CPDB_ECOLI
ID CPDB_ECOLI Reviewed; 647 AA.
AC P08331; Q2M692;
DT 01-AUG-1988, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 2.
DT 03-AUG-2022, entry version 184.
DE RecName: Full=2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase;
DE EC=3.1.3.6;
DE EC=3.1.4.16;
DE Flags: Precursor;
GN Name=cpdB; OrderedLocusNames=b4213, JW4171;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, AND
RP SUBCELLULAR LOCATION.
RX PubMed=3005231; DOI=10.1128/jb.165.3.1002-1010.1986;
RA Liu J., Burns D.M., Beacham I.R.;
RT "Isolation and sequence analysis of the gene (cpdB) encoding periplasmic
RT 2',3'-cyclic phosphodiesterase.";
RL J. Bacteriol. 165:1002-1010(1986).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=7610040; DOI=10.1093/nar/23.12.2105;
RA Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.;
RT "Analysis of the Escherichia coli genome VI: DNA sequence of the region
RT from 92.8 through 100 minutes.";
RL Nucleic Acids Res. 23:2105-2119(1995).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-20.
RC STRAIN=K12;
RX PubMed=2172762; DOI=10.1007/bf00283039;
RA Liu J., Beacham I.R.;
RT "Transcription and regulation of the cpdB gene in Escherichia coli K12 and
RT Salmonella typhimurium LT2: evidence for modulation of constitutive
RT promoters by cyclic AMP-CRP complex.";
RL Mol. Gen. Genet. 222:161-165(1990).
RN [6]
RP PROTEIN SEQUENCE OF 20-31.
RC STRAIN=K12 / EMG2;
RX PubMed=9298646; DOI=10.1002/elps.1150180807;
RA Link A.J., Robison K., Church G.M.;
RT "Comparing the predicted and observed properties of proteins encoded in the
RT genome of Escherichia coli K-12.";
RL Electrophoresis 18:1259-1313(1997).
CC -!- FUNCTION: This bifunctional enzyme catalyzes two consecutive reactions
CC during ribonucleic acid degradation. Converts a 2',3'-cyclic nucleotide
CC to a 3'-nucleotide and then the 3'-nucleotide to the corresponding
CC nucleoside and phosphate. {ECO:0000269|PubMed:3005231}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a nucleoside 2',3'-cyclic phosphate + H2O = a nucleoside 3'-
CC phosphate + H(+); Xref=Rhea:RHEA:19621, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:66949, ChEBI:CHEBI:66954; EC=3.1.4.16;
CC Evidence={ECO:0000269|PubMed:3005231};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 3'-phosphate + H2O = a ribonucleoside +
CC phosphate; Xref=Rhea:RHEA:10144, ChEBI:CHEBI:13197,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:18254, ChEBI:CHEBI:43474; EC=3.1.3.6;
CC Evidence={ECO:0000269|PubMed:3005231};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000250};
CC -!- SUBCELLULAR LOCATION: Periplasm {ECO:0000269|PubMed:3005231}.
CC -!- MISCELLANEOUS: Two kinetically distinguishable active sites for the two
CC substrates (2',3'-cyclic nucleotides and 3'-nucleotides) have been
CC identified.
CC -!- SIMILARITY: Belongs to the 5'-nucleotidase family. {ECO:0000305}.
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DR EMBL; M13464; AAA23597.1; -; Genomic_DNA.
DR EMBL; U14003; AAA97109.1; -; Genomic_DNA.
DR EMBL; U00096; AAC77170.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE78214.1; -; Genomic_DNA.
DR EMBL; X54008; CAA37954.1; -; Genomic_DNA.
DR PIR; H65232; ESECPC.
DR RefSeq; NP_418634.1; NC_000913.3.
DR RefSeq; WP_000589431.1; NZ_LN832404.1.
DR AlphaFoldDB; P08331; -.
DR SMR; P08331; -.
DR BioGRID; 4262719; 40.
DR DIP; DIP-9311N; -.
DR IntAct; P08331; 4.
DR STRING; 511145.b4213; -.
DR jPOST; P08331; -.
DR PaxDb; P08331; -.
DR PRIDE; P08331; -.
DR EnsemblBacteria; AAC77170; AAC77170; b4213.
DR EnsemblBacteria; BAE78214; BAE78214; BAE78214.
DR GeneID; 948729; -.
DR KEGG; ecj:JW4171; -.
DR KEGG; eco:b4213; -.
DR PATRIC; fig|1411691.4.peg.2488; -.
DR EchoBASE; EB0158; -.
DR eggNOG; COG0737; Bacteria.
DR HOGENOM; CLU_005854_4_1_6; -.
DR InParanoid; P08331; -.
DR OMA; EKAQYPM; -.
