RegulonDB RegulonDB 10.9: Gene Form
   

cpdB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

cpdB cysQ ytfH CRP cpdBp cpdBp TSS_5071 (cluster) TSS_5071 (cluster)

Gene      
Name: cpdB    Texpresso search in the literature
Synonym(s): ECK4209, EG10160, b4213
Genome position(nucleotides): 4434622 <-- 4436565 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
49.49
Reference(s): [1] Beacham IR., et al., 1980
External database links:  
ASAP:
ABE-0013782
CGSC:
909
ECHOBASE:
EB0158
ECOLIHUB:
cpdB
OU-MICROARRAY:
b4213
STRING:
511145.b4213
COLOMBOS: cpdB


Shine dalgarno      
Sequence: cccgatgataAAAGGAtgtccctGAT


Product      
Name: 2'3' cyclic nucleotide phosphodiesterase/3' nucleotidase
Synonym(s): CpdB
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space
Molecular weight: 70.832
Isoelectric point: 5.423
Motif(s):
 
Type Positions Sequence
20 -> 647 ATVDLRIMETTDLHSNMMDFDYYKDTATEKFGLVRTASLINDARNEVKNSVLVDNGDLIQGSPLADYMSAKGLKAGDIHPVYKALNTLDYTVGTLGNHEFNYGLDYLKNALAGAKFPYVNANVIDARTKQPMFTPYLIKDTEVVDKDGKKQTLKIGYIGVVPPQIMGWDKANLSGKVTVNDITETVRKYVPEMREKGADVVVVLAHSGLSADPYKVMAENSVYYLSEIPGVNAIMFGHAHAVFPGKDFADIEGADIAKGTLNGVPAVMPGMWGDHLGVVDLQLSNDSGKWQVTQAKAEARPIYDIANKKSLAAEDSKLVETLKADHDATRQFVSKPIGKSADNMYSYLALVQDDPTVQVVNNAQKAYVEHYIQGDPDLAKLPVLSAAAPFKVGGRKNDPASYVEVEKGQLTFRNAADLYLYPNTLIVVKASGKEVKEWLECSAGQFNQIDPNSTKPQSLINWDGFRTYNFDVIDGVNYQIDVTQPARYDGECQMINANAERIKNLTFNGKPIDPNAMFLVATNNYRAYGGKFAGTGDSHIAFASPDENRSVLAAWIADESKRAGEIHPAADNNWRLAPIAGDKKLDIRFETSPSDKAAAFIKEKGQYPMNKVATDDIGFAIYQVDLSK
355 -> 550 PIGKSADNMYSYLALVQDDPTVQVVNNAQKAYVEHYIQGDPDLAKLPVLSAAAPFKVGGRKNDPASYVEVEKGQLTFRNAADLYLYPNTLIVVKASGKEVKEWLECSAGQFNQIDPNSTKPQSLINWDGFRTYNFDVIDGVNYQIDVTQPARYDGECQMINANAERIKNLTFNGKPIDPNAMFLVATNNYRAYGGK
1 -> 19 MIKFSATLLATLIAASVNA
544 -> 550 YRAYGGK
316 -> 316 A

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.33 - nucleotide and nucleoside conversions
Gene Ontology Terms (GO)  
cellular_component GO:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space
molecular_function GO:0003824 - catalytic activity
GO:0016788 - hydrolase activity, acting on ester bonds
GO:0016787 - hydrolase activity
GO:0046872 - metal ion binding
GO:0000166 - nucleotide binding
GO:0008254 - 3'-nucleotidase activity
GO:0008663 - 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity
biological_process GO:0008152 - metabolic process
GO:0009117 - nucleotide metabolic process
GO:0006974 - cellular response to DNA damage stimulus
GO:0016311 - dephosphorylation
GO:0009166 - nucleotide catabolic process
Note(s): Note(s): ...[more].
External database links:  
DIP:
DIP-9311N
ECOCYC:
CPDB-MONOMER
ECOLIWIKI:
b4213
INTERPRO:
IPR004843
INTERPRO:
IPR041827
INTERPRO:
IPR036907
INTERPRO:
IPR029052
INTERPRO:
IPR008334
INTERPRO:
IPR006294
INTERPRO:
IPR006146
INTERPRO:
IPR006179
MODBASE:
P08331
PANTHER:
PTHR11575
PFAM:
PF02872
PFAM:
PF00149
PRIDE:
P08331
PRINTS:
PR01607
PRODB:
PRO_000022322
PROSITE:
PS00786
PROSITE:
PS00785
REFSEQ:
NP_418634
SMR:
P08331
UNIPROT:
P08331


Operon      
Name: cpdB         
Operon arrangement:
Transcription unit        Promoter
cpdB


Transcriptional Regulation      
Display Regulation             
Activated by: CRP


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_5071 (cluster) 4436564 forward For this promoter, there
Read more >
[RS-EPT-CBR] [2]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates



Reference(s)    

 [1] Beacham IR., Garrett S., 1980, Isolation of Escherichia coli mutants (cpdB) deficient in periplasmic 2':3'-cyclic phosphodiesterase and genetic mapping of the cpdB locus., J Gen Microbiol 119(1):31-4

 [2] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.


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