
Cytidine aminohydrolase
CDA
NP_416648.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_490382.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF00383 (dCMP_cyt_deam_1)
PF08211 (dCMP_cyt_deam_2)
[Graphical View]

KEGG enzyme name
cytidine deaminase
cytosine nucleoside deaminase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P0ABF6 CDD_ECOLI Cytidine + H(2)O = uridine + NH(3). Homodimer. Binds 1 zinc ion.

KEGG Pathways
Map code Pathways E.C.
MAP00983 Drug metabolism - other enzymes
MAP00240 Pyrimidine metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00038 C00475 C00001 C00299 C00014 I00148
E.C.
Compound Zinc Cytidine H2O Uridine NH3 4-hydroxy-cytidine
Type heavy metal amine group,nucleoside H2O amide group,nucleoside amine group,organic ion
ChEBI 29105
17562
15377
16704
16134
PubChem 32051
6175
22247451
962
6029
222
1af2A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Bound:__U Unbound Unbound
1alnA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Analogue:CTD Unbound Unbound Unbound
1cttA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Analogue:DHZ Unbound Unbound
1ctuA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Analogue:ZEB Unbound Unbound
1af2A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1alnA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1cttA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ctuA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P0ABF6

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1af2A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 104 HIS 102;CYS 129;CYS 132(Zn2+ binding) THR 127
1alnA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 104 HIS 102;CYS 129;CYS 132(Zn2+ binding) THR 127
1cttA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 104 HIS 102;CYS 129;CYS 132(Zn2+ binding) THR 127
1ctuA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 104 HIS 102;CYS 129;CYS 132(Zn2+ binding) THR 127
1af2A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1alnA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1cttA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ctuA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
p.651-653, Fig.12 3
[2]
p.6471-6472
[3]
Fig.7, p.97 3
[4]
p.4223-4224
[5]
p.4522
[6]
p.954
[7]
p.1338-1341, Fig.4
[9]
p.4772-4774
[15]
p.662-663
[17]
p.3928-3930

