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P13518 (CSRD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 112. 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:
RNase E specificity factor CsrD
Alternative name(s):
Regulator of CsrB and CsrC decay CsrD
Gene names
Name:csrD
Synonyms:yhdA
Ordered Locus Names:b3252, JW3221
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length646 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Serves as a specificity factor required for RNase E-mediated decay of the small global regulatory RNAs CsrB and CsrC, it is probably not a nuclease. Nor does its activity involve c-di-GMP, despite its domain composition. Positively modulates motility gene expression, is also required for curli expression. Ref.4 Ref.5 Ref.6

Subcellular location

Cell membrane; Multi-pass membrane protein Potential.

Induction

Expressed at low levels at both 28 and 37 degrees Celsius. Ref.6

Domain

Removal of the transmembrane regions (residues 1-156) has no effect on csrB translation, however removal of either the HAMP-like region, EAL or GGDEF domains obviates the activity of CsrD. Ref.5

Disruption phenotype

Dramatically stabilizes CsrB and CsrC RNAs, small RNAs that sequester the global carbon storage regulator CsrA; also decreased transcription of CsrB/C (Ref.5). Decreased biofilm formation, decreased expression of AdrA, a probable diguanylate cyclase and of the curli regulator CsgD. Decreased expression of the curlin subunit CsgB, decreased curli expression at 28 degrees Celsius (Ref.6). Ref.4 Ref.5 Ref.6

Sequence similarities

Contains 1 EAL domain.

Contains 1 GGDEF domain.

Caution

Although this protein contains both EAL and GGDEF domains it is unlikely to have either c-di-GMP phosphodiesterase or diguanylate cyclase activities as amino acids known to be important to these activities are not conserved.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 646646RNase E specificity factor CsrD
PRO_0000169492

Regions

Transmembrane10 – 3021Helical; Potential
Transmembrane135 – 15521Helical; Potential
Domain254 – 387134GGDEF
Domain396 – 644249EAL
Region152 – 21968HAMP-like
Coiled coil194 – 22431 Potential

Experimental info

Mutagenesis5841L → A: Decreased transcription of csrB. Ref.5

Sequences

Sequence LengthMass (Da)Tools
P13518 [UniParc].

Last modified November 1, 1995. Version 2.
Checksum: 0387E011BC4D06B8

FASTA64673,339
        10         20         30         40         50         60 
MRLTTKFSAF VTLLTGLTIF VTLLGCSLSF YNAIQYKFSH RVQAVATAID THLVSNDFSV 

        70         80         90        100        110        120 
LRPQITELMM SADIVRVDLL HGDKQVYTLA RNGSYRPVGS SDLFRELSVP LIKHPGMSLR 

       130        140        150        160        170        180 
LVYQDPMGNY FHSLMTTAPL TGAIGFIIVM LFLAVRWLQR QLAGQELLET RATRILNGER 

       190        200        210        220        230        240 
GSNVLGTIYE WPPRTSSALD TLLREIQNAR EQHSRLDTLI RSYAAQDVKT GLNNRLFFDN 

       250        260        270        280        290        300 
QLATLLEDQE KVGTHGIVMM IRLPDFNMLS DTWGHSQVEE QFFTLTNLLS TFMMRYPGAL 

       310        320        330        340        350        360 
LARYHRSDFA ALLPHRTLKE AESIAGQLIK AVDTLPNNKM LDRDDMIHIG ICAWRSGQDT 

       370        380        390        400        410        420 
EQVMEHAESA TRNAGLQGGN SWAIYDDSLP EKGRGNVRWR TLIEQMLSRG GPRLYQKPAV 

       430        440        450        460        470        480 
TREGQVHHRE LMCRIFDGNE EVSSAEYMPM VLQFGLSEEY DRLQISRLIP LLRYWPEENL 

       490        500        510        520        530        540 
AIQVTVESLI RPRFQRWLRD TLMQCEKSQR KRIIIELAEA DVGQHISRLQ PVIRLVNALG 

       550        560        570        580        590        600 
VRVAVNQAGL TLVSTSWIKE LNVELLKLHP GLVRNIEKRT ENQLLVQSLV EACSGTSTQV 

