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csrD:On One Page

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Standard Name

csrD

Gene Synonym(s)

yhdA, ECK3240, b3252, JW3221[1][2]

Product Desc.

regulator of CsrB and CsrC decay[2][3]

Targets csrB/C sRNAs for degradation by RNase E; carbon flux regulator; mechanism unknown; indirectly affects CsrA function[4]

Product Synonyms(s)

conserved inner membrane protein[1], B3252[2][1], YhdA[2][1], CsrD[2][1]

Function from GO
Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yhdA[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(csrD)    Textpresso(csrD)

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Notes

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CsrD has a central GGDEF putative diguanylate cyclase, then a C-terminal putative cyclic-di-GMP phosphodiesterase EAL domain. CsrD's role in csrB/C destabilization does not involve cyclic-di-GMP metabolism; very low level of CsrD expression; CsrD may work at substoichiometric concentrations (Suzuki, 2006). False positive lipoprotein prediction, Cys not conserved.[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

csrD

Mnemonic

Carbon storage regulator

Synonyms

yhdA, ECK3240, b3252, JW3221[1][2]

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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

73.27 minutes 

MG1655: 3401354..3399414
gbrowse_img.php?coord=3399414..3401354&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 3403187..3401247
gbrowse_img.php?coord=3401247..3403187&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

BW2952

NC_012759: 3286562..3288502
gbrowse_img.php?coord=3286562..3288502&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
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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

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

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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:EG10018

EchoBASE (EcoliWiki Page)

EchoBASE:EB0018

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3252

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4008

EcoGene (EcoliWiki Page)

EcoGene:EG10018

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YHDA

ASAP (EcoliWikiPage)

ASAP:ABE-0010663


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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

YhdA

Synonyms

conserved inner membrane protein[1], B3252[2][1], YhdA[2][1], CsrD[2][1]

Product description

regulator of CsrB and CsrC decay[2][3]

Targets csrB/C sRNAs for degradation by RNase E; carbon flux regulator; mechanism unknown; indirectly affects CsrA function[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
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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
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Notes

Localization

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

CompartmentDescriptionEvidenceSourceNotes

plasma membrane

C-terminus localized in the cytoplasm with 2 predicted transmembrane domains

Daley et al. (2005) [5]


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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 

MRLTTKFSAF VTLLTGLTIF VTLLGCSLSF YNAIQYKFSH RVQAVATAID THLVSNDFSV
LRPQITELMM SADIVRVDLL HGDKQVYTLA RNGSYRPVGS SDLFRELSVP LIKHPGMSLR
LVYQDPMGNY FHSLMTTAPL TGAIGFIIVM LFLAVRWLQR QLAGQELLET RATRILNGER
GSNVLGTIYE WPPRTSSALD TLLREIQNAR EQHSRLDTLI RSYAAQDVKT GLNNRLFFDN
QLATLLEDQE KVGTHGIVMM IRLPDFNMLS DTWGHSQVEE QFFTLTNLLS TFMMRYPGAL
LARYHRSDFA ALLPHRTLKE AESIAGQLIK AVDTLPNNKM LDRDDMIHIG ICAWRSGQDT
EQVMEHAESA TRNAGLQGGN SWAIYDDSLP EKGRGNVRWR TLIEQMLSRG GPRLYQKPAV
TREGQVHHRE LMCRIFDGNE EVSSAEYMPM VLQFGLSEEY DRLQISRLIP LLRYWPEENL
AIQVTVESLI RPRFQRWLRD TLMQCEKSQR KRIIIELAEA DVGQHISRLQ PVIRLVNALG
VRVAVNQAGL TLVSTSWIKE LNVELLKLHP GLVRNIEKRT ENQLLVQSLV EACSGTSTQV
YATGVRSRSE WQTLIQRGVT GGQGDFFASS QPLDTNVKKY SQRYSV
Length

646

Mol. Wt

73.34 kDa

pI

8.9 (calculated)

Extinction coefficient

81,820 - 82,445 (calc based on 18 Y, 10 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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tmhmm.php?gene=csrD&show=pic&.jpg
Click the image to view raw output from TMHMM.

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:EG10018-MONOMER

UniProt (EcoliWiki Page)

UniProt:P13518

PFAM (EcoliWiki Page)

PFAM:PF00990

RefSeq (EcoliWiki Page)

RefSeq:NP_417718


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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)

yhdA

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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=3401334..3401374&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:b3252 (EcoliWiki Page)

NCBI GEO profiles for csrD

microarray

GenExpDB:b3252 (EcoliWiki Page)

Summary of data for csrD 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 (3400889..3401142) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ08; Well:E7[6]

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Notes

Accessions Related to csrD Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10018

EchoBASE (EcoliWiki Page)

EchoBASE:EB0018

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3252

EcoGene (EcoliWiki Page)

EcoGene:EG10018


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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

Shigella flexneri

YHDA

From SHIGELLACYC

E. coli O157

YHDA

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:PF00990


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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. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 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. ↑ Daley DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308: 1321-3 PubMed EcoliWiki page
  6. ↑ 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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