CDD_VIBCH
ID CDD_VIBCH Reviewed; 295 AA.
AC Q9KSM5;
DT 10-JAN-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 109.
DE RecName: Full=Cytidine deaminase {ECO:0000255|HAMAP-Rule:MF_01558};
DE EC=3.5.4.5 {ECO:0000255|HAMAP-Rule:MF_01558};
DE AltName: Full=Cytidine aminohydrolase {ECO:0000255|HAMAP-Rule:MF_01558};
DE Short=CDA {ECO:0000255|HAMAP-Rule:MF_01558};
GN Name=cdd {ECO:0000255|HAMAP-Rule:MF_01558}; OrderedLocusNames=VC_1231;
OS Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Vibrio.
OX NCBI_TaxID=243277;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 39315 / El Tor Inaba N16961;
RX PubMed=10952301; DOI=10.1038/35020000;
RA Heidelberg J.F., Eisen J.A., Nelson W.C., Clayton R.A., Gwinn M.L.,
RA Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Umayam L.A., Gill S.R.,
RA Nelson K.E., Read T.D., Tettelin H., Richardson D.L., Ermolaeva M.D.,
RA Vamathevan J.J., Bass S., Qin H., Dragoi I., Sellers P., McDonald L.A.,
RA Utterback T.R., Fleischmann R.D., Nierman W.C., White O., Salzberg S.L.,
RA Smith H.O., Colwell R.R., Mekalanos J.J., Venter J.C., Fraser C.M.;
RT "DNA sequence of both chromosomes of the cholera pathogen Vibrio
RT cholerae.";
RL Nature 406:477-483(2000).
CC -!- FUNCTION: This enzyme scavenges exogenous and endogenous cytidine and
CC 2'-deoxycytidine for UMP synthesis. {ECO:0000255|HAMAP-Rule:MF_01558}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine + H(+) + H2O = NH4(+) + uridine;
CC Xref=Rhea:RHEA:16069, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16704, ChEBI:CHEBI:17562, ChEBI:CHEBI:28938; EC=3.5.4.5;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01558};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2'-deoxycytidine + H(+) + H2O = 2'-deoxyuridine + NH4(+);
CC Xref=Rhea:RHEA:13433, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:15698, ChEBI:CHEBI:16450, ChEBI:CHEBI:28938; EC=3.5.4.5;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01558};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01558};
CC Note=Binds 1 zinc ion. {ECO:0000255|HAMAP-Rule:MF_01558};
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_01558}.
CC -!- SIMILARITY: Belongs to the cytidine and deoxycytidylate deaminase
CC family. {ECO:0000255|HAMAP-Rule:MF_01558}.
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DR EMBL; AE003852; AAF94390.1; -; Genomic_DNA.
DR PIR; G82226; G82226.
DR RefSeq; NP_230876.1; NC_002505.1.
DR RefSeq; WP_001245905.1; NZ_LT906614.1.
DR PDB; 4EG2; X-ray; 2.20 A; A/B/C/D/E/F/G/H=1-295.
DR PDBsum; 4EG2; -.
DR AlphaFoldDB; Q9KSM5; -.
DR SMR; Q9KSM5; -.
DR STRING; 243277.VC_1231; -.
DR DNASU; 2614668; -.
DR EnsemblBacteria; AAF94390; AAF94390; VC_1231.
DR GeneID; 66939137; -.
DR KEGG; vch:VC_1231; -.
DR PATRIC; fig|243277.26.peg.1173; -.
DR eggNOG; COG0295; Bacteria.
DR HOGENOM; CLU_052424_0_0_6; -.
DR OMA; NYSPCGH; -.
DR BioCyc; VCHO:VC1231-MON; -.
DR Proteomes; UP000000584; Chromosome 1.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0004126; F:cytidine deaminase activity; IBA:GO_Central.
DR GO; GO:0047844; F:deoxycytidine deaminase activity; IEA:RHEA.
DR GO; GO:0008270; F:zinc ion binding; IBA:GO_Central.
DR GO; GO:0009972; P:cytidine deamination; IBA:GO_Central.
DR HAMAP; MF_01558; Cyt_deam; 1.
DR InterPro; IPR016192; APOBEC/CMP_deaminase_Zn-bd.
DR InterPro; IPR002125; CMP_dCMP_dom.
DR InterPro; IPR013171; Cyd/dCyd_deaminase_Zn-bd.
DR InterPro; IPR006263; Cyt_deam_dimer.
