Reviewed, UniProtKB/Swiss-Prot P0ABF6 (CDD_ECOLI)

Names and origin

Protein names

Recommended name:
    Cytidine deaminase
    EC=3.5.4.5
Alternative name(s):
    Cytidine aminohydrolase
      Short name=CDA

Gene names

Name:	cdd
Ordered Locus Names:	b2143, JW2131

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	294 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	This enzyme scavenge exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis. HAMAP MF_01558
Catalytic activity	Cytidine + H2O = uridine + NH3. HAMAP MF_01558
Cofactor	Binds 1 zinc ion. HAMAP MF_01558
Subunit structure	Homodimer. HAMAP MF_01558
Domain	Each monomer is composed of a small N-terminal alpha-helical domain and two larger core domains that have nearly identical tertiary structures and are related by approximate two-fold symmetry, but lack homology. HAMAP MF_01558
Sequence similarities	Belongs to the cytidine and deoxycytidylate deaminase family.
Sequence caution	The sequence CAA44849.1 differs from that shown. Reason: Frameshift at position 255.

Ontologies

Keywords
Ligand	Metal-binding Zinc
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	cytidine metabolic process Inferred from electronic annotation. Source: InterPro
Cellular component	cytosol Inferred from direct assay. Source: UniProtKB
Molecular function	cytidine deaminase activity Inferred from electronic annotation. Source: HAMAP zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 294

294

Cytidine deaminase HAMAP MF_01558

PRO_0000171649

Regions

Region

89 – 91

3

Substrate binding HAMAP MF_01558

Sites

Active site

104

1

Proton donor HAMAP MF_01558

Metal binding

102

1

Zinc; catalytic HAMAP MF_01558

Metal binding

129

1

Zinc; catalytic HAMAP MF_01558

Metal binding

132

1

Zinc; catalytic HAMAP MF_01558

Experimental info

Sequence conflict

4

1

R → I AA sequence Ref.9

Sequence conflict

58 – 77

20

PLAAA…VGAIA → RWRRPVRVRHCRILMLAQLR Ref.6

Secondary structure

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294

Helix Strand Turn

Details...

