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Protein

Cytidine deaminase

Gene

cdd

Organism
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Status
Reviewed-Annotation score: Annotation score: 3 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

Zn2+UniRule annotationNote: Binds 1 zinc ion.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi102Zinc; catalyticUniRule annotation1
Active sitei104Proton donorUniRule annotation1
Metal bindingi129Zinc; catalyticUniRule annotation1
Metal bindingi132Zinc; catalyticUniRule annotation1

GO - Molecular functioni

  • cytidine deaminase activity Source: TIGR
  • zinc ion binding Source: GO_Central

GO - Biological processi

  • cytidine deamination Source: GO_Central
  • pyrimidine-containing compound salvage Source: TIGR
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciVCHO:VC1231-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Cytidine deaminaseUniRule annotation (EC:3.5.4.5UniRule annotation)
Alternative name(s):
Cytidine aminohydrolaseUniRule annotation
Short name:
CDAUniRule annotation
Gene namesi
Name:cddUniRule annotation
Ordered Locus Names:VC_1231
OrganismiVibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Taxonomic identifieri243277 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
Proteomesi
  • UP000000584 Componenti: Chromosome 1

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001716691 – 295Cytidine deaminaseAdd BLAST295

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi243277.VC1231.

Structurei

Secondary structure

1295
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi2 – 11Combined sources10
Turni14 – 16Combined sources3
Helixi17 – 24Combined sources8
Beta strandi31 – 33Combined sources3
Helixi35 – 45Combined sources11
Helixi49 – 61Combined sources13
Turni67 – 69Combined sources3
Beta strandi74 – 79Combined sources6
Beta strandi84 – 88Combined sources5
Helixi97 – 99Combined sources3
Helixi103 – 113Combined sources11
Beta strandi119 – 126Combined sources8
Helixi130 – 136Combined sources7
Turni140 – 144Combined sources5
Beta strandi146 – 148Combined sources3
Beta strandi150 – 152Combined sources3
Helixi157 – 160Combined sources4
Helixi167 – 170Combined sources4
Helixi191 – 200Combined sources10
Turni206 – 208Combined sources3
Beta strandi212 – 218Combined sources7
Beta strandi223 – 227Combined sources5
Helixi240 – 250Combined sources11
Helixi255 – 257Combined sources3
Beta strandi258 – 265Combined sources8
Helixi274 – 284Combined sources11
Beta strandi290 – 294Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4EG2X-ray2.20A/B/C/D/E/F/G/H1-295[»]
ProteinModelPortaliQ9KSM5.
SMRiQ9KSM5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini48 – 168CMP/dCMP-type deaminase 1PROSITE-ProRule annotationAdd BLAST121
Domaini187 – 295CMP/dCMP-type deaminase 2PROSITE-ProRule annotationAdd BLAST109

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni89 – 91Substrate bindingUniRule annotation3

Sequence similaritiesi

Belongs to the cytidine and deoxycytidylate deaminase family.UniRule annotation
Contains 2 CMP/dCMP-type deaminase domains.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4107T42. Bacteria.
COG0295. LUCA.
KOiK01489.
OMAiNQSHAPY.

Family and domain databases

HAMAPiMF_01558. Cyt_deam. 1 hit.
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. 1 hit.
PS51747. CYT_DCMP_DEAMINASES_2. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9KSM5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRNRIEQALQ QMPASFAPYL RELVLAKDFD ATFSAEQYQQ LLTLSGLEDA
60 70 80 90 100
DLRVALLPIA AAYSYAPISE FYVGAIVRGI SGRLYLGANM EFTGAQLGQT
110 120 130 140 150
VHAEQCAISH AWMKGEKGVA DITINFSPCG HCRQFMNELT TASSLKIQLP
160 170 180 190 200
KRAAKTLQEY LPESFGPADL GIDSGLMSPV NHGKTSDDDE ELIQQALRAM
210 220 230 240 250
NISHSPYTQN FSGVALKMRS GAIYLGAYAE NAAFNPSLPP LQVALAQAMM
260 270 280 290
MGESFEDIEA AALVESATGK ISHLADTQAT LEVINPDIPL SYLSL
Length:295
Mass (Da):31,955
Last modified:October 1, 2000 - v1
Checksum:i7AA766021089D736
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003852 Genomic DNA. Translation: AAF94390.1.
PIRiG82226.
RefSeqiNP_230876.1. NC_002505.1.
WP_001245905.1. NC_002505.1.

Genome annotation databases

EnsemblBacteriaiAAF94390; AAF94390; VC_1231.
GeneIDi2614668.
KEGGivch:VC1231.
PATRICi20081548. VBIVibCho83274_1173.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003852 Genomic DNA. Translation: AAF94390.1.
PIRiG82226.
RefSeqiNP_230876.1. NC_002505.1.
WP_001245905.1. NC_002505.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4EG2X-ray2.20A/B/C/D/E/F/G/H1-295[»]
ProteinModelPortaliQ9KSM5.
SMRiQ9KSM5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243277.VC1231.

Protocols and materials databases

DNASUi2614668.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAF94390; AAF94390; VC_1231.
GeneIDi2614668.
KEGGivch:VC1231.
PATRICi20081548. VBIVibCho83274_1173.

Phylogenomic databases

eggNOGiENOG4107T42. Bacteria.
COG0295. LUCA.
KOiK01489.
OMAiNQSHAPY.

Enzyme and pathway databases

BioCyciVCHO:VC1231-MONOMER.

Family and domain databases

HAMAPiMF_01558. Cyt_deam. 1 hit.
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. 1 hit.
PS51747. CYT_DCMP_DEAMINASES_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiCDD_VIBCH
AccessioniPrimary (citable) accession number: Q9KSM5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: October 1, 2000
Last modified: November 2, 2016
This is version 91 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

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 one 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.