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P0ABF6

- CDD_ECOLI

UniProt

P0ABF6 - CDD_ECOLI

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Protein
Cytidine deaminase
Gene
cdd, b2143, JW2131
Organism
Escherichia coli (strain K12)
Status
Reviewed - 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.UniRule annotation

Catalytic activityi

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

Cofactori

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
Complete GO annotation...

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.

Names & Taxonomyi

Protein namesi
Recommended name:
Cytidine deaminase (EC:3.5.4.5)
Alternative name(s):
Cytidine aminohydrolase
Short name:
CDA
Gene namesi
Name:cdd
Ordered Locus Names:b2143, JW2131
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: 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 deaminaseUniRule annotation
PRO_0000171649Add
BLAST

Proteomic databases

PaxDbiP0ABF6.
PRIDEiP0ABF6.

2D gel databases

SWISS-2DPAGEP0ABF6.

Expressioni

Gene expression databases

GenevestigatoriP0ABF6.

Interactioni

Subunit structurei

Homodimer.

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

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1AF2X-ray2.30A1-294[»]
1ALNX-ray2.30A1-294[»]
1CTTX-ray2.20A1-294[»]
1CTUX-ray2.30A1-294[»]
ProteinModelPortaliP0ABF6.

Miscellaneous databases

EvolutionaryTraceiP0ABF6.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini56 – 13984CMP/dCMP deaminase zinc-binding
Add
BLAST

Region

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

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.UniRule annotation

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0295.
HOGENOMiHOG000218617.
KOiK01489.
OMAiNRSHAPY.
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 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0ABF6-1 [UniParc]FASTAAdd to Basket

« Hide

MHPRFQTAFA QLADNLQSAL EPILADKYFP ALLTGEQVSS LKSATGLDED    50
ALAFALLPLA AACARTPLSN FNVGAIARGV SGTWYFGANM EFIGATMQQT 100
VHAEQSAISH AWLSGEKALA AITVNYTPCG HCRQFMNELN SGLDLRIHLP 150
GREAHALRDY LPDAFGPKDL EIKTLLMDEQ DHGYALTGDA LSQAAIAAAN 200
RSHMPYSKSP SGVALECKDG RIFSGSYAEN AAFNPTLPPL QGALILLNLK 250
GYDYPDIQRA VLAEKADAPL IQWDATSATL KALGCHSIDR VLLA 294
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.

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti4 – 41R → I AA sequence 1 Publication
Sequence conflicti58 – 7720PLAAA…VGAIA → RWRRPVRVRHCRILMLAQLR1 Publication
Add
BLAST

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
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 .
PIRi F64982.
RefSeqi NP_416648.1. NC_000913.3.
YP_490382.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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 [» ]
ProteinModelPortali P0ABF6.
ModBasei Search...

Protein-protein interaction databases

DIPi DIP-36169N.
IntActi P0ABF6. 2 interactions.
MINTi MINT-1283574.
STRINGi 511145.b2143.

2D gel databases

SWISS-2DPAGE P0ABF6.

Proteomic databases

PaxDbi P0ABF6.
PRIDEi P0ABF6.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC75204 ; AAC75204 ; b2143 .
BAE76620 ; BAE76620 ; BAE76620 .
GeneIDi 12934044.
946663.
KEGGi ecj:Y75_p2105.
eco:b2143.
PATRICi 32119629. VBIEscCol129921_2225.

Organism-specific databases

EchoBASEi EB0135.
EcoGenei EG10137. cdd.

Phylogenomic databases

eggNOGi COG0295.
HOGENOMi HOG000218617.
KOi K01489.
OMAi NRSHAPY.
OrthoDBi EOG6XDH25.
PhylomeDBi P0ABF6.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTracei P0ABF6.
PROi P0ABF6.

Gene expression databases

Genevestigatori P0ABF6.

Family and domain databases

HAMAPi MF_01558. Cyt_deam.
InterProi 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 ]
Pfami PF00383. dCMP_cyt_deam_1. 1 hit.
PF08211. dCMP_cyt_deam_2. 1 hit.
[Graphical view ]
PIRSFi PIRSF006334. Cdd_plus_pseudo. 1 hit.
SUPFAMi SSF53927. SSF53927. 2 hits.
TIGRFAMsi TIGR01355. cyt_deam_dimer. 1 hit.
PROSITEi PS00903. CYT_DCMP_DEAMINASES. 1 hit.
[Graphical view ]
ProtoNeti Search...

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: September 3, 2014
This is version 82 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

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