P19079 (CDD_BACSU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Cytidine deaminase
Short name=CDA
EC=3.5.4.5

Alternative name(s):
Cytidine aminohydrolase

Gene names

Name:	cdd
Ordered Locus Names:	BSU25300

Organism

Bacillus subtilis (strain 168) [Reference proteome] [HAMAP]

Taxonomic identifier

224308 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus › Bacillus subtilis group › Bacillus subtilis › Bacillus subtilis subsp. subtilis

Protein attributes

Sequence length	136 AA.
Sequence status	Complete.
Protein existence	Evidence 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.
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
Ligand	Metal-binding Zinc
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Molecular_function	cytidine deaminase activity Inferred from electronic annotation. Source: EC zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 136

136

Cytidine deaminase

PRO_0000171678

Regions

Domain

3 – 104

102

CMP/dCMP deaminase zinc-binding

Region

42 – 44

3

Substrate binding

Sites

Active site

55

1

Proton donor

Metal binding

53

1

Zinc; catalytic

Metal binding

86

1

Zinc; catalytic

Metal binding

89

1

Zinc; catalytic

Experimental info

Mutagenesis

53

1

C → H: Loss of activity. Reduces activity 500-fold, without effect on zinc binding; when associated with Q-56. Ref.6

Mutagenesis

56

1

R → A: No effect on zinc binding. Strongly reduces Vmax. Ref.6

Mutagenesis

56

1

R → D: Loss of activity. Reduces zinc binding by 80%. Ref.6

Mutagenesis

56

1

R → Q: No effect on zinc binding. Strongly reduces Vmax. Reduces activity 500-fold; when associated with H-53. Ref.6

Secondary structure

1

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136

Helix Strand Turn

Details...

Helix

3 – 14

12

Turn

20 – 22

3

Beta strand

26 – 32

7

Beta strand

37 – 41

5

Helix

48 – 50

3

Helix

54 – 64

11

Beta strand

70 – 78

9

Beta strand

80 – 82

3

Helix

87 – 96

10

Beta strand

102 – 106

5

Beta strand

108 – 110

3

Beta strand

112 – 116

5

Helix

117 – 120

4

Helix

127 – 129

3

Sequences

	Sequence		Length	Mass (Da)
	P19079 [UniParc]. Last modified November 1, 1990. Version 1. Checksum: 83755B1CDB2A534A	FASTA	136	14,854
	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

References

	« Hide 'large scale' referencesShow '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. , 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.

PIR

JE0022.

RefSeq

NP_390408.1. NC_000964.3.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P19079.

SMR

P19079. Positions 1-131.

ModBase

Search...

Protein-protein interaction databases

STRING

224308.BSU25300.

Proteomic databases

PaxDb

P19079.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

CAB14459; CAB14459; BSU25300.

GeneID

937885.

KEGG

bsu:BSU25300.

PATRIC

18976898. VBIBacSub10457_2638.

Organism-specific databases

GenoList

BSU25300. [Micado]

Phylogenomic databases

eggNOG

COG0295.

HOGENOM

HOG000014707.

KO

K01489.

OMA

KLVKMAL.

ProtClustDB

CLSK887594.

Enzyme and pathway databases

BioCyc

BSUB:BSU25300-MONOMER.

Family and domain databases

InterPro

IPR016192. APOBEC/CMP_deaminase_Zn-bd.
IPR002125. CMP_dCMP_Zn-bd.
IPR006262. Cyt_deam_tetra.
IPR016193. Cytidine_deaminase-like.
[Graphical view]

Pfam

PF00383. dCMP_cyt_deam_1. 1 hit.
[Graphical view]

SUPFAM

SSF53927. Cytidine_deaminase-like. 1 hit.

TIGRFAMs

TIGR01354. cyt_deam_tetra. 1 hit.

PROSITE

PS00903. CYT_DCMP_DEAMINASES. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P19079.

Entry information

Entry name

CDD_BACSU

Accession

Primary (citable) accession number: P19079

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1990
Last sequence update:	November 1, 1990
Last modified:	May 1, 2013
This is version 114 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program