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P19079

- CDD_BACSU

UniProt

P19079 - CDD_BACSU

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Protein
Cytidine deaminase
Gene
cdd, BSU25300
Organism
Bacillus subtilis (strain 168)
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.

Catalytic activityi

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

Cofactori

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.

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: 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 deaminase
PRO_0000171678Add
BLAST

Proteomic databases

PaxDbiP19079.

Interactioni

Subunit structurei

Homotetramer.2 Publications

Protein-protein interaction databases

STRINGi224308.BSU25300.

Structurei

Secondary structure

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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.

Miscellaneous databases

EvolutionaryTraceiP19079.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini3 – 104102CMP/dCMP deaminase zinc-binding
Add
BLAST

Region

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

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0295.
HOGENOMiHOG000014707.
KOiK01489.
OMAiIADTPRP.
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 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P19079-1 [UniParc]FASTAAdd to Basket

« Hide

MNRQELITEA LKARDMAYAP YSKFQVGAAL LTKDGKVYRG CNIENAAYSM    50
CNCAERTALF KAVSEGDTEF QMLAVAADTP GPVSPCGACR QVISELCTKD 100
VIVVLTNLQG QIKEMTVEEL LPGAFSSEDL HDERKL 136
Length:136
Mass (Da):14,854
Last modified:November 1, 1990 - v1
Checksum:i83755B1CDB2A534A
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
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 .
PIRi JE0022.
RefSeqi NP_390408.1. NC_000964.3.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1JTK X-ray 2.04 A/B 1-136 [» ]
1UWZ X-ray 1.99 A/B 1-136 [» ]
1UX0 X-ray 1.99 A/B 1-136 [» ]
1UX1 X-ray 2.36 A/B/C/D 1-136 [» ]
ProteinModelPortali P19079.
SMRi P19079. Positions 1-131.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 224308.BSU25300.

Proteomic databases

PaxDbi P19079.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai CAB14459 ; CAB14459 ; BSU25300 .
GeneIDi 937885.
KEGGi bsu:BSU25300.
PATRICi 18976898. VBIBacSub10457_2638.

Organism-specific databases

GenoListi BSU25300. [Micado ]

Phylogenomic databases

eggNOGi COG0295.
HOGENOMi HOG000014707.
KOi K01489.
OMAi IADTPRP.
OrthoDBi EOG6XDH25.
PhylomeDBi P19079.

Enzyme and pathway databases

BioCyci BSUB:BSU25300-MONOMER.
MetaCyc:BSU25300-MONOMER.
RETL1328306-WGS:GSTH-198-MONOMER.

Miscellaneous databases

EvolutionaryTracei P19079.

Family and domain databases

InterProi IPR016192. APOBEC/CMP_deaminase_Zn-bd.
IPR002125. CMP_dCMP_Zn-bd.
IPR006262. Cyt_deam_tetra.
IPR016193. Cytidine_deaminase-like.
[Graphical view ]
Pfami PF00383. dCMP_cyt_deam_1. 1 hit.
[Graphical view ]
SUPFAMi SSF53927. SSF53927. 1 hit.
TIGRFAMsi TIGR01354. cyt_deam_tetra. 1 hit.
PROSITEi PS00903. CYT_DCMP_DEAMINASES. 1 hit.
[Graphical view ]
ProtoNeti Search...

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(1989) [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(1996) [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(1997) [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 (JUL-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(2002) [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(2004) [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: November 1, 1990
Last sequence update: November 1, 1990
Last modified: July 9, 2014
This is version 120 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

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