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P08331 (CPDB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 138. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase

EC=3.1.3.6
EC=3.1.4.16
Gene names
Name:cpdB
Ordered Locus Names:b4213, JW4171
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length647 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.1

Catalytic activity

Nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 3'-phosphate. Ref.1

A 3'-ribonucleotide + H2O = a ribonucleoside + phosphate. Ref.1

Cofactor

Divalent cations By similarity.

Subcellular location

Periplasm Ref.1.

Miscellaneous

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

Sequence similarities

Belongs to the 5'-nucleotidase family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 1919 Ref.6
Chain20 – 6476282',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase
PRO_0000000035

Regions

Region544 – 5507Substrate binding By similarity

Sites

Metal binding311Divalent metal cation 1 By similarity
Metal binding331Divalent metal cation 1 By similarity
Metal binding761Divalent metal cation 1 By similarity
Metal binding761Divalent metal cation 2 By similarity
Metal binding1161Divalent metal cation 2 By similarity
Metal binding2251Divalent metal cation 2 By similarity
Metal binding2571Divalent metal cation 2 By similarity
Metal binding2591Divalent metal cation 1 By similarity
Binding site4401Substrate By similarity

Experimental info

Sequence conflict3161A → G in AAA23597. Ref.1
Sequence conflict528 – 55225GKPID…GGKFA → ASRLIRTPCSWLPPITIALT GQIC in AAA23597. Ref.1

Sequences

Sequence LengthMass (Da)Tools
P08331 [UniParc].

Last modified February 1, 1995. Version 2.
Checksum: 4B26DC3563473827

FASTA64770,832
        10         20         30         40         50         60 
MIKFSATLLA TLIAASVNAA TVDLRIMETT DLHSNMMDFD YYKDTATEKF GLVRTASLIN 

        70         80         90        100        110        120 
DARNEVKNSV LVDNGDLIQG SPLADYMSAK GLKAGDIHPV YKALNTLDYT VGTLGNHEFN 

       130        140        150        160        170        180 
YGLDYLKNAL AGAKFPYVNA NVIDARTKQP MFTPYLIKDT EVVDKDGKKQ TLKIGYIGVV 

       190        200        210        220        230        240 
PPQIMGWDKA NLSGKVTVND ITETVRKYVP EMREKGADVV VVLAHSGLSA DPYKVMAENS 

       250        260        270        280        290        300 
VYYLSEIPGV NAIMFGHAHA VFPGKDFADI EGADIAKGTL NGVPAVMPGM WGDHLGVVDL 

       310        320        330        340        350        360 
QLSNDSGKWQ VTQAKAEARP IYDIANKKSL AAEDSKLVET LKADHDATRQ FVSKPIGKSA 

       370        380        390        400        410        420 
DNMYSYLALV QDDPTVQVVN NAQKAYVEHY IQGDPDLAKL PVLSAAAPFK VGGRKNDPAS 

       430        440        450        460        470        480 
YVEVEKGQLT FRNAADLYLY PNTLIVVKAS GKEVKEWLEC SAGQFNQIDP NSTKPQSLIN 

       490        500        510        520        530        540 
WDGFRTYNFD VIDGVNYQID VTQPARYDGE CQMINANAER IKNLTFNGKP IDPNAMFLVA 

       550        560        570        580        590        600 
TNNYRAYGGK FAGTGDSHIA FASPDENRSV LAAWIADESK RAGEIHPAAD NNWRLAPIAG 

       610        620        630        640 
DKKLDIRFET SPSDKAAAFI KEKGQYPMNK VATDDIGFAI YQVDLSK 

« Hide

References

« Hide 'large scale' references
[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]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRESECPC. H65232.
RefSeqNP_418634.1. NC_000913.3.
YP_492355.1. NC_007779.1.

3D structure databases

ProteinModelPortalP08331.
SMRP08331. Positions 19-550.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-9311N.
IntActP08331. 2 interactions.
MINTMINT-1228170.
STRING511145.b4213.

Proteomic databases

PaxDbP08331.
PRIDEP08331.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC77170; AAC77170; b4213.
BAE78214; BAE78214; BAE78214.
GeneID12933725.
948729.
KEGGecj:Y75_p4099.
eco:b4213.
PATRIC32124001. VBIEscCol129921_4345.

Organism-specific databases

EchoBASEEB0158.
EcoGeneEG10160. cpdB.

Phylogenomic databases

eggNOGCOG0737.
HOGENOMHOG000248800.
KOK01119.
OMAEKAQYPM.
OrthoDBEOG696BW0.

Enzyme and pathway databases

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

Gene expression databases

GenevestigatorP08331.

Family and domain databases

Gene3D3.60.21.10. 1 hit.
3.90.780.10. 1 hit.
InterProIPR008334. 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]
PANTHERPTHR11575. PTHR11575. 1 hit.
PfamPF02872. 5_nucleotid_C. 1 hit.
PF00149. Metallophos. 1 hit.
[Graphical view]
PRINTSPR01607. APYRASEFAMLY.
SUPFAMSSF55816. SSF55816. 1 hit.
SSF56300. SSF56300. 1 hit.
TIGRFAMsTIGR01390. CycNucDiestase. 1 hit.
PROSITEPS00785. 5_NUCLEOTIDASE_1. 1 hit.
PS00786. 5_NUCLEOTIDASE_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

PROP08331.

Entry information

Entry nameCPDB_ECOLI
AccessionPrimary (citable) accession number: P08331
Secondary accession number(s): Q2M692
Entry history
Integrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: February 1, 1995
Last modified: June 11, 2014
This is version 138 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene