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Protein

Cytidine deaminase

Gene

cdd

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis.

Catalytic activityi

Cytidine + H2O = uridine + NH3.UniRule annotation
2'deoxycytidine + H2O = 2'-deoxyuridine + NH3.UniRule annotation

Cofactori

Zn2+Note: Binds 1 zinc ion.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi102 – 1021Zinc; catalytic
Active sitei104 – 1041Proton donor
Metal bindingi129 – 1291Zinc; catalytic
Metal bindingi132 – 1321Zinc; catalytic

GO - Molecular functioni

  1. cytidine deaminase activity Source: EcoCyc
  2. deoxycytidine deaminase activity Source: EcoCyc
  3. identical protein binding Source: IntAct
  4. pyrimidine nucleoside binding Source: EcoliWiki
  5. zinc ion binding Source: EcoCyc

GO - Biological processi

  1. cytidine deamination Source: EcoCyc
  2. deoxycytidine catabolic process Source: EcoCyc
  3. nucleobase-containing small molecule interconversion Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:CYTIDEAM-MONOMER.
ECOL316407:JW2131-MONOMER.
MetaCyc:CYTIDEAM-MONOMER.
BRENDAi3.5.4.5. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
Cytidine deaminaseUniRule annotation (EC:3.5.4.5UniRule annotation)
Alternative name(s):
Cytidine aminohydrolaseUniRule annotation
Short name:
CDAUniRule annotation
Gene namesi
Name:cddUniRule annotation
Ordered Locus Names:b2143, JW2131
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10137. cdd.

Subcellular locationi

GO - Cellular componenti

  1. cytosol Source: UniProtKB
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 294294Cytidine deaminasePRO_0000171649Add
BLAST

Proteomic databases

PaxDbiP0ABF6.
PRIDEiP0ABF6.

2D gel databases

SWISS-2DPAGEP0ABF6.

Expressioni

Gene expression databases

GenevestigatoriP0ABF6.

Interactioni

Subunit structurei

Homodimer.UniRule annotation3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
itself2EBI-550703,EBI-550703

Protein-protein interaction databases

DIPiDIP-36169N.
IntActiP0ABF6. 2 interactions.
MINTiMINT-1283574.
STRINGi511145.b2143.

Structurei

Secondary structure

1
294
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 53Combined sources
Helixi6 – 105Combined sources
Helixi14 – 207Combined sources
Turni21 – 255Combined sources
Beta strandi31 – 333Combined sources
Helixi35 – 4410Combined sources
Helixi49 – 6214Combined sources
Turni67 – 693Combined sources
Beta strandi74 – 796Combined sources
Beta strandi84 – 885Combined sources
Helixi97 – 993Combined sources
Helixi103 – 11311Combined sources
Beta strandi119 – 1268Combined sources
Helixi130 – 1367Combined sources
Helixi142 – 1443Combined sources
Beta strandi146 – 1483Combined sources
Helixi157 – 1604Combined sources
Helixi167 – 1704Combined sources
Helixi190 – 20011Combined sources
Turni205 – 2073Combined sources
Beta strandi211 – 2177Combined sources
Beta strandi222 – 2265Combined sources
Helixi239 – 24911Combined sources
Helixi254 – 2563Combined sources
Beta strandi257 – 2648Combined sources
Helixi273 – 28311Combined sources
Beta strandi288 – 2925Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1AF2X-ray2.30A1-294[»]
1ALNX-ray2.30A1-294[»]
1CTTX-ray2.20A1-294[»]
1CTUX-ray2.30A1-294[»]
SMRiP0ABF6. Positions 1-294.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0ABF6.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini48 – 168121CMP/dCMP-type deaminase 1PROSITE-ProRule annotationAdd
BLAST
Domaini186 – 294109CMP/dCMP-type deaminase 2PROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni89 – 913Substrate binding

Domaini

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.

Sequence similaritiesi

Belongs to the cytidine and deoxycytidylate deaminase family.UniRule annotation
Contains 2 CMP/dCMP-type deaminase domains.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG0295.
HOGENOMiHOG000218617.
InParanoidiP0ABF6.
KOiK01489.
OMAiSHAPYSK.
OrthoDBiEOG6XDH25.
PhylomeDBiP0ABF6.

