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P08331

- CPDB_ECOLI

UniProt

P08331 - CPDB_ECOLI

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Protein

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

Gene

cpdB

Organism
Escherichia coli (strain K12)
Status
Reviewed - 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

Divalent cations.By similarity

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

  1. 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity Source: EcoCyc
  2. 3'-nucleotidase activity Source: EcoCyc
  3. metal ion binding Source: UniProtKB-KW
  4. nucleotide binding Source: UniProtKB-KW

GO - Biological processi

  1. cellular response to DNA damage stimulus Source: EcoliWiki
  2. dephosphorylation Source: GOC
  3. 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: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10160. cpdB.

Subcellular locationi

Periplasm 1 Publication

GO - Cellular componenti

  1. 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.

Expressioni

Gene expression databases

GenevestigatoriP08331.

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.
OMAiEKAQYPM.
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:
EMBL
GenBank
DDBJ
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.
YP_492355.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC77170; AAC77170; b4213.
BAE78214; BAE78214; BAE78214.
GeneIDi12933725.
948729.
KEGGiecj:Y75_p4099.
eco:b4213.
PATRICi32124001. VBIEscCol129921_4345.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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 .
PIRi H65232. ESECPC.
RefSeqi NP_418634.1. NC_000913.3.
YP_492355.1. NC_007779.1.

3D structure databases

ProteinModelPortali P08331.
SMRi P08331. Positions 19-550.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-9311N.
IntActi P08331. 2 interactions.
MINTi MINT-1228170.
STRINGi 511145.b4213.

Proteomic databases

PaxDbi P08331.
PRIDEi P08331.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC77170 ; AAC77170 ; b4213 .
BAE78214 ; BAE78214 ; BAE78214 .
GeneIDi 12933725.
948729.
KEGGi ecj:Y75_p4099.
eco:b4213.
PATRICi 32124001. VBIEscCol129921_4345.

Organism-specific databases

EchoBASEi EB0158.
EcoGenei EG10160. cpdB.

Phylogenomic databases

eggNOGi COG0737.
HOGENOMi HOG000248800.
InParanoidi P08331.
KOi K01119.
OMAi EKAQYPM.
OrthoDBi EOG696BW0.

Enzyme and pathway databases

BioCyci EcoCyc:CPDB-MONOMER.
ECOL316407:JW4171-MONOMER.
MetaCyc:CPDB-MONOMER.

Miscellaneous databases

PROi P08331.

Gene expression databases

Genevestigatori P08331.

Family and domain databases

Gene3Di 3.60.21.10. 1 hit.
3.90.780.10. 1 hit.
InterProi IPR008334. 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 ]
PANTHERi PTHR11575. PTHR11575. 1 hit.
Pfami PF02872. 5_nucleotid_C. 1 hit.
PF00149. Metallophos. 1 hit.
[Graphical view ]
PRINTSi PR01607. APYRASEFAMLY.
SUPFAMi SSF55816. SSF55816. 1 hit.
SSF56300. SSF56300. 1 hit.
TIGRFAMsi TIGR01390. CycNucDiestase. 1 hit.
PROSITEi PS00785. 5_NUCLEOTIDASE_1. 1 hit.
PS00786. 5_NUCLEOTIDASE_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

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: October 29, 2014
This is version 140 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