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P0ABF6 (CDD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 78. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length294 AA.
Sequence statusComplete.
Protein existenceEvidence 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

2'deoxycytidine + H2O = 2'-deoxyuridine + 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.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

itself2EBI-550703,EBI-550703

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 294294Cytidine deaminase HAMAP-Rule MF_01558
PRO_0000171649

Regions

Domain56 – 13984CMP/dCMP deaminase zinc-binding
Region89 – 913Substrate binding HAMAP-Rule MF_01558

Sites

Active site1041Proton donor
Metal binding1021Zinc; catalytic
Metal binding1291Zinc; catalytic
Metal binding1321Zinc; catalytic

Experimental info

Sequence conflict41R → I AA sequence Ref.9
Sequence conflict58 – 7720PLAAA…VGAIA → RWRRPVRVRHCRILMLAQLR Ref.6

Secondary structure

.................................................... 294
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P0ABF6 [UniParc].

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

FASTA29431,540
        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' 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 277:1453-1462(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.
PIRF64982.
RefSeqNP_416648.1. NC_000913.3.
YP_490382.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1AF2X-ray2.30A1-294[»]
1ALNX-ray2.30A1-294[»]
1CTTX-ray2.20A1-294[»]
1CTUX-ray2.30A1-294[»]
ProteinModelPortalP0ABF6.
SMRP0ABF6. Positions 1-294.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-36169N.
IntActP0ABF6. 2 interactions.
MINTMINT-1283574.
STRING511145.b2143.

2D gel databases

SWISS-2DPAGEP0ABF6.

Proteomic databases

PaxDbP0ABF6.
PRIDEP0ABF6.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC75204; AAC75204; b2143.
BAE76620; BAE76620; BAE76620.
GeneID12934044.
946663.
KEGGecj:Y75_p2105.
eco:b2143.
PATRIC32119629. VBIEscCol129921_2225.

Organism-specific databases

EchoBASEEB0135.
EcoGeneEG10137. cdd.

Phylogenomic databases

eggNOGCOG0295.
HOGENOMHOG000218617.
KOK01489.
OMANRSHAPY.
OrthoDBEOG6XDH25.
PhylomeDBP0ABF6.
ProtClustDBPRK09027.

Enzyme and pathway databases

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

Gene expression databases

GenevestigatorP0ABF6.

Family and domain databases

HAMAPMF_01558. Cyt_deam.
InterProIPR016192. 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]
PfamPF00383. dCMP_cyt_deam_1. 1 hit.
PF08211. dCMP_cyt_deam_2. 1 hit.
[Graphical view]
PIRSFPIRSF006334. Cdd_plus_pseudo. 1 hit.
SUPFAMSSF53927. SSF53927. 2 hits.
TIGRFAMsTIGR01355. cyt_deam_dimer. 1 hit.
PROSITEPS00903. CYT_DCMP_DEAMINASES. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP0ABF6.
PROP0ABF6.

Entry information

Entry nameCDD_ECOLI
AccessionPrimary (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: April 16, 2014
This is version 78 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

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