References
[1]
Resource
Comments X-ray crystallography (2.3 Angstroms)
Medline ID 94118314
PubMed ID 8289286
Journal J Mol Biol
Year 1994
Volume 235
Pages 635-56
Authors Betts L, Xiang S, Short SA, Wolfenden R, Carter CW Jr
Title Cytidine deaminase. The 2.3 A crystal structure of an enzyme: transition-state analog complex.
Related PDB
Related UniProtKB P0ABF6
[2]
Resource
Comments
Medline ID
PubMed ID 8204580
Journal Biochemistry
Year 1994
Volume 33
Pages 6468-74
Authors Smith AA, Carlow DC, Wolfenden R, Short SA
Title Mutations affecting transition-state stabilization by residues coordinating zinc at the active site of cytidine deaminase.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 7599282
Journal Biochimie
Year 1995
Volume 77
Pages 92-8
Authors Carter CW Jr
Title The nucleoside deaminases for cytidine and adenosine: structure, transition state stabilization, mechanism, and evolution.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 7703234
Journal Biochemistry
Year 1995
Volume 34
Pages 4220-4
Authors Carlow DC, Smith AA, Yang CC, Short SA, Wolfenden R
Title Major contribution of a carboxymethyl group to transition-state stabilization by cytidine deaminase: mutation and rescue.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 7718553
Journal Biochemistry
Year 1995
Volume 34
Pages 4516-23
Authors Xiang S, Short SA, Wolfenden R, Carter CW Jr
Title Transition-state selectivity for a single hydroxyl group during catalysis by cytidine deaminase.
Related PDB 1ctt 1ctu
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 8547277
Journal Biochemistry
Year 1996
Volume 35
Pages 948-54
Authors Carlow DC, Short SA, Wolfenden R
Title Role of glutamate-104 in generating a transition state analogue inhibitor at the active site of cytidine deaminase.
Related PDB
Related UniProtKB
[7]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 8634261
Journal Biochemistry
Year 1996
Volume 35
Pages 1335-41
Authors Xiang S, Short SA, Wolfenden R, Carter CW Jr
Title Cytidine deaminase complexed to 3-deazacytidine: a "valence buffer" in zinc enzyme catalysis.
Related PDB 1aln
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 8664259
Journal Biochemistry
Year 1996
Volume 35
Pages 4697-703
Authors Shih P, Wolfenden R
Title Enzyme-substrate complexes of adenosine and cytidine deaminases: absence of accumulation of water adducts.
Related PDB
Related UniProtKB
[9]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 9125497
Journal Biochemistry
Year 1997
Volume 36
Pages 4768-74
Authors Xiang S, Short SA, Wolfenden R, Carter CW Jr
Title The structure of the cytidine deaminase-product complex provides evidence for efficient proton transfer and ground-state destabilization.
Related PDB 1af2
Related UniProtKB
[10]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 9477944
Journal Biochemistry
Year 1998
Volume 37
Pages 1199-203
Authors Carlow DC, Short SA, Wolfenden R
Title Complementary truncations of a hydrogen bond to ribose involved in transition-state stabilization by cytidine deaminase.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 9579661
Journal Protein Eng
Year 1998
Volume 11
Pages 59-63
Authors Cambi A, Vincenzetti S, Neuhard J, Costanzi S, Natalini P, Vita A
Title Identification of four amino acid residues essential for catalysis in human cytidine deaminase by site-directed mutagenesis and chemical modifications.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 10933791
Journal Biochemistry
Year 2000
Volume 39
Pages 9746-53
Authors Snider MJ, Gaunitz S, Ridgway C, Short SA, Wolfenden R
Title Temperature effects on the catalytic efficiency, rate enhancement, and transition state affinity of cytidine deaminase, and the thermodynamic consequences for catalysis of removing a substrate "anchor".
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 11292850
Journal Nucleic Acids Res
Year 2001
Volume 29
Pages 1772-80
Authors Dance GS, Beemiller P, Yang Y, Mater DV, Mian IS, Smith HC
Title Identification of the yeast cytidine deaminase CDD1 as an orphan C-->U RNA editase.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 11420434
Journal Protein Sci
Year 2001
Volume 10
Pages 1319-30
Authors Alper KO, Singla M, Stone JL, Bagdassarian CK
Title Correlated conformational fluctuations during enzymatic catalysis: Implications for catalytic rate enhancement.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 11751045
Journal Curr Opin Struct Biol
Year 2001
Volume 11
Pages 657-65
Authors Schramm VL, Shi W
Title Atomic motion in enzymatic reaction coordinates.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 11851403
Journal Biochemistry
Year 2002
Volume 41
Pages 2563-70
Authors Johansson E, Mejlhede N, Neuhard J, Larsen S
Title Crystal structure of the tetrameric cytidine deaminase from Bacillus subtilis at 2.0 A resolution.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 11900535
Journal Biochemistry
Year 2002
Volume 41
Pages 3925-30
Authors Snider MJ, Lazarevic D, Wolfenden R
Title Catalysis by entropic effects: the action of cytidine deaminase on 5,6-dihydrocytidine.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 12906827
Journal Structure (Camb)
Year 2003
Volume 11
Pages 961-72
Authors Ireton GC, Black ME, Stoddard BL
Title The 1.14 A crystal structure of yeast cytosine deaminase: evolution of nucleotide salvage enzymes and implications for genetic chemotherapy.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 14565461
Journal Nucleosides Nucleotides Nucleic Acids
Year 2003
Volume 22
Pages 1539-43
Authors Costanzi S, Vincenzetti S, Vita A, Lambertucci C, Taffi S, Volpini R, Vittori S, Cristalli G
Title Human cytidine deaminase: understanding the catalytic mechanism.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to the cytidine and deoxyxytidylate deaminase family.
According to the literature [1] & [3], this enzyme catalyzes two successive reactions (rather than hydrolysis) as follows:
(A) Addition of water to imine carbon to form a tetrahedral intermediate (I00148).
(B) Elimination of amine group from the intermediate, forming a carbonyl group.
####
(A) Addition of water to imine carbon to form a tetrahedral intermediate (I00148).
(A1) Glu104 play unusual multiple roles in this reaction, by abstracting a proton from the zinc-bound hydroxide, and subsequently by protonating to N-3 atom of the substrate.
(A2) Nucleophilic attack by the zinc bound hydroxide on C-4 atom of the substrate leads to a succession of two tetrahedral intermediate at the carbon atom.
(A3) Formation of the first tetrahedral intermediate with 4-amino group (-NH2) and hydroxy group (-OH) at C-4 atom (I00148); The leaving 4-amino group is stabilized by the carbonyl oxygen atom of Thr127.
(B) Elimination of amine group from the intermediate, forming a carbonyl group.
(B1) Glu104 acts as a general base to deprotonate the hydroxyl group of the first tetrahedral intermediate, forming the second intermediate.
(B2) Glu104 now acts as a general acid to protonate the amine group of the second tetrahedral intermediate, releasing ammonia. (Glu104 plays the shuttling role in the proton transfer.)
According to the paper [15], this nucleophilic displacement involves SN2-like reaction.
More interestingly, this unusual enzyme with zinc ligated by two cysteine residues and a histidine residue adopts an essential strategy, according to the literature [7] & [9]. The Zn-S gamma (Cys132) bond, which lengthens in transition state, shortens as the O-4 atom returns to a state of lower negative charge in the planar product, was proposed to function as a "valence buffer" which can accommodate changing negative charge on the hydroxy group.

Created Updated
2002-09-27 2012-10-16