Family and domain databases

HAMAPiMF_01558. Cyt_deam.
InterProiIPR016192. 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]
PfamiPF00383. dCMP_cyt_deam_1. 1 hit.
PF08211. dCMP_cyt_deam_2. 1 hit.
[Graphical view]
PIRSFiPIRSF006334. Cdd_plus_pseudo. 1 hit.
SUPFAMiSSF53927. SSF53927. 2 hits.
TIGRFAMsiTIGR01355. cyt_deam_dimer. 1 hit.
PROSITEiPS00903. CYT_DCMP_DEAMINASES_1. 1 hit.
PS51747. CYT_DCMP_DEAMINASES_2. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0ABF6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHPRFQTAFA QLADNLQSAL EPILADKYFP ALLTGEQVSS LKSATGLDED
60 70 80 90 100
ALAFALLPLA AACARTPLSN FNVGAIARGV SGTWYFGANM EFIGATMQQT
110 120 130 140 150
VHAEQSAISH AWLSGEKALA AITVNYTPCG HCRQFMNELN SGLDLRIHLP
160 170 180 190 200
GREAHALRDY LPDAFGPKDL EIKTLLMDEQ DHGYALTGDA LSQAAIAAAN
210 220 230 240 250
RSHMPYSKSP SGVALECKDG RIFSGSYAEN AAFNPTLPPL QGALILLNLK
260 270 280 290
GYDYPDIQRA VLAEKADAPL IQWDATSATL KALGCHSIDR VLLA
Length:294
Mass (Da):31,540
Last modified:October 25, 2005 - v1
Checksum:iF0B5CD68AB145D7D
GO

Sequence cautioni

The sequence CAA44849.1 differs from that shown. Reason: Frameshift at position 255. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti4 – 41R → I AA sequence (PubMed:8899705).Curated
Sequence conflicti58 – 7720PLAAA…VGAIA → RWRRPVRVRHCRILMLAQLR (PubMed:2575702).CuratedAdd
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiF64982.
RefSeqiNP_416648.1. NC_000913.3.
YP_490382.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC75204; AAC75204; b2143.
BAE76620; BAE76620; BAE76620.
GeneIDi12934044.
946663.
KEGGiecj:Y75_p2105.
eco:b2143.
PATRICi32119629. VBIEscCol129921_2225.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiF64982.
RefSeqiNP_416648.1. NC_000913.3.
YP_490382.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1AF2X-ray2.30A1-294[»]
1ALNX-ray2.30A1-294[»]
1CTTX-ray2.20A1-294[»]
1CTUX-ray2.30A1-294[»]
SMRiP0ABF6. Positions 1-294.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-36169N.
IntActiP0ABF6. 2 interactions.
MINTiMINT-1283574.
STRINGi511145.b2143.

2D gel databases

SWISS-2DPAGEP0ABF6.

Proteomic databases

PaxDbiP0ABF6.
PRIDEiP0ABF6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75204; AAC75204; b2143.
BAE76620; BAE76620; BAE76620.
GeneIDi12934044.
946663.
KEGGiecj:Y75_p2105.
eco:b2143.
PATRICi32119629. VBIEscCol129921_2225.

Organism-specific databases

EchoBASEiEB0135.
EcoGeneiEG10137. cdd.

Phylogenomic databases

eggNOGiCOG0295.
HOGENOMiHOG000218617.
InParanoidiP0ABF6.
KOiK01489.
OMAiSHAPYSK.
OrthoDBiEOG6XDH25.
PhylomeDBiP0ABF6.

Enzyme and pathway databases

BioCyciEcoCyc:CYTIDEAM-MONOMER.
ECOL316407:JW2131-MONOMER.
MetaCyc:CYTIDEAM-MONOMER.
BRENDAi3.5.4.5. 2026.

Miscellaneous databases

EvolutionaryTraceiP0ABF6.
PROiP0ABF6.

Gene expression databases

GenevestigatoriP0ABF6.

Family and domain databases

HAMAPiMF_01558. Cyt_deam.
InterProiIPR016192. 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]
PfamiPF00383. dCMP_cyt_deam_1. 1 hit.
PF08211. dCMP_cyt_deam_2. 1 hit.
[Graphical view]
PIRSFiPIRSF006334. Cdd_plus_pseudo. 1 hit.
SUPFAMiSSF53927. SSF53927. 2 hits.
TIGRFAMsiTIGR01355. cyt_deam_dimer. 1 hit.
PROSITEiPS00903. CYT_DCMP_DEAMINASES_1. 1 hit.
PS51747. CYT_DCMP_DEAMINASES_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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. 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.

Entry informationi

Entry nameiCDD_ECOLI
AccessioniPrimary (citable) accession number: P0ABF6
Secondary accession number(s): P13652, Q2MAT6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 25, 2005
Last sequence update: October 25, 2005
Last modified: April 1, 2015
This is version 87 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.