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Protein

Cytidine deaminase

Gene

cdd

Organism
Bacillus subtilis (strain 168)
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.
2'deoxycytidine + H2O = 2'-deoxyuridine + NH3.

Cofactori

Zn2+Note: Binds 1 zinc ion per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi53 – 531Zinc; catalytic
Active sitei55 – 551Proton donor
Metal bindingi86 – 861Zinc; catalytic
Metal bindingi89 – 891Zinc; catalytic

GO - Molecular functioni

  1. cytidine deaminase activity Source: UniProtKB-EC
  2. zinc ion binding Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciBSUB:BSU25300-MONOMER.
MetaCyc:BSU25300-MONOMER.
RETL1328306-WGS:GSTH-198-MONOMER.
BRENDAi3.5.4.5. 658.

Names & Taxonomyi

Protein namesi
Recommended name:
Cytidine deaminase (EC:3.5.4.5)
Short name:
CDA
Alternative name(s):
Cytidine aminohydrolase
Gene namesi
Name:cdd
Ordered Locus Names:BSU25300
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
ProteomesiUP000001570 Componenti: Chromosome

Organism-specific databases

GenoListiBSU25300. [Micado]

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi53 – 531C → H: Loss of activity. Reduces activity 500-fold, without effect on zinc binding; when associated with Q-56. 1 Publication
Mutagenesisi56 – 561R → A: No effect on zinc binding. Strongly reduces Vmax. 1 Publication
Mutagenesisi56 – 561R → D: Loss of activity. Reduces zinc binding by 80%. 1 Publication
Mutagenesisi56 – 561R → Q: No effect on zinc binding. Strongly reduces Vmax. Reduces activity 500-fold; when associated with H-53. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 136136Cytidine deaminasePRO_0000171678Add
BLAST

Proteomic databases

PaxDbiP19079.

Interactioni

Subunit structurei

Homotetramer.2 Publications

Protein-protein interaction databases

STRINGi224308.BSU25300.

Structurei

Secondary structure

1
136
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 1412Combined sources
Turni20 – 223Combined sources
Beta strandi26 – 327Combined sources
Beta strandi37 – 415Combined sources
Helixi48 – 503Combined sources
Helixi54 – 6411Combined sources
Beta strandi70 – 789Combined sources
Beta strandi80 – 823Combined sources
Helixi87 – 9610Combined sources
Beta strandi102 – 1065Combined sources
Beta strandi108 – 1103Combined sources
Beta strandi112 – 1165Combined sources
Helixi117 – 1204Combined sources
Helixi127 – 1293Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1JTKX-ray2.04A/B1-136[»]
1UWZX-ray1.99A/B1-136[»]
1UX0X-ray1.99A/B1-136[»]
1UX1X-ray2.36A/B/C/D1-136[»]
ProteinModelPortaliP19079.
SMRiP19079. Positions 1-131.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP19079.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 128128CMP/dCMP-type deaminasePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni42 – 443Substrate binding

Sequence similaritiesi

Contains 1 CMP/dCMP-type deaminase domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG0295.
HOGENOMiHOG000014707.
InParanoidiP19079.
KOiK01489.
OMAiGCRQRIR.
OrthoDBiEOG6XDH25.
PhylomeDBiP19079.

Family and domain databases

InterProiIPR016192. APOBEC/CMP_deaminase_Zn-bd.
IPR002125. CMP_dCMP_Zn-bd.
IPR006262. Cyt_deam_tetra.
IPR016193. Cytidine_deaminase-like.
[Graphical view]
PfamiPF00383. dCMP_cyt_deam_1. 1 hit.
[Graphical view]
SUPFAMiSSF53927. SSF53927. 1 hit.
TIGRFAMsiTIGR01354. cyt_deam_tetra. 1 hit.
PROSITEiPS00903. CYT_DCMP_DEAMINASES_1. 1 hit.
PS51747. CYT_DCMP_DEAMINASES_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P19079-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNRQELITEA LKARDMAYAP YSKFQVGAAL LTKDGKVYRG CNIENAAYSM
60 70 80 90 100
CNCAERTALF KAVSEGDTEF QMLAVAADTP GPVSPCGACR QVISELCTKD
110 120 130
VIVVLTNLQG QIKEMTVEEL LPGAFSSEDL HDERKL
Length:136
Mass (Da):14,854
Last modified:October 31, 1990 - v1
Checksum:i83755B1CDB2A534A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18532 Genomic DNA. Translation: AAB59993.1.
X17430 Genomic DNA. Translation: CAB57856.1.
D84432 Genomic DNA. Translation: BAA12481.1.
K02174 Genomic DNA. Translation: AAB05347.1.
AL009126 Genomic DNA. Translation: CAB14459.1.
U29177 Genomic DNA. Translation: AAA70045.1.
PIRiJE0022.
RefSeqiNP_390408.1. NC_000964.3.

