Cytidine deaminase - Escherichia coli (strain K12)

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P0ABF6 (CDD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 71. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

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) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	294 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	This enzyme scavenge exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis. HAMAP-Rule MF_01558
Catalytic activity	Cytidine + H₂O = uridine + NH₃. HAMAP-Rule MF_01558
Cofactor	Binds 1 zinc ion.
Subunit structure	Homodimer.
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-Rule MF_01558
Sequence similarities	Belongs to the cytidine and deoxycytidylate deaminase family. Contains 1 CMP/dCMP deaminase zinc-binding domain.
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 Reference proteome
Gene Ontology (GO)
Biological_process	deoxycytidine catabolic process Inferred from direct assay PubMed 6386817. Source: EcoCyc nucleobase-containing small molecule interconversion Inferred from direct assay PubMed 4944311 PubMed 4944312. Source: EcoliWiki
Cellular_component	cytosol Inferred from direct assay PubMed 16858726. Source: UniProtKB
Molecular_function	cytidine deaminase activity Inferred from direct assay PubMed 2651432. Source: EcoCyc deoxycytidine deaminase activity Inferred from direct assay PubMed 6386817. Source: EcoCyc pyrimidine nucleoside binding Inferred from direct assay PubMed 3910086. Source: EcoliWiki zinc ion binding Inferred from direct assay Ref.1. Source: EcoCyc
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-Rule MF_01558

PRO_0000171649

Regions

Domain

56 – 139

CMP/dCMP deaminase zinc-binding

Region

89 – 91

Substrate binding HAMAP-Rule MF_01558

Sites

Active site

104

Proton donor

Metal binding

102

Zinc; catalytic

Metal binding

129

Zinc; catalytic

Metal binding

132

Zinc; catalytic

Experimental info

Sequence conflict

R → I AA sequence Ref.9

Sequence conflict

58 – 77

PLAAA…VGAIA → RWRRPVRVRHCRILMLAQLR Ref.6

Secondary structure

294

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P0ABF6 [UniParc].

Last modified October 25, 2005. Version 1.
Checksum: F0B5CD68AB145D7D
Show »

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

« Hide

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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH URIDINE AND ZINC IONS.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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

NP_416648.1. NC_000913.2.
YP_490382.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P0ABF6.

SMR

P0ABF6. Positions 1-294.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-36169N.

IntAct

P0ABF6. 1 interaction.

MINT

MINT-1283574.

STRING

511145.b2143.

2D gel databases

SWISS-2DPAGE

P0ABF6.

Proteomic databases

PaxDb

P0ABF6.

PRIDE

P0ABF6.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC75204; AAC75204; b2143.
BAE76620; BAE76620; BAE76620.

GeneID

12934044.
946663.

KEGG

ecj:Y75_p2105.
eco:b2143.

PATRIC

32119629. VBIEscCol129921_2225.

Organism-specific databases

EchoBASE

EB0135.

EcoGene

EG10137. cdd.

Phylogenomic databases

eggNOG

COG0295.

HOGENOM

HOG000218617.

K01489.

OMA

NRSHAPY.

ProtClustDB

PRK09027.

Enzyme and pathway databases

BioCyc

EcoCyc:CYTIDEAM-MONOMER.
ECOL316407:JW2131-MONOMER.
MetaCyc:CYTIDEAM-MONOMER.

Gene expression databases

Genevestigator

P0ABF6.

Family and domain databases

HAMAP

MF_01558. Cyt_deam.

InterPro

IPR016192. APOBEC/CMP_deaminase_Zn-bd.
IPR002125. CMP_dCMP_Zn-bd.
IPR013171. Cyd/dCyd_deaminase_Zn-bd.
IPR006263. Cyt_deam_dimer.
IPR016193. Cytidine_deaminase-like.
IPR020797. Cytidine_deaminase_bacteria.
[Graphical view]

PANTHER

PTHR11644:SF12. PTHR11644:SF12. 1 hit.

Pfam

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

PIRSF

PIRSF006334. Cdd_plus_pseudo. 1 hit.

SUPFAM

SSF53927. Cytidine_deaminase-like. 2 hits.

TIGRFAMs

TIGR01355. cyt_deam_dimer. 1 hit.

PROSITE

PS00903. CYT_DCMP_DEAMINASES. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P0ABF6.

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:	May 1, 2013
This is version 71 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2D gel databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents