CDA1_ARATH
ID CDA1_ARATH Reviewed; 301 AA.
AC O65896; Q8LEF2; Q9XEX5;
DT 14-MAY-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 151.
DE RecName: Full=Cytidine deaminase 1 {ECO:0000303|PubMed:10024464, ECO:0000303|PubMed:10469156};
DE Short=At-CDA1 {ECO:0000303|PubMed:10024464, ECO:0000303|PubMed:10469156};
DE EC=3.5.4.5 {ECO:0000269|PubMed:10024464, ECO:0000269|PubMed:10469156, ECO:0000269|Ref.3};
GN Name=CDA1; Synonyms=CDD, DESZ; OrderedLocusNames=At2g19570; ORFNames=F3P11;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
RP ACTIVITY REGULATION, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=cv. Columbia;
RX PubMed=10024464; DOI=10.1006/prep.1998.0959;
RA Vincenzetti S., Cambi A., Neuhard J., Schnorr K., Grelloni M., Vita A.;
RT "Cloning, expression, and purification of cytidine deaminase from
RT Arabidopsis thaliana.";
RL Protein Expr. Purif. 15:8-15(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CATALYTIC ACTIVITY, ACTIVITY
RP REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Landsberg erecta;
RX PubMed=10469156; DOI=10.1046/j.1432-1327.1999.00591.x;
RA Faivre-Nitschke E.S., Grienenberger J.M., Gualberto J.M.;
RT "A prokaryotic-type cytidine deaminase from Arabidopsis thaliana.";
RL Eur. J. Biochem. 263:896-903(1999).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CATALYTIC ACTIVITY, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RA Kafer C., Thornburg R.W.;
RT "Arabidopsis thaliana cytidine deaminase 1 shows more similarity to
RT prokaryotic enzymes than to eukaryotic enzymes.";
RL J. Plant Biol. 43:162-170(2000).
RN [4]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Columbia;
RA Sanchez H., Schuster W.;
RL Submitted (JAN-1999) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
RN [6]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [8]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: This enzyme scavenges exogenous and endogenous cytidine and
CC 2'-deoxycytidine for UMP synthesis. Functions as a conventional
CC cytidine deaminase. Has no affinity for RNA and is not involved in RNA-
CC editing by C-to-U deamination. {ECO:0000269|PubMed:10024464,
CC ECO:0000269|PubMed:10469156, ECO:0000269|Ref.3}.
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:0000269|PubMed:10024464, ECO:0000269|PubMed:10469156,
CC ECO:0000269|Ref.3};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:16070;
CC Evidence={ECO:0000269|PubMed:10024464, ECO:0000269|PubMed:10469156,
CC ECO:0000269|Ref.3};
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:10024464, ECO:0000269|PubMed:10469156,
CC ECO:0000269|Ref.3};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:13434;
CC Evidence={ECO:0000269|PubMed:10024464, ECO:0000269|PubMed:10469156,
CC ECO:0000269|Ref.3};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000305|PubMed:10024464};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000305|PubMed:10024464};
CC -!- ACTIVITY REGULATION: Inhibited by uridine, CMP and dCMP.
CC {ECO:0000269|PubMed:10024464, ECO:0000269|PubMed:10469156}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=150 uM for cytidine (at pH 7.5 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:10024464};
CC KM=250 uM for cytidine (at pH 7.5 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:10469156};
CC KM=226.1 uM for cytidine (at pH 8.0 and 25 degrees Celsius)
CC {ECO:0000269|Ref.3};
CC KM=75 uM for 2'-deoxycytidine (at pH 7.5 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:10024464};
CC KM=120 uM for 2'-deoxycytidine (at pH 7.5 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:10469156};
CC KM=49.3 uM for 2'-deoxycytidine (at pH 8.0 and 25 degrees Celsius)
CC {ECO:0000269|Ref.3};
CC Vmax=59.5 umol/min/mg enzyme toward cytidine (at pH 7.5 and 37
CC degrees Celsius) {ECO:0000269|PubMed:10024464};
CC Vmax=58 umol/min/mg enzyme toward cytidine (at pH 7.5 and 25 degrees
CC Celsius) {ECO:0000269|PubMed:10469156};
CC Vmax=39.7 umol/min/mg enzyme toward cytidine (at pH 8.0 and 25
CC degrees Celsius) {ECO:0000269|Ref.3};
CC Vmax=49 umol/min/mg enzyme toward 2'-deoxycytidine (at pH 7.5 and 37
CC degrees Celsius) {ECO:0000269|PubMed:10024464};
CC Vmax=38 umol/min/mg enzyme toward 2'-deoxycytidine (at pH 7.5 and 25
CC degrees Celsius) {ECO:0000269|PubMed:10469156};
CC Vmax=24.4 umol/min/mg enzyme toward 2'-deoxycytidine (at pH 8.0 and
CC 25 degrees Celsius, Ref.3) {ECO:0000269|PubMed:10024464,
CC ECO:0000269|PubMed:10469156, ECO:0000269|Ref.3};
CC pH dependence:
CC Optimum pH is 7.5-8.0. {ECO:0000269|PubMed:10024464,
CC ECO:0000269|PubMed:10469156, ECO:0000269|Ref.3};
CC -!- SUBUNIT: Homodimer. {ECO:0000305|PubMed:10469156}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, rosette leaves, stems and
CC flowers. {ECO:0000269|PubMed:10469156}.
CC -!- SIMILARITY: Belongs to the cytidine and deoxycytidylate deaminase
CC family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD30449.1; Type=Miscellaneous discrepancy; Note=Sequencing errors.; Evidence={ECO:0000305};
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DR EMBL; AJ005261; CAA06460.1; -; mRNA.
DR EMBL; AJ005687; CAA06671.1; -; Genomic_DNA.
DR EMBL; AF134487; AAF03358.1; -; mRNA.
DR EMBL; AF121878; AAD30449.1; ALT_SEQ; mRNA.
DR EMBL; AC005917; AAD10156.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC06896.1; -; Genomic_DNA.
DR EMBL; AY128366; AAM91569.1; -; mRNA.
DR EMBL; BT008708; AAP42721.1; -; mRNA.
DR EMBL; AY085453; AAM62679.1; -; mRNA.
DR PIR; T51733; T51733.
DR RefSeq; NP_179547.1; NM_127515.4.
DR PDB; 6L08; X-ray; 3.00 A; A/B=1-301.
DR PDBsum; 6L08; -.
DR AlphaFoldDB; O65896; -.
DR SMR; O65896; -.
DR IntAct; O65896; 1.
DR STRING; 3702.AT2G19570.1; -.
DR iPTMnet; O65896; -.
DR PaxDb; O65896; -.
DR PRIDE; O65896; -.
DR ProteomicsDB; 223879; -.
DR EnsemblPlants; AT2G19570.1; AT2G19570.1; AT2G19570.
DR GeneID; 816476; -.
DR Gramene; AT2G19570.1; AT2G19570.1; AT2G19570.
DR KEGG; ath:AT2G19570; -.
DR Araport; AT2G19570; -.
DR TAIR; locus:2050429; AT2G19570.
DR eggNOG; KOG0833; Eukaryota.
DR HOGENOM; CLU_052424_1_0_1; -.
DR InParanoid; O65896; -.
DR OMA; NYSPCGH; -.
DR OrthoDB; 1054992at2759; -.
DR PhylomeDB; O65896; -.
DR BioCyc; ARA:AT2G19570-MON; -.
DR BioCyc; MetaCyc:AT2G19570-MON; -.
DR PRO; PR:O65896; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; O65896; differential.
DR Genevisible; O65896; AT.
DR GO; GO:0005829; C:cytosol; IDA:TAIR.
DR GO; GO:0005739; C:mitochondrion; HDA:TAIR.
DR GO; GO:0004126; F:cytidine deaminase activity; IDA:TAIR.
DR GO; GO:0047844; F:deoxycytidine deaminase activity; IDA:TAIR.
DR GO; GO:0042803; F:protein homodimerization activity; IPI:UniProtKB.
