CDD_MYCTU
ID CDD_MYCTU Reviewed; 133 AA.
AC P9WPH3; L0TEZ3; O53367; Q7D5Q5;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 38.
DE RecName: Full=Cytidine deaminase {ECO:0000303|PubMed:20035876};
DE Short=CDD;
DE EC=3.5.4.5 {ECO:0000269|PubMed:20035876};
DE AltName: Full=Cytidine aminohydrolase;
DE Short=CDA;
GN Name=cdd; OrderedLocusNames=Rv3315c;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
RN [3] {ECO:0007744|PDB:3IJF}
RP X-RAY CRYSTALLOGRAPHY (1.99 ANGSTROMS) IN COMPLEX WITH ZINC IONS, PROTEIN
RP SEQUENCE OF 2-31, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, COFACTOR, MASS SPECTROMETRY, AND SUBUNIT.
RX PubMed=20035876; DOI=10.1016/j.jsb.2009.12.019;
RA Sanchez-Quitian Z.A., Schneider C.Z., Ducati R.G., de Azevedo W.F.,
RA Bloch C., Basso L.A., Santos D.S.;
RT "Structural and functional analyses of Mycobacterium tuberculosis Rv3315c-
RT encoded metal-dependent homotetrameric cytidine deaminase.";
RL J. Struct. Biol. 169:413-423(2010).
CC -!- FUNCTION: Recycles cytidine and 2-deoxycytidine for uridine and 2-
CC deoxyuridine synthesis, respectively. Catalyzes the hydrolytic
CC deamination of cytidine and 2-deoxycytidine to form, respectively,
CC uridine and 2-deoxyuridine. {ECO:0000269|PubMed:20035876}.
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:20035876};
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:20035876};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:20035876};
CC Note=Binds 1 Zn(2+) ion per subunit. {ECO:0000269|PubMed:20035876};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1004 uM for cytidine {ECO:0000269|PubMed:20035876};
CC KM=1059 uM for 2-deoxycytidine {ECO:0000269|PubMed:20035876};
CC Note=kcat is 4.8 and 3.5 sec(-1) with cytidine and 2-deoxycytidine as
CC substrate, respectively.;
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:20035876}.
CC -!- MASS SPECTROMETRY: Mass=13938; Method=Electrospray;
CC Evidence={ECO:0000269|PubMed:20035876};
CC -!- SIMILARITY: Belongs to the cytidine and deoxycytidylate deaminase
CC family. {ECO:0000305}.
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DR EMBL; AL123456; CCP46135.1; -; Genomic_DNA.
DR PIR; B70843; B70843.
DR RefSeq; NP_217832.1; NC_000962.3.
DR RefSeq; WP_003417264.1; NZ_NVQJ01000003.1.
DR PDB; 3IJF; X-ray; 1.99 A; X=1-133.
DR PDB; 4WIF; X-ray; 1.80 A; A/B=1-133.
DR PDB; 4WIG; X-ray; 1.76 A; A/B=1-133.
DR PDBsum; 3IJF; -.
DR PDBsum; 4WIF; -.
DR PDBsum; 4WIG; -.
DR AlphaFoldDB; P9WPH3; -.
DR SMR; P9WPH3; -.
DR STRING; 83332.Rv3315c; -.
DR PaxDb; P9WPH3; -.
DR GeneID; 45427315; -.
DR GeneID; 887975; -.
DR KEGG; mtu:Rv3315c; -.
DR TubercuList; Rv3315c; -.
DR eggNOG; COG0295; Bacteria.
DR OMA; LTHFTCV; -.
DR PhylomeDB; P9WPH3; -.
DR BRENDA; 3.5.4.5; 3445.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005886; C:plasma membrane; HDA:MTBBASE.
DR GO; GO:0004126; F:cytidine deaminase activity; IDA:MTBBASE.
DR GO; GO:0047844; F:deoxycytidine deaminase activity; IDA:MTBBASE.
DR GO; GO:0008270; F:zinc ion binding; IDA:MTBBASE.
DR GO; GO:0009972; P:cytidine deamination; IDA:MTBBASE.
DR GO; GO:0043100; P:pyrimidine nucleobase salvage; IDA:MTBBASE.
DR GO; GO:0046109; P:uridine biosynthetic process; IDA:MTBBASE.
DR InterPro; IPR002125; CMP_dCMP_dom.
DR InterPro; IPR016193; Cytidine_deaminase-like.
DR Pfam; PF00383; dCMP_cyt_deam_1; 1.
DR SUPFAM; SSF53927; SSF53927; 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; Direct protein sequencing; Hydrolase; Metal-binding;
KW Reference proteome; Zinc.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:20035876"
FT CHAIN 2..133
FT /note="Cytidine deaminase"
FT /id="PRO_0000420699"
FT DOMAIN 4..126
FT /note="CMP/dCMP-type deaminase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01083"
FT ACT_SITE 58
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 45..47
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 56
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:20035876,
FT ECO:0007744|PDB:3IJF"
FT BINDING 89
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:20035876,
FT ECO:0007744|PDB:3IJF"
FT BINDING 92
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:20035876,
FT ECO:0007744|PDB:3IJF"
FT HELIX 6..17
FT /evidence="ECO:0007829|PDB:4WIG"
FT TURN 23..25
FT /evidence="ECO:0007829|PDB:4WIG"
FT STRAND 29..35
FT /evidence="ECO:0007829|PDB:4WIG"
FT STRAND 40..44
FT /evidence="ECO:0007829|PDB:4WIG"
FT HELIX 51..53
FT /evidence="ECO:0007829|PDB:4WIG"
FT HELIX 57..67
FT /evidence="ECO:0007829|PDB:4WIG"
FT STRAND 73..80
FT /evidence="ECO:0007829|PDB:4WIG"
FT HELIX 90..100
FT /evidence="ECO:0007829|PDB:4WIG"
FT STRAND 109..111
FT /evidence="ECO:0007829|PDB:4WIG"
FT HELIX 115..118
FT /evidence="ECO:0007829|PDB:4WIG"
FT HELIX 125..127
FT /evidence="ECO:0007829|PDB:4WIG"
SQ SEQUENCE 133 AA; 14072 MW; B21C0B188CB8080E CRC64;
MPDVDWNMLR GNATQAAAGA YVPYSRFAVG AAALVDDGRV VTGCNVENVS YGLTLCAECA
VVCALHSTGG GRLLALACVD GHGSVLMPCG RCRQVLLEHG GSELLIDHPV RPRRLGDLLP
DAFGLDDLPR ERR