Genome annotation databases

EnsemblBacteriaiCAB14459; CAB14459; BSU25300.
GeneIDi937885.
KEGGibsu:BSU25300.
PATRICi18976898. VBIBacSub10457_2638.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18532 Genomic DNA. Translation: AAB59993.1.
X17430 Genomic DNA. Translation: CAB57856.1.
D84432 Genomic DNA. Translation: BAA12481.1.
K02174 Genomic DNA. Translation: AAB05347.1.
AL009126 Genomic DNA. Translation: CAB14459.1.
U29177 Genomic DNA. Translation: AAA70045.1.
PIRiJE0022.
RefSeqiNP_390408.1. NC_000964.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1JTKX-ray2.04A/B1-136[»]
1UWZX-ray1.99A/B1-136[»]
1UX0X-ray1.99A/B1-136[»]
1UX1X-ray2.36A/B/C/D1-136[»]
ProteinModelPortaliP19079.
SMRiP19079. Positions 1-131.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.BSU25300.

Proteomic databases

PaxDbiP19079.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB14459; CAB14459; BSU25300.
GeneIDi937885.
KEGGibsu:BSU25300.
PATRICi18976898. VBIBacSub10457_2638.

Organism-specific databases

GenoListiBSU25300. [Micado]

Phylogenomic databases

eggNOGiCOG0295.
HOGENOMiHOG000014707.
InParanoidiP19079.
KOiK01489.
OMAiGCRQRIR.
OrthoDBiEOG6XDH25.
PhylomeDBiP19079.

Enzyme and pathway databases

BioCyciBSUB:BSU25300-MONOMER.
MetaCyc:BSU25300-MONOMER.
RETL1328306-WGS:GSTH-198-MONOMER.
BRENDAi3.5.4.5. 658.

Miscellaneous databases

EvolutionaryTraceiP19079.

Family and domain databases

InterProiIPR016192. APOBEC/CMP_deaminase_Zn-bd.
IPR002125. CMP_dCMP_Zn-bd.
IPR006262. Cyt_deam_tetra.
IPR016193. Cytidine_deaminase-like.
[Graphical view]
PfamiPF00383. dCMP_cyt_deam_1. 1 hit.
[Graphical view]
SUPFAMiSSF53927. SSF53927. 1 hit.
TIGRFAMsiTIGR01354. cyt_deam_tetra. 1 hit.
PROSITEiPS00903. CYT_DCMP_DEAMINASES_1. 1 hit.
PS51747. CYT_DCMP_DEAMINASES_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Chromosomal location, cloning and nucleotide sequence of the Bacillus subtilis cdd gene encoding cytidine/deoxycytidine deaminase."
    Song B.-H., Neuhard J.
    Mol. Gen. Genet. 216:462-468(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168.
  2. "Systematic sequencing of the 283 kb 210 degrees-232 degrees region of the Bacillus subtilis genome containing the skin element and many sporulation genes."
    Mizuno M., Masuda S., Takemaru K., Hosono S., Sato T., Takeuchi M., Kobayashi Y.
    Microbiology 142:3103-3111(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168 / JH642.
  3. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
    Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
    , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
    Nature 390:249-256(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.
  4. "Nucleotide sequence upstream of the cdd locus in Bacillus subtilis."
    Kim K., Hwang S., Suh J., Song B.-H., Hong S., Kim J.
    Submitted (JUN-1995) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-10.
    Strain: ED40.
  5. "Crystal structure of the tetrameric cytidine deaminase from Bacillus subtilis at 2.0 A resolution."
    Johansson E., Mejlhede N., Neuhard J., Larsen S.
    Biochemistry 41:2563-2570(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG AND ZINC IONS, SUBUNIT.
  6. "Structural, kinetic, and mutational studies of the zinc ion environment in tetrameric cytidine deaminase."
    Johansson E., Neuhard J., Willemoes M., Larsen S.
    Biochemistry 43:6020-6029(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.99 ANGSTROMS) OF MUTANTS IN COMPLEX WITH SUBSTRATE ANALOG AND ZINC IONS, SUBUNIT, MUTAGENESIS OF CYS-53 AND ARG-56.

Entry informationi

Entry nameiCDD_BACSU
AccessioniPrimary (citable) accession number: P19079
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 31, 1990
Last sequence update: October 31, 1990
Last modified: March 31, 2015
This is version 125 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, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  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.