       610        620        630        640 
YATGVRSRSE WQTLIQRGVT GGQGDFFASS QPLDTNVKKY SQRYSV 

« Hide

References

« Hide 'large scale' references
[1]"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.
[2]"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.
[3]"Determinations of the DNA sequence of the mreB gene and of the gene products of the mre region that function in formation of the rod shape of Escherichia coli cells."
Doi M., Wachi M., Ishino F., Tomioka S., Ito M., Sakagami Y., Suzuki A., Matsuhashi M.
J. Bacteriol. 170:4619-4624(1988) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 545-646.
Strain: K12.
[4]"Identification of YhdA as a regulator of the Escherichia coli carbon storage regulation system."
Jonas K., Tomenius H., Romling U., Georgellis D., Melefors O.
FEMS Microbiol. Lett. 264:232-237(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN REGULATION OF CARBON STORAGE REGULATION SYSTEM, DISRUPTION PHENOTYPE.
Strain: K12 / MG1655 / CF7789.
[5]"Identification of a novel regulatory protein (CsrD) that targets the global regulatory RNAs CsrB and CsrC for degradation by RNase E."
Suzuki K., Babitzke P., Kushner S.R., Romeo T.
Genes Dev. 20:2605-2617(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, MUTAGENESIS OF LEU-584, DOMAIN EAL AND GGDEF, DISRUPTION PHENOTYPE.
Strain: K12 / MG1655 / CF7789.
[6]"Gene expression patterns and differential input into curli fimbriae regulation of all GGDEF/EAL domain proteins in Escherichia coli."
Sommerfeldt N., Possling A., Becker G., Pesavento C., Tschowri N., Hengge R.
Microbiology 155:1318-1331(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN CURLI EXPRESSION, INDUCTION, DISRUPTION PHENOTYPE.
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U18997 Genomic DNA. Translation: AAA58055.1.
U00096 Genomic DNA. Translation: AAC76284.1.
AP009048 Genomic DNA. Translation: BAE77294.1.
M22055 Genomic DNA. Translation: AAA83890.1.
PIRQQECE5. F65117.
RefSeqNP_417718.1. NC_000913.3.
YP_491435.1. NC_007779.1.

3D structure databases

ProteinModelPortalP13518.
SMRP13518. Positions 210-634.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-12292N.
IntActP13518. 1 interaction.
MINTMINT-1286606.
STRING511145.b3252.

Proteomic databases

PaxDbP13518.
PRIDEP13518.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC76284; AAC76284; b3252.
BAE77294; BAE77294; BAE77294.
GeneID12932949.
947702.
KEGGecj:Y75_p3171.
eco:b3252.
PATRIC32121930. VBIEscCol129921_3349.

Organism-specific databases

EchoBASEEB0018.
EcoGeneEG10018. csrD.

Phylogenomic databases

eggNOGCOG2199.
HOGENOMHOG000270419.
OMARMDTLIR.
OrthoDBEOG64V28B.
PhylomeDBP13518.
ProtClustDBPRK11059.

Enzyme and pathway databases

BioCycEcoCyc:EG10018-MONOMER.
ECOL316407:JW3221-MONOMER.

Gene expression databases

GenevestigatorP13518.

Family and domain databases

Gene3D3.20.20.450. 1 hit.
InterProIPR001054. A/G_cyclase.
IPR001633. Diguanylate_PEstase_EAL_dom.
IPR000160. GGDEF_dom.
[Graphical view]
PfamPF00563. EAL. 1 hit.
PF00990. GGDEF. 1 hit.
[Graphical view]
SMARTSM00052. EAL. 1 hit.
SM00267. GGDEF. 1 hit.
[Graphical view]
SUPFAMSSF141868. SSF141868. 1 hit.
SSF55073. SSF55073. 1 hit.
TIGRFAMsTIGR00254. GGDEF. 1 hit.
PROSITEPS50883. EAL. 1 hit.
PS50887. GGDEF. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

PROP13518.

Entry information

Entry nameCSRD_ECOLI
AccessionPrimary (citable) accession number: P13518
Secondary accession number(s): Q2M8W2
Entry history
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: November 1, 1995
Last modified: April 16, 2014
This is version 112 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