P08331 (CPDB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	647 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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.

Ontologies

Keywords
Cellular component	Periplasm
Domain	Signal
Ligand	Metal-binding Nucleotide-binding
Molecular function	Hydrolase
Technical term	Complete proteome Direct protein sequencing Multifunctional enzyme Reference proteome
Gene Ontology (GO)
Biological process	nucleotide catabolic process Inferred from electronic annotation. Source: InterPro
Cellular component	periplasmic space Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	2',3'-cyclic-nucleotide 2'-phosphodiesterase activity Inferred from electronic annotation. Source: EC 3'-nucleotidase activity Inferred from electronic annotation. Source: EC metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW nucleotide binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Signal peptide	1 – 19	19	Ref.6
	Chain	20 – 647	628	2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase		PRO_0000000035
Regions
	Region	544 – 550	7	Substrate binding By similarity
Sites
	Metal binding	31	1	Divalent metal cation 1 By similarity
	Metal binding	33	1	Divalent metal cation 1 By similarity
	Metal binding	76	1	Divalent metal cation 1 By similarity
	Metal binding	76	1	Divalent metal cation 2 By similarity
	Metal binding	116	1	Divalent metal cation 2 By similarity
	Metal binding	225	1	Divalent metal cation 2 By similarity
	Metal binding	257	1	Divalent metal cation 2 By similarity
	Metal binding	259	1	Divalent metal cation 1 By similarity
	Binding site	440	1	Substrate By similarity
Experimental info
	Sequence conflict	316	1	A → G in AAA23597. Ref.1
	Sequence conflict	528 – 552	25	GKPID…GGKFA → ASRLIRTPCSWLPPITIALT GQIC in AAA23597. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P08331 [UniParc]. Last modified February 1, 1995. Version 2. Checksum: 4B26DC3563473827	FASTA	647	70,832
	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

References

	« Hide 'large scale' referencesShow '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: 3005231] [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: 7610040] [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 277:1453-1474(1997) [PubMed: 9278503] [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: 16738553] [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: 2172762] [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: 9298646] [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.
PIR	ESECPC. H65232.
RefSeq	NP_418634.1. NC_000913.2.
3D structure databases
ProteinModelPortal	P08331.
SMR	P08331. Positions 19-354.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-9311N.
IntAct	P08331. 2 interactions.
MINT	MINT-1228170.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	EBESCT00000003401; EBESCP00000003401; EBESCG00000002787. EBESCT00000014549; EBESCP00000013840; EBESCG00000013610.
GeneID	948729.
GenomeReviews	Gene locus JW4171 in contig AP009048_GR. Gene locus b4213 in contig U00096_GR.
KEGG	ecj:JW4171. eco:b4213.
PATRIC	32124001. VBIEscCol129921_4345.
Organism-specific databases
EchoBASE	EB0158.
EcoGene	EG10160. cpdB.
Phylogenomic databases
eggNOG	COG0737.
GeneTree	EBGT00050000009523.
HOGENOM	HBG510269.
OMA	DHDATRE.
ProtClustDB	PRK09420.
Enzyme and pathway databases
BioCyc	EcoCyc:CPDB-MONOMER. MetaCyc:CPDB-MONOMER.
Gene expression databases
Genevestigator	P08331.
Family and domain databases
InterPro	IPR008334. 5'-Nucleotdase_C. IPR006146. 5'-Nucleotdase_CS. IPR006179. 5_nucleotidase/apyrase. IPR006294. Cyc_nuc_PDE_nucleotidase. IPR004843. Metallo_PEstase_dom. [Graphical view]
Gene3D	G3DSA:3.90.780.10. 5'-Nucleotdase_C. 1 hit.
KO	K01119.
PANTHER	PTHR11575. 5_nucleotidase. 1 hit.
Pfam	PF02872. 5_nucleotid_C. 1 hit. PF00149. Metallophos. 1 hit. [Graphical view]
PRINTS	PR01607. APYRASEFAMLY.
SUPFAM	SSF55816. 5'-Nucleotdase_C. 1 hit.
TIGRFAMs	TIGR01390. CycNucDiestase. 1 hit.
PROSITE	PS00785. 5_NUCLEOTIDASE_1. 1 hit. PS00786. 5_NUCLEOTIDASE_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

CPDB_ECOLI

Accession

Primary (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:	January 25, 2012
This is version 118 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program