DB code: D00406

RLCP classification	4.12.642300.465 : Addition
RLCP classification	5.201.1660000.464 : Elimination
CATH domain	3.40.140.10 : Cytidine Deaminase; domain 2	Catalytic domain
CATH 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.
MAP00240	Pyrimidine metabolism
MAP00983	Drug metabolism - other enzymes

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 29105	17562 17562	15377 15377	16704 16704	16134 16134
PubChem	32051 32051	6175 6175	22247451 962 22247451 962	6029 6029	222 222

1af2A01	Bound:_ZN	Unbound		Bound:__U	Unbound	Unbound
1alnA01	Bound:_ZN	Analogue:CTD		Unbound	Unbound	Unbound
1cttA01	Bound:_ZN	Unbound		Analogue:DHZ	Unbound	Unbound
1ctuA01	Bound:_ZN	Unbound		Analogue:ZEB	Unbound	Unbound
1af2A02	Unbound	Unbound		Unbound	Unbound	Unbound
1alnA02	Unbound	Unbound		Unbound	Unbound	Unbound
1cttA02	Unbound	Unbound		Unbound	Unbound	Unbound
1ctuA02	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	GLU 104	HIS 102;CYS 129;CYS 132(Zn2+ binding)		THR 127
1alnA01	GLU 104	HIS 102;CYS 129;CYS 132(Zn2+ binding)		THR 127
1cttA01	GLU 104	HIS 102;CYS 129;CYS 132(Zn2+ binding)		THR 127
1ctuA01	GLU 104	HIS 102;CYS 129;CYS 132(Zn2+ binding)		THR 127
1af2A02
1alnA02
1cttA02
1ctuA02

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.

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