CDD_YEAST
ID CDD_YEAST Reviewed; 142 AA.
AC Q06549; D6VYP3;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 188.
DE RecName: Full=Cytidine deaminase;
DE Short=CDA;
DE EC=3.5.4.5 {ECO:0000269|PubMed:10501935};
DE AltName: Full=Cytidine aminohydrolase;
GN Name=CDD1; OrderedLocusNames=YLR245C; ORFNames=L9672.13;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION, AND CATALYTIC
RP ACTIVITY.
RC STRAIN=ATCC 28383 / FL100 / VTT C-80102;
RX PubMed=10501935; DOI=10.1007/s002940050482;
RA Kurtz J.-E., Exinger F., Erbs P., Jund R.;
RT "New insights into the pyrimidine salvage pathway of Saccharomyces
RT cerevisiae: requirement of six genes for cytidine metabolism.";
RL Curr. Genet. 36:130-136(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169871;
RA Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
RA Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
RA Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
RA Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
RA Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
RA Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
RA Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
RA Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
RA Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
RA Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
RA Zollner A., Hani J., Hoheisel J.D.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
RL Nature 387:87-90(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [5]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH ZINC IONS, AND
RP SUBUNIT.
RX PubMed=15148397; DOI=10.1073/pnas.0400493101;
RA Xie K., Sowden M.P., Dance G.S., Torelli A.T., Smith H.C., Wedekind J.E.;
RT "The structure of a yeast RNA-editing deaminase provides insight into the
RT fold and function of activation-induced deaminase and APOBEC-1.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:8114-8119(2004).
CC -!- FUNCTION: This enzyme scavenges exogenous and endogenous cytidine and
CC 2'-deoxycytidine for UMP synthesis.
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 -!- 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:0000269|PubMed:10501935};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:13434;
CC Evidence={ECO:0000305|PubMed:10501935};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:15148397}.
CC -!- INTERACTION:
CC Q06549; Q06549: CDD1; NbExp=4; IntAct=EBI-4455, EBI-4455;
CC -!- MISCELLANEOUS: Present with 3120 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the cytidine and deoxycytidylate deaminase
CC family. {ECO:0000305}.
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DR EMBL; AF080089; AAD04031.1; -; Genomic_DNA.
DR EMBL; U20865; AAB67399.1; -; Genomic_DNA.
DR EMBL; AY557930; AAS56256.1; -; Genomic_DNA.
DR EMBL; BK006945; DAA09559.1; -; Genomic_DNA.
DR PIR; S59391; S59391.
DR RefSeq; NP_013346.1; NM_001182132.1.
DR PDB; 1R5T; X-ray; 2.00 A; A/B/C/D=1-142.
DR PDBsum; 1R5T; -.
DR AlphaFoldDB; Q06549; -.
DR SMR; Q06549; -.
DR BioGRID; 31512; 71.
DR DIP; DIP-1252N; -.
DR IntAct; Q06549; 10.
DR MINT; Q06549; -.
DR STRING; 4932.YLR245C; -.
DR MaxQB; Q06549; -.
DR PaxDb; Q06549; -.
DR PRIDE; Q06549; -.
DR TopDownProteomics; Q06549; -.
DR EnsemblFungi; YLR245C_mRNA; YLR245C; YLR245C.
DR GeneID; 850946; -.
DR KEGG; sce:YLR245C; -.
DR SGD; S000004235; CDD1.
DR VEuPathDB; FungiDB:YLR245C; -.
DR eggNOG; KOG0833; Eukaryota.
DR GeneTree; ENSGT00940000168030; -.
DR HOGENOM; CLU_097262_1_2_1; -.
DR InParanoid; Q06549; -.
DR OMA; LTHFTCV; -.
DR BioCyc; MetaCyc:YLR245C-MON; -.
DR BioCyc; YEAST:YLR245C-MON; -.
DR Reactome; R-SCE-6798695; Neutrophil degranulation.
DR Reactome; R-SCE-73614; Pyrimidine salvage.
DR EvolutionaryTrace; Q06549; -.
DR PRO; PR:Q06549; -.
DR Proteomes; UP000002311; Chromosome XII.
DR RNAct; Q06549; protein.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0004126; F:cytidine deaminase activity; IDA:SGD.
DR GO; GO:0047844; F:deoxycytidine deaminase activity; IEA:RHEA.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0008270; F:zinc ion binding; IBA:GO_Central.
DR GO; GO:0006216; P:cytidine catabolic process; IDA:SGD.
DR GO; GO:0009972; P:cytidine deamination; IBA:GO_Central.
DR GO; GO:0006217; P:deoxycytidine catabolic process; IDA:SGD.
DR GO; GO:0008655; P:pyrimidine-containing compound salvage; IDA:SGD.
DR InterPro; IPR016192; APOBEC/CMP_deaminase_Zn-bd.
DR InterPro; IPR002125; CMP_dCMP_dom.
DR InterPro; IPR006262; Cyt_deam_tetra.
DR InterPro; IPR016193; Cytidine_deaminase-like.
DR Pfam; PF00383; dCMP_cyt_deam_1; 1.
DR SUPFAM; SSF53927; SSF53927; 1.
DR TIGRFAMs; TIGR01354; cyt_deam_tetra; 1.
DR PROSITE; PS00903; CYT_DCMP_DEAMINASES_1; 1.
DR PROSITE; PS51747; CYT_DCMP_DEAMINASES_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Metal-binding; Reference proteome; Zinc.
FT CHAIN 1..142
FT /note="Cytidine deaminase"
FT /id="PRO_0000171685"
FT DOMAIN 9..139
FT /note="CMP/dCMP-type deaminase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01083"
FT ACT_SITE 63
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 50..52
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 61
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT BINDING 96
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT BINDING 99
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT HELIX 8..21
FT /evidence="ECO:0007829|PDB:1R5T"
FT HELIX 22..24
FT /evidence="ECO:0007829|PDB:1R5T"
FT TURN 28..30
FT /evidence="ECO:0007829|PDB:1R5T"
FT STRAND 34..39
FT /evidence="ECO:0007829|PDB:1R5T"
FT STRAND 45..49
FT /evidence="ECO:0007829|PDB:1R5T"
FT HELIX 56..58
FT /evidence="ECO:0007829|PDB:1R5T"
FT HELIX 62..72
FT /evidence="ECO:0007829|PDB:1R5T"
FT STRAND 81..87
FT /evidence="ECO:0007829|PDB:1R5T"
FT STRAND 89..91
FT /evidence="ECO:0007829|PDB:1R5T"
FT HELIX 97..104
FT /evidence="ECO:0007829|PDB:1R5T"
FT STRAND 112..116
FT /evidence="ECO:0007829|PDB:1R5T"
FT STRAND 118..127
FT /evidence="ECO:0007829|PDB:1R5T"
FT HELIX 128..131
FT /evidence="ECO:0007829|PDB:1R5T"
FT HELIX 138..140
FT /evidence="ECO:0007829|PDB:1R5T"
SQ SEQUENCE 142 AA; 15536 MW; 962BD69CCB30D51F CRC64;
MKVGGIEDRQ LEALKRAALK ACELSYSPYS HFRVGCSILT NNDVIFTGAN VENASYSNCI
CAERSAMIQV LMAGHRSGWK CMVICGDSED QCVSPCGVCR QFINEFVVKD FPIVMLNSTG
SRSKVMTMGE LLPMAFGPSH LN
