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P19079 (CDD_BACSU) Reviewed, UniProtKB/Swiss-Prot

Last modified November 13, 2013. Version 118. 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·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Cytidine deaminase

Short name=CDA
EC=3.5.4.5
Alternative name(s):
Cytidine aminohydrolase
Gene names
Name:cdd
Ordered Locus Names:BSU25300
OrganismBacillus subtilis (strain 168) [Reference proteome] [HAMAP]
Taxonomic identifier224308 [NCBI]
Taxonomic lineageBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus

Protein attributes

Sequence length136 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.

Catalytic activity

Cytidine + H2O = uridine + NH3.

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

Cofactor

Binds 1 zinc ion per subunit.

Subunit structure

Homotetramer. Ref.5 Ref.6

Sequence similarities

Belongs to the cytidine and deoxycytidylate deaminase family.

Contains 1 CMP/dCMP deaminase zinc-binding domain.

Ontologies

Keywords
   LigandMetal-binding
Zinc
   Molecular functionHydrolase
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Molecular_functioncytidine deaminase activity

Inferred from electronic annotation. Source: UniProtKB-EC

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 136136Cytidine deaminase
PRO_0000171678

Regions

Domain3 – 104102CMP/dCMP deaminase zinc-binding
Region42 – 443Substrate binding

Sites

Active site551Proton donor
Metal binding531Zinc; catalytic
Metal binding861Zinc; catalytic
Metal binding891Zinc; catalytic

Experimental info

Mutagenesis531C → H: Loss of activity. Reduces activity 500-fold, without effect on zinc binding; when associated with Q-56. Ref.6
Mutagenesis561R → A: No effect on zinc binding. Strongly reduces Vmax. Ref.6
Mutagenesis561R → D: Loss of activity. Reduces zinc binding by 80%. Ref.6
Mutagenesis561R → Q: No effect on zinc binding. Strongly reduces Vmax. Reduces activity 500-fold; when associated with H-53. Ref.6

Secondary structure

............................ 136
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P19079 [UniParc].

Last modified November 1, 1990. Version 1.
Checksum: 83755B1CDB2A534A

FASTA13614,854
        10         20         30         40         50         60 
MNRQELITEA LKARDMAYAP YSKFQVGAAL LTKDGKVYRG CNIENAAYSM CNCAERTALF 

        70         80         90        100        110        120 
KAVSEGDTEF QMLAVAADTP GPVSPCGACR QVISELCTKD VIVVLTNLQG QIKEMTVEEL 

       130 
LPGAFSSEDL HDERKL 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRJE0022.
RefSeqNP_390408.1. NC_000964.3.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalP19079.
SMRP19079. Positions 1-131.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING224308.BSU25300.

Proteomic databases

PaxDbP19079.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaCAB14459; CAB14459; BSU25300.
GeneID937885.
KEGGbsu:BSU25300.
PATRIC18976898. VBIBacSub10457_2638.

Organism-specific databases

GenoListBSU25300. [Micado]

Phylogenomic databases

eggNOGCOG0295.
HOGENOMHOG000014707.
KOK01489.
OMADLHDERK.
OrthoDBEOG6XDH25.
ProtClustDBCLSK887594.

Enzyme and pathway databases

BioCycBSUB:BSU25300-MONOMER.
MetaCyc:BSU25300-MONOMER.

Family and domain databases

InterProIPR016192. APOBEC/CMP_deaminase_Zn-bd.
IPR002125. CMP_dCMP_Zn-bd.
IPR006262. Cyt_deam_tetra.
IPR016193. Cytidine_deaminase-like.
[Graphical view]
PfamPF00383. dCMP_cyt_deam_1. 1 hit.
[Graphical view]
SUPFAMSSF53927. SSF53927. 1 hit.
TIGRFAMsTIGR01354. cyt_deam_tetra. 1 hit.
PROSITEPS00903. CYT_DCMP_DEAMINASES. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP19079.

Entry information

Entry nameCDD_BACSU
AccessionPrimary (citable) accession number: P19079
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1990
Last sequence update: November 1, 1990
Last modified: November 13, 2013
This is version 118 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

Bacillus subtilis

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