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cpdA:On One Page

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See Help:Quickview for help with entering information in the Quickview table.

Standard Name

cpdA

Gene Synonym(s)

ECK3023, b3032, JW3000, icc[1]

Product Desc.

cAMP phosphodiesterase[2][3]

3',5' cAMP phosphodiesterase; mutants have elevated cAMP levels[4]

Product Synonyms(s)

cyclic 3',5'-adenosine monophosphate phosphodiesterase[1], B3032[2][1], CpdA[2][1], Icc[2][1]

Function from GO
Knock-Out Phenotype
Regulation/Expression

transcription unit(s): parE[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(cpdA)    Textpresso(cpdA)

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Notes

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CpdA is defective in Crooke's strain (ATCC 8739).[4]



Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

cpdA

Mnemonic

Cyclic nucleotide P-Diesterase

Synonyms

ECK3023, b3032, JW3000, icc[1]

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

68.41 minutes 

MG1655: 3174855..3174028
gbrowse_img.php?coord=3174028..3174855&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 3111005..3110178
gbrowse_img.php?coord=3110178..3111005&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 3175489..3174662
gbrowse_img.php?coord=3174662..3175489&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 3272600..3271773
gbrowse_img.php?coord=3271773..3272600&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 3061176..3062003
gbrowse_img.php?coord=3061176..3062003&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature typeLocationDescription
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

ΔcpdA (Keio:JW3000)

deletion

deletion

PMID:16738554

Shigen
CGSC10300[5]

ΔcpdA729::kan

PMID:16738554

CGSC:100378


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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

ResourceResource TypeSourceNotes/Reference

JW3000

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGAAAGCCTGTTAACCCTTCC

Primer 2:CCGTAGCCTTCTGAAGCGGTATC

metC162::Tn10

Linked marker

CAG18475 = CGSC7435[5]

est. P1 cotransduction: 41% [6]

tolC210::Tn10

Linked marker

CAG12184 = CGSC7437[5]

est. P1 cotransduction: 87% [6]

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G7579

EchoBASE (EcoliWiki Page)

EchoBASE:EB2104

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3032

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3778

EcoGene (EcoliWiki Page)

EcoGene:EG12187

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:ICC

ASAP (EcoliWikiPage)

ASAP:ABE-0009957


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Notes

Links

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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

CpdA

Synonyms

cyclic 3',5'-adenosine monophosphate phosphodiesterase[1], B3032[2][1], CpdA[2][1], Icc[2][1]

Product description

cAMP phosphodiesterase[2][3]

3',5' cAMP phosphodiesterase; mutants have elevated cAMP levels[4]

EC number (for enzymes)
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Notes

Function

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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0016787

hydrolase activity

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004843

F

Seeded from EcoCyc [7]

complete

GO:0005737

cytoplasm

C

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0016052

carbohydrate catabolic process

P

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0008233

peptidase activity

F

Seeded from Riley et al 2006 [1].

required fields missing

GO:0016788

hydrolase activity, acting on ester bonds

F

Seeded from EcoCyc 11.1[3].

required fields missing

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner TypePartnerNotesReferencesEvidence

Protein

gadX

PMID:16606699

Experiment(s):EBI-1144597

Protein

ribB

PMID:16606699

Experiment(s):EBI-1144597

Protein

lldR

PMID:16606699

Experiment(s):EBI-1144597

Protein

dam

PMID:16606699

Experiment(s):EBI-1144597

Protein

groL

PMID:16606699

Experiment(s):EBI-1144597

Protein

kdsA

PMID:16606699

Experiment(s):EBI-1144597

Protein

yafY

PMID:16606699

Experiment(s):EBI-1144597

Protein

yfeT

PMID:16606699

Experiment(s):EBI-1144597

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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

CompartmentDescriptionEvidenceSourceNotes
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Notes

Structure and Physical Properties

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Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Sequence

at EcoCyc 

MESLLTLPLA GEARVRILQI TDTHLFAQKH EALLGVNTWE SYQAVLEAIR PHQHEFDLIV
ATGDLAQDQS SAAYQHFAEG IASFRAPCVW LPGNHDFQPA MYSALQDAGI SPAKRVFIGE
QWQILLLDSQ VFGVPHGELS EFQLEWLERK LADAPERHTL LLLHHHPLPA GCSWLDQHSL
RNAGELDTVL AKFPHVKYLL CGHIHQELDL DWNGRRLLAT PSTCVQFKPH CSNFTLDTIA
PGWRTLELHA DGTLTTEVHR LADTRFQPDT ASEGY
Length

275

Mol. Wt

30.937 kDa

pI

5.9 (calculated)

Extinction coefficient

45,950 - 46,575 (calc based on 5 Y, 7 W, and 5 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

TypeResiduesDescriptionNotesReferences
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Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures
Models

View models at:

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Structure figures

Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource typeSourceNotes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G7579-MONOMER

UniProt (EcoliWiki Page)

UniProt:P0AEW4

PFAM (EcoliWiki Page)

PFAM:PF00149

RefSeq (EcoliWiki Page)

RefSeq:NP_417504


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Notes

Links

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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

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See Help:Cellular levels

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

parE

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Figure courtesy of RegulonDB

Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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gbrowse_img.php?coord=3174835..3174875&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein+flip&width=400&figure=Nterm&.png
This picture shows the sequence around the N-terminus.

Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele NameMutationPhenotypeReference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

TypeReferenceNotes

microarray

GEO Profiles:b3032 (EcoliWiki Page)

NCBI GEO profiles for cpdA

microarray

GenExpDB:b3032 (EcoliWiki Page)

Summary of data for cpdA from multiple microarray studies

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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource NameResource TypeDescriptionSourceNotes

GFP Fusion

Intergenic region (3174753..3174913) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ12; Well:B2[8]

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Notes

Accessions Related to cpdA Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G7579

EchoBASE (EcoliWiki Page)

EchoBASE:EB2104

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3032

EcoGene (EcoliWiki Page)

EcoGene:EG12187


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Notes

Links

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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

OrganismHomologs (Statistics)Comments

Anopheles gambiae

  • ENSANGP00000026900 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

ICC

From SHIGELLACYC

E. coli O157

ICC

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF00149


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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 3.4 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
  7. ↑ EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  8. ↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

Categories

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