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Protein

2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase

Gene

cpdB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

This bifunctional enzyme catalyzes two consecutive reactions during ribonucleic acid degradation. Converts a 2',3'-cyclic nucleotide to a 3'-nucleotide and then the 3'-nucleotide to the corresponding nucleoside and phosphate.1 Publication

Catalytic activityi

Nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 3'-phosphate.1 Publication
A 3'-ribonucleotide + H2O = a ribonucleoside + phosphate.1 Publication

Cofactori

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi31 – 311Divalent metal cation 1By similarity
Metal bindingi33 – 331Divalent metal cation 1By similarity
Metal bindingi76 – 761Divalent metal cation 1By similarity
Metal bindingi76 – 761Divalent metal cation 2By similarity
Metal bindingi116 – 1161Divalent metal cation 2By similarity
Metal bindingi225 – 2251Divalent metal cation 2By similarity
Metal bindingi257 – 2571Divalent metal cation 2By similarity
Metal bindingi259 – 2591Divalent metal cation 1By similarity
Binding sitei440 – 4401SubstrateBy similarity

GO - Molecular functioni

  • 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity Source: EcoCyc
  • 3'-nucleotidase activity Source: EcoCyc
  • metal ion binding Source: UniProtKB-KW
  • nucleotide binding Source: UniProtKB-KW

GO - Biological processi

  • cellular response to DNA damage stimulus Source: EcoliWiki
  • dephosphorylation Source: GOC
  • nucleotide catabolic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:CPDB-MONOMER.
ECOL316407:JW4171-MONOMER.
MetaCyc:CPDB-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase (EC:3.1.3.6, EC:3.1.4.16)
Gene namesi
Name:cpdB
Ordered Locus Names:b4213, JW4171
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10160. cpdB.

Subcellular locationi

  • Periplasm 1 Publication

GO - Cellular componenti

  • periplasmic space Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 19191 PublicationAdd
BLAST
Chaini20 – 6476282',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidasePRO_0000000035Add
BLAST

Proteomic databases

PaxDbiP08331.
PRIDEiP08331.

Interactioni

Protein-protein interaction databases

DIPiDIP-9311N.
IntActiP08331. 2 interactions.
MINTiMINT-1228170.
STRINGi511145.b4213.

Structurei

3D structure databases

ProteinModelPortaliP08331.
SMRiP08331. Positions 19-550.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni544 – 5507Substrate bindingBy similarity

Sequence similaritiesi

Belongs to the 5'-nucleotidase family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiCOG0737.
HOGENOMiHOG000248800.
InParanoidiP08331.
KOiK01119.
OMAiMVWDKAN.
OrthoDBiEOG696BW0.

Family and domain databases

Gene3Di3.60.21.10. 1 hit.
3.90.780.10. 1 hit.
InterProiIPR008334. 5'-Nucleotdase_C.
IPR006146. 5'-Nucleotdase_CS.
IPR006179. 5_nucleotidase/apyrase.
IPR004843. Calcineurin-like_PHP_apaH.
IPR006294. Cyc_nuc_PDE_nucleotidase.
IPR029052. Metallo-depent_PP-like.
[Graphical view]
PANTHERiPTHR11575. PTHR11575. 1 hit.
PfamiPF02872. 5_nucleotid_C. 1 hit.
PF00149. Metallophos. 1 hit.
[Graphical view]
PRINTSiPR01607. APYRASEFAMLY.
SUPFAMiSSF55816. SSF55816. 1 hit.
SSF56300. SSF56300. 1 hit.
TIGRFAMsiTIGR01390. CycNucDiestase. 1 hit.
PROSITEiPS00785. 5_NUCLEOTIDASE_1. 1 hit.
PS00786. 5_NUCLEOTIDASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P08331-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIKFSATLLA TLIAASVNAA TVDLRIMETT DLHSNMMDFD YYKDTATEKF
60 70 80 90 100
GLVRTASLIN DARNEVKNSV LVDNGDLIQG SPLADYMSAK GLKAGDIHPV
110 120 130 140 150
YKALNTLDYT VGTLGNHEFN YGLDYLKNAL AGAKFPYVNA NVIDARTKQP
160 170 180 190 200
MFTPYLIKDT EVVDKDGKKQ TLKIGYIGVV PPQIMGWDKA NLSGKVTVND
210 220 230 240 250
ITETVRKYVP EMREKGADVV VVLAHSGLSA DPYKVMAENS VYYLSEIPGV
260 270 280 290 300
NAIMFGHAHA VFPGKDFADI EGADIAKGTL NGVPAVMPGM WGDHLGVVDL
310 320 330 340 350
QLSNDSGKWQ VTQAKAEARP IYDIANKKSL AAEDSKLVET LKADHDATRQ
360 370 380 390 400
FVSKPIGKSA DNMYSYLALV QDDPTVQVVN NAQKAYVEHY IQGDPDLAKL
410 420 430 440 450
PVLSAAAPFK VGGRKNDPAS YVEVEKGQLT FRNAADLYLY PNTLIVVKAS
460 470 480 490 500
GKEVKEWLEC SAGQFNQIDP NSTKPQSLIN WDGFRTYNFD VIDGVNYQID
510 520 530 540 550
VTQPARYDGE CQMINANAER IKNLTFNGKP IDPNAMFLVA TNNYRAYGGK
560 570 580 590 600
FAGTGDSHIA FASPDENRSV LAAWIADESK RAGEIHPAAD NNWRLAPIAG
610 620 630 640
DKKLDIRFET SPSDKAAAFI KEKGQYPMNK VATDDIGFAI YQVDLSK
Length:647
Mass (Da):70,832
Last modified:February 1, 1995 - v2
Checksum:i4B26DC3563473827
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti316 – 3161A → G in AAA23597 (PubMed:3005231).Curated
Sequence conflicti528 – 55225GKPID…GGKFA → ASRLIRTPCSWLPPITIALT GQIC in AAA23597 (PubMed:3005231).CuratedAdd
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M13464 Genomic DNA. Translation: AAA23597.1.
U14003 Genomic DNA. Translation: AAA97109.1.
U00096 Genomic DNA. Translation: AAC77170.1.
AP009048 Genomic DNA. Translation: BAE78214.1.
X54008 Genomic DNA. Translation: CAA37954.1.
PIRiH65232. ESECPC.
RefSeqiNP_418634.1. NC_000913.3.
WP_000589431.1. NZ_CP010445.1.