DR PhylomeDB; P08331; -.
DR BioCyc; EcoCyc:CPDB-MON; -.
DR BioCyc; MetaCyc:CPDB-MON; -.
DR BRENDA; 3.1.3.6; 2026.
DR PHI-base; PHI:7020; -.
DR PRO; PR:P08331; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0030288; C:outer membrane-bounded periplasmic space; IDA:EcoCyc.
DR GO; GO:0042597; C:periplasmic space; IDA:EcoCyc.
DR GO; GO:0008663; F:2',3'-cyclic-nucleotide 2'-phosphodiesterase activity; IDA:EcoCyc.
DR GO; GO:0008254; F:3'-nucleotidase activity; IDA:EcoCyc.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; IEP:EcoliWiki.
DR GO; GO:0009166; P:nucleotide catabolic process; IEP:EcoCyc.
DR CDD; cd07410; MPP_CpdB_N; 1.
DR Gene3D; 3.60.21.10; -; 1.
DR Gene3D; 3.90.780.10; -; 1.
DR InterPro; IPR008334; 5'-Nucleotdase_C.
DR InterPro; IPR036907; 5'-Nucleotdase_C_sf.
DR InterPro; IPR006146; 5'-Nucleotdase_CS.
DR InterPro; IPR006179; 5_nucleotidase/apyrase.
DR InterPro; IPR004843; Calcineurin-like_PHP_ApaH.
DR InterPro; IPR041827; CpdB_N.
DR InterPro; IPR006294; Cyc_nuc_PDE_nucleotidase.
DR InterPro; IPR029052; Metallo-depent_PP-like.
DR PANTHER; PTHR11575; PTHR11575; 1.
DR Pfam; PF02872; 5_nucleotid_C; 1.
DR Pfam; PF00149; Metallophos; 1.
DR PRINTS; PR01607; APYRASEFAMLY.
DR SUPFAM; SSF55816; SSF55816; 1.
DR SUPFAM; SSF56300; SSF56300; 1.
DR TIGRFAMs; TIGR01390; CycNucDiestase; 1.
DR PROSITE; PS00785; 5_NUCLEOTIDASE_1; 1.
DR PROSITE; PS00786; 5_NUCLEOTIDASE_2; 1.
PE 1: Evidence at protein level;
KW Direct protein sequencing; Hydrolase; Metal-binding;
KW Multifunctional enzyme; Nucleotide-binding; Periplasm; Reference proteome;
KW Signal.
FT SIGNAL 1..19
FT /evidence="ECO:0000269|PubMed:9298646"
FT CHAIN 20..647
FT /note="2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-
FT nucleotidase"
FT /id="PRO_0000000035"
FT BINDING 31
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 33
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 76
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 76
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 116
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 225
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 257
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 259
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 440
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 544..550
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT CONFLICT 316
FT /note="A -> G (in Ref. 1; AAA23597)"
FT /evidence="ECO:0000305"
FT CONFLICT 528..552
FT /note="GKPIDPNAMFLVATNNYRAYGGKFA -> ASRLIRTPCSWLPPITIALTGQI
FT C (in Ref. 1; AAA23597)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 647 AA; 70832 MW; 4B26DC3563473827 CRC64;
MIKFSATLLA TLIAASVNAA TVDLRIMETT DLHSNMMDFD YYKDTATEKF GLVRTASLIN
DARNEVKNSV LVDNGDLIQG SPLADYMSAK GLKAGDIHPV YKALNTLDYT VGTLGNHEFN
YGLDYLKNAL AGAKFPYVNA NVIDARTKQP MFTPYLIKDT EVVDKDGKKQ TLKIGYIGVV
PPQIMGWDKA NLSGKVTVND ITETVRKYVP EMREKGADVV VVLAHSGLSA DPYKVMAENS
VYYLSEIPGV NAIMFGHAHA VFPGKDFADI EGADIAKGTL NGVPAVMPGM WGDHLGVVDL
QLSNDSGKWQ VTQAKAEARP IYDIANKKSL AAEDSKLVET LKADHDATRQ FVSKPIGKSA
DNMYSYLALV QDDPTVQVVN NAQKAYVEHY IQGDPDLAKL PVLSAAAPFK VGGRKNDPAS
YVEVEKGQLT FRNAADLYLY PNTLIVVKAS GKEVKEWLEC SAGQFNQIDP NSTKPQSLIN
WDGFRTYNFD VIDGVNYQID VTQPARYDGE CQMINANAER IKNLTFNGKP IDPNAMFLVA
TNNYRAYGGK FAGTGDSHIA FASPDENRSV LAAWIADESK RAGEIHPAAD NNWRLAPIAG
DKKLDIRFET SPSDKAAAFI KEKGQYPMNK VATDDIGFAI YQVDLSK