Helix

5 – 10

6

Helix

14 – 20

7

Helix

23 – 25

3

Beta strand

31 – 33

3

Helix

35 – 45

11

Helix

49 – 61

13

Turn

67 – 69

3

Beta strand

74 – 79

6

Beta strand

84 – 88

5

Helix

97 – 99

3

Helix

103 – 114

12

Beta strand

119 – 126

8

Helix

130 – 136

7

Helix

142 – 144

3

Beta strand

146 – 148

3

Helix

157 – 160

4

Helix

167 – 170

4

Helix

190 – 200

11

Turn

205 – 207

3

Beta strand

211 – 217

7

Beta strand

222 – 226

5

Helix

239 – 249

11

Helix

254 – 256

3

Beta strand

257 – 265

9

Helix

273 – 283

11

Beta strand

288 – 293

6

Sequences

	Sequence		Length	Mass (Da)
	P0ABF6-1 [UniParc]. Last modified October 25, 2005. Version 1. Checksum: F0B5CD68AB145D7D	FASTA	294	31,540
	10 20 30 40 50 60 MHPRFQTAFA QLADNLQSAL EPILADKYFP ALLTGEQVSS LKSATGLDED ALAFALLPLA 70 80 90 100 110 120 AACARTPLSN FNVGAIARGV SGTWYFGANM EFIGATMQQT VHAEQSAISH AWLSGEKALA 130 140 150 160 170 180 AITVNYTPCG HCRQFMNELN SGLDLRIHLP GREAHALRDY LPDAFGPKDL EIKTLLMDEQ 190 200 210 220 230 240 DHGYALTGDA LSQAAIAAAN RSHMPYSKSP SGVALECKDG RIFSGSYAEN AAFNPTLPPL 250 260 270 280 290 QGALILLNLK GYDYPDIQRA VLAEKADAPL IQWDATSATL KALGCHSIDR VLLA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and nucleotide sequence of the Escherichia coli cytidine deaminase (ccd) gene." Yang C., Carlow D., Wolfenden R., Short S.A. Biochemistry 31:4168-4174(1992) [PubMed: 1567863] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE. Strain: K12.
[2]	"Complete sequence of Escherichia coli cytidine deaminase gene." Montgomery D.S., Drake C., Purvis I.J. Submitted (NOV-1991) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[3]	"Automated multiplex sequencing of the E.coli genome." Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K., Church G.M. Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / BHB2600.
[4]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]	"CRP/cAMP- and CytR-regulated promoters in Escherichia coli K12: the cdd promoter." Valentin-Hansen P., Holst B., Josephsen J., Hammer K., Albrechtsen B. Mol. Microbiol. 3:1385-1390(1989) [PubMed: 2575702] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-77. Strain: K12.
[7]	"Binding of pyrimidin-2-one ribonucleoside by cytidine deaminase as the transition-state analogue 3,4-dihydrouridine and the contribution of the 4-hydroxyl group to its binding affinity." Frick L., Yang C., Marquez V.E., Wolfenden R. Biochemistry 28:9423-9430(1989) [PubMed: 2692708] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-22, CHARACTERIZATION.
[8]	"Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases." Henzel W.J., Billeci T.M., Stults J.T., Wong S.C., Grimley C., Watanabe C. Proc. Natl. Acad. Sci. U.S.A. 90:5011-5015(1993) [PubMed: 8506346] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-17.
[9]	"FIS is a regulator of metabolism in Escherichia coli." Gonzalez-Gil G., Bringmann P., Kahmann R. Mol. Microbiol. 22:21-29(1996) [PubMed: 8899705] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-15. Strain: K12.
[10]	"Amplification of a novel gene, sanA, abolishes a vancomycin-sensitive defect in Escherichia coli." Rida S., Caillet J., Alix J.-H. J. Bacteriol. 178:94-102(1996) [PubMed: 8550448] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 256-294. Strain: K12.
[11]	"Cytidine deaminase. The 2.3 A crystal structure of an enzyme: transition-state analog complex." Betts L., Xiang S., Short S.A., Wolfenden R., Carter C.W. Jr. J. Mol. Biol. 235:635-656(1994) [PubMed: 8289286] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG AND ZINC IONS.
[12]	"Cytidine deaminase complexed to 3-deazacytidine: a 'valence buffer' in zinc enzyme catalysis." Xiang S., Short S.A., Wolfenden R., Carter C.W. Jr. Biochemistry 35:1335-1341(1996) [PubMed: 8634261] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG AND ZINC IONS.
[13]	"The structure of the cytidine deaminase-product complex provides evidence for efficient proton transfer and ground-state destabilization." Xiang S., Short S.A., Wolfenden R., Carter C.W. Jr. Biochemistry 36:4768-4774(1997) [PubMed: 9125497] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH URIDINE AND ZINC IONS.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

M60916 Genomic DNA. Translation: AAA23542.1.
X63144 Genomic DNA. Translation: CAA44849.1. Frameshift.
U00007 Genomic DNA. Translation: AAA60533.1.
U00096 Genomic DNA. Translation: AAC75204.1.
AP009048 Genomic DNA. Translation: BAE76620.1.
X16419 Genomic DNA. Translation: CAA34441.1.
Z47804 Genomic DNA. Translation: CAA87765.1.

PIR

F64982.

RefSeq

AP_002740.1.
NP_416648.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1AF2	X-ray	2.30	A	1-294	[»]
1ALN	X-ray	2.30	A	1-294	[»]
1CTT	X-ray	2.20	A	1-294	[»]
1CTU	X-ray	2.30	A	1-294	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P0ABF6. 1 interaction.

STRING

P0ABF6.

2-D gel databases

SWISS-2DPAGE

P0ABF6.

Proteomic databases

PRIDE

P0ABF6.

Genome annotation databases

GeneID

946663.

GenomeReviews

Gene locus JW2131 in contig AP009048_GR.
Gene locus b2143 in contig U00096_GR.

KEGG

ecj:JW2131.
eco:b2143.

Organism-specific databases

EchoBASE

EB0135.

EcoGene

EG10137. cdd.

CMR

Search...

Phylogenomic databases

HOGENOM

P0ABF6.

OMA

FSPCGHC.

Enzyme and pathway databases

BioCyc

EcoCyc:CYTIDEAM-MON.
MetaCyc:CYTIDEAM-MON.

Gene expression databases

Genevestigator

P0ABF6.

Family and domain databases

HAMAP

MF_01558.
[Tree]

InterPro

IPR016192. APOBEC/CMP_deaminase_Zn-bd.
IPR002125. CMP_dCMP_Zn_bd.
IPR013171. Cyd/dCyd_deaminase_Zn_bd.
IPR006263. Cyt_deam_dimer.
[Graphical view]

Pfam

PF00383. dCMP_cyt_deam_1. 1 hit.
PF08211. dCMP_cyt_deam_2. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01355. cyt_deam_dimer. 1 hit.

PROSITE

PS00903. CYT_DCMP_DEAMINASES. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

CDD_ECOLI

Accession

Primary (citable) accession number: P0ABF6
Secondary accession number(s): P13652, Q2MAT6

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 25, 2005
Last sequence update:	October 25, 2005
Last modified:	November 3, 2009
This is version 40 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)