Genome annotation databases

EnsemblBacteriaiAAC77170; AAC77170; b4213.
BAE78214; BAE78214; BAE78214.
GeneIDi948729.
KEGGieco:b4213.
PATRICi32124001. VBIEscCol129921_4345.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M13464 Genomic DNA. Translation: AAA23597.1.
U14003 Genomic DNA. Translation: AAA97109.1.
U00096 Genomic DNA. Translation: AAC77170.1.
AP009048 Genomic DNA. Translation: BAE78214.1.
X54008 Genomic DNA. Translation: CAA37954.1.
PIRiH65232. ESECPC.
RefSeqiNP_418634.1. NC_000913.3.
WP_000589431.1. NZ_CP010445.1.

3D structure databases

ProteinModelPortaliP08331.
SMRiP08331. Positions 19-550.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-9311N.
IntActiP08331. 2 interactions.
MINTiMINT-1228170.
STRINGi511145.b4213.

Proteomic databases

PaxDbiP08331.
PRIDEiP08331.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC77170; AAC77170; b4213.
BAE78214; BAE78214; BAE78214.
GeneIDi948729.
KEGGieco:b4213.
PATRICi32124001. VBIEscCol129921_4345.

Organism-specific databases

EchoBASEiEB0158.
EcoGeneiEG10160. cpdB.

Phylogenomic databases

eggNOGiCOG0737.
HOGENOMiHOG000248800.
InParanoidiP08331.
KOiK01119.
OMAiMVWDKAN.
OrthoDBiEOG696BW0.

Enzyme and pathway databases

BioCyciEcoCyc:CPDB-MONOMER.
ECOL316407:JW4171-MONOMER.
MetaCyc:CPDB-MONOMER.

Miscellaneous databases

PROiP08331.

Family and domain databases

Gene3Di3.60.21.10. 1 hit.
3.90.780.10. 1 hit.
InterProiIPR008334. 5'-Nucleotdase_C.
IPR006146. 5'-Nucleotdase_CS.
IPR006179. 5_nucleotidase/apyrase.
IPR004843. Calcineurin-like_PHP_apaH.
IPR006294. Cyc_nuc_PDE_nucleotidase.
IPR029052. Metallo-depent_PP-like.
[Graphical view]
PANTHERiPTHR11575. PTHR11575. 1 hit.
PfamiPF02872. 5_nucleotid_C. 1 hit.
PF00149. Metallophos. 1 hit.
[Graphical view]
PRINTSiPR01607. APYRASEFAMLY.
SUPFAMiSSF55816. SSF55816. 1 hit.
SSF56300. SSF56300. 1 hit.
TIGRFAMsiTIGR01390. CycNucDiestase. 1 hit.
PROSITEiPS00785. 5_NUCLEOTIDASE_1. 1 hit.
PS00786. 5_NUCLEOTIDASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Isolation and sequence analysis of the gene (cpdB) encoding periplasmic 2',3'-cyclic phosphodiesterase."
    Liu J., Burns D.M., Beacham I.R.
    J. Bacteriol. 165:1002-1010(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION.
  2. "Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes."
    Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.
    Nucleic Acids Res. 23:2105-2119(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Transcription and regulation of the cpdB gene in Escherichia coli K12 and Salmonella typhimurium LT2: evidence for modulation of constitutive promoters by cyclic AMP-CRP complex."
    Liu J., Beacham I.R.
    Mol. Gen. Genet. 222:161-165(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-20.
    Strain: K12.
  6. "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12."
    Link A.J., Robison K., Church G.M.
    Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 20-31.
    Strain: K12 / EMG2.

Entry informationi

Entry nameiCPDB_ECOLI
AccessioniPrimary (citable) accession number: P08331
Secondary accession number(s): Q2M692
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: February 1, 1995
Last modified: July 22, 2015
This is version 145 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Two kinetically distinguishable active sites for the two substrates (2',3'-cyclic nucleotides and 3'-nucleotides) have been identified.

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Multifunctional enzyme, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.