DR InterPro; IPR016193; Cytidine_deaminase-like.
DR InterPro; IPR020797; Cytidine_deaminase_bacteria.
DR Pfam; PF00383; dCMP_cyt_deam_1; 1.
DR Pfam; PF08211; dCMP_cyt_deam_2; 1.
DR SUPFAM; SSF53927; SSF53927; 2.
DR TIGRFAMs; TIGR01355; cyt_deam_dimer; 1.
DR PROSITE; PS00903; CYT_DCMP_DEAMINASES_1; 1.
DR PROSITE; PS51747; CYT_DCMP_DEAMINASES_2; 2.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Metal-binding; Reference proteome; Zinc.
FT CHAIN 1..295
FT /note="Cytidine deaminase"
FT /id="PRO_0000171669"
FT DOMAIN 48..168
FT /note="CMP/dCMP-type deaminase 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01083"
FT DOMAIN 187..295
FT /note="CMP/dCMP-type deaminase 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01083"
FT ACT_SITE 104
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01558"
FT BINDING 89..91
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01558"
FT BINDING 102
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01558"
FT BINDING 129
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01558"
FT BINDING 132
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01558"
FT HELIX 2..11
FT /evidence="ECO:0007829|PDB:4EG2"
FT TURN 14..16
FT /evidence="ECO:0007829|PDB:4EG2"
FT HELIX 17..24
FT /evidence="ECO:0007829|PDB:4EG2"
FT STRAND 31..33
FT /evidence="ECO:0007829|PDB:4EG2"
FT HELIX 35..45
FT /evidence="ECO:0007829|PDB:4EG2"
FT HELIX 49..61
FT /evidence="ECO:0007829|PDB:4EG2"
FT TURN 67..69
FT /evidence="ECO:0007829|PDB:4EG2"
FT STRAND 74..79
FT /evidence="ECO:0007829|PDB:4EG2"
FT STRAND 84..88
FT /evidence="ECO:0007829|PDB:4EG2"
FT HELIX 97..99
FT /evidence="ECO:0007829|PDB:4EG2"
FT HELIX 103..113
FT /evidence="ECO:0007829|PDB:4EG2"
FT STRAND 119..126
FT /evidence="ECO:0007829|PDB:4EG2"
FT HELIX 130..136
FT /evidence="ECO:0007829|PDB:4EG2"
FT TURN 140..144
FT /evidence="ECO:0007829|PDB:4EG2"
FT STRAND 146..148
FT /evidence="ECO:0007829|PDB:4EG2"
FT STRAND 150..152
FT /evidence="ECO:0007829|PDB:4EG2"
FT HELIX 157..160
FT /evidence="ECO:0007829|PDB:4EG2"
FT HELIX 167..170
FT /evidence="ECO:0007829|PDB:4EG2"
FT HELIX 191..200
FT /evidence="ECO:0007829|PDB:4EG2"
FT TURN 206..208
FT /evidence="ECO:0007829|PDB:4EG2"
FT STRAND 212..218
FT /evidence="ECO:0007829|PDB:4EG2"
FT STRAND 223..227
FT /evidence="ECO:0007829|PDB:4EG2"
FT HELIX 240..250
FT /evidence="ECO:0007829|PDB:4EG2"
FT HELIX 255..257
FT /evidence="ECO:0007829|PDB:4EG2"
FT STRAND 258..265
FT /evidence="ECO:0007829|PDB:4EG2"
FT HELIX 274..284
FT /evidence="ECO:0007829|PDB:4EG2"
FT STRAND 290..294
FT /evidence="ECO:0007829|PDB:4EG2"
SQ SEQUENCE 295 AA; 31955 MW; 7AA766021089D736 CRC64;
MRNRIEQALQ QMPASFAPYL RELVLAKDFD ATFSAEQYQQ LLTLSGLEDA DLRVALLPIA
AAYSYAPISE FYVGAIVRGI SGRLYLGANM EFTGAQLGQT VHAEQCAISH AWMKGEKGVA
DITINFSPCG HCRQFMNELT TASSLKIQLP KRAAKTLQEY LPESFGPADL GIDSGLMSPV
NHGKTSDDDE ELIQQALRAM NISHSPYTQN FSGVALKMRS GAIYLGAYAE NAAFNPSLPP
LQVALAQAMM MGESFEDIEA AALVESATGK ISHLADTQAT LEVINPDIPL SYLSL