DR GO; GO:0008270; F:zinc ion binding; IDA:UniProtKB.
DR GO; GO:0006216; P:cytidine catabolic process; IMP:TAIR.
DR GO; GO:0009972; P:cytidine deamination; IDA:TAIR.
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 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..301
FT /note="Cytidine deaminase 1"
FT /id="PRO_0000429143"
FT DOMAIN 23..156
FT /note="CMP/dCMP-type deaminase 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01083"
FT DOMAIN 188..301
FT /note="CMP/dCMP-type deaminase 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01083"
FT ACT_SITE 79
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 64..66
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 77
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 104
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 107
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT CONFLICT 270
FT /note="E -> K (in Ref. 8; AAM62679)"
FT /evidence="ECO:0000305"
FT CONFLICT 293
FT /note="F -> Y (in Ref. 8; AAM62679)"
FT /evidence="ECO:0000305"
FT STRAND 6..8
FT /evidence="ECO:0007829|PDB:6L08"
FT HELIX 10..20
FT /evidence="ECO:0007829|PDB:6L08"
FT TURN 25..27
FT /evidence="ECO:0007829|PDB:6L08"
FT HELIX 28..31
FT /evidence="ECO:0007829|PDB:6L08"
FT HELIX 32..35
FT /evidence="ECO:0007829|PDB:6L08"
FT HELIX 36..38
FT /evidence="ECO:0007829|PDB:6L08"
FT TURN 42..44
FT /evidence="ECO:0007829|PDB:6L08"
FT STRAND 49..57
FT /evidence="ECO:0007829|PDB:6L08"
FT STRAND 59..63
FT /evidence="ECO:0007829|PDB:6L08"
FT HELIX 72..74
FT /evidence="ECO:0007829|PDB:6L08"
FT HELIX 78..88
FT /evidence="ECO:0007829|PDB:6L08"
FT STRAND 94..101
FT /evidence="ECO:0007829|PDB:6L08"
FT HELIX 105..110
FT /evidence="ECO:0007829|PDB:6L08"
FT HELIX 111..113
FT /evidence="ECO:0007829|PDB:6L08"
FT HELIX 117..119
FT /evidence="ECO:0007829|PDB:6L08"
FT STRAND 121..124
FT /evidence="ECO:0007829|PDB:6L08"
FT STRAND 139..141
FT /evidence="ECO:0007829|PDB:6L08"
FT HELIX 145..148
FT /evidence="ECO:0007829|PDB:6L08"
FT HELIX 155..157
FT /evidence="ECO:0007829|PDB:6L08"
FT STRAND 165..167
FT /evidence="ECO:0007829|PDB:6L08"
FT HELIX 194..202
FT /evidence="ECO:0007829|PDB:6L08"
FT STRAND 207..210
FT /evidence="ECO:0007829|PDB:6L08"
FT STRAND 233..237
FT /evidence="ECO:0007829|PDB:6L08"
FT HELIX 243..250
FT /evidence="ECO:0007829|PDB:6L08"
FT STRAND 253..255
FT /evidence="ECO:0007829|PDB:6L08"
FT HELIX 277..287
FT /evidence="ECO:0007829|PDB:6L08"
SQ SEQUENCE 301 AA; 32582 MW; 91C17F09AA70CBB2 CRC64;
MDKPSFVIQS KEAESAAKQL GVSVIQLLPS LVKPAQSYAR TPISKFNVAV VGLGSSGRIF
LGVNVEFPNL PLHHSIHAEQ FLVTNLTLNG ERHLNFFAVS AAPCGHCRQF LQEIRDAPEI
KILITDPNNS ADSDSAADSD GFLRLGSFLP HRFGPDDLLG KDHPLLLESH DNHLKISDLD
SICNGNTDSS ADLKQTALAA ANRSYAPYSL CPSGVSLVDC DGKVYRGWYM ESAAYNPSMG
PVQAALVDYV ANGGGGGYER IVGAVLVEKE DAVVRQEHTA RLLLETISPK CEFKVFHCYE
A
