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P13518

- CSRD_ECOLI

UniProt

P13518 - CSRD_ECOLI

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Protein

RNase E specificity factor CsrD

Gene
csrD, yhdA, b3252, JW3221
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 4 out of 5 - Experimental evidence at protein leveli

Functioni

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.3 Publications

GO - Molecular functioni

  1. phosphorus-oxygen lyase activity Source: InterPro

GO - Biological processi

  1. cyclic nucleotide biosynthetic process Source: InterPro
  2. intracellular signal transduction Source: InterPro
  3. ncRNA catabolic process Source: EcoCyc
  4. regulation of RNA metabolic process Source: EcoCyc
Complete GO annotation...

Enzyme and pathway databases

BioCyciEcoCyc:EG10018-MONOMER.
ECOL316407:JW3221-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
RNase E specificity factor CsrD
Alternative name(s):
Regulator of CsrB and CsrC decay CsrD
Gene namesi
Name:csrD
Synonyms:yhdA
Ordered Locus Names:b3252, JW3221
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10018. csrD.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei10 – 3021Helical; Reviewed predictionAdd
BLAST
Transmembranei135 – 15521Helical; Reviewed predictionAdd
BLAST

GO - Cellular componenti

  1. integral component of membrane Source: UniProtKB-KW
  2. plasma membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Disruption phenotypei

Dramatically stabilizes CsrB and CsrC RNAs, small RNAs that sequester the global carbon storage regulator CsrA; also decreased transcription of CsrB/C (1 Publication). 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 (1 Publication).3 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi584 – 5841L → A: Decreased transcription of csrB. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 646646RNase E specificity factor CsrDPRO_0000169492Add
BLAST

Proteomic databases

PaxDbiP13518.
PRIDEiP13518.

Expressioni

Inductioni

Expressed at low levels at both 28 and 37 degrees Celsius.1 Publication

Gene expression databases

GenevestigatoriP13518.

Interactioni

Protein-protein interaction databases

DIPiDIP-12292N.
IntActiP13518. 1 interaction.
MINTiMINT-1286606.
STRINGi511145.b3252.

Structurei

3D structure databases

ProteinModelPortaliP13518.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini254 – 387134GGDEFAdd
BLAST
Domaini396 – 644249EALAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni152 – 21968HAMP-likeAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili194 – 22431 Reviewed predictionAdd
BLAST

Domaini

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.1 Publication

Sequence similaritiesi

Contains 1 EAL domain.
Contains 1 GGDEF domain.

Keywords - Domaini

Coiled coil, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiCOG2199.
HOGENOMiHOG000270419.
OMAiRMDTLIR.
OrthoDBiEOG64V28B.
PhylomeDBiP13518.

Family and domain databases

Gene3Di3.20.20.450. 1 hit.
InterProiIPR001054. A/G_cyclase.
IPR001633. Diguanylate_PEstase_EAL_dom.
IPR000160. GGDEF_dom.
[Graphical view]
PfamiPF00563. EAL. 1 hit.
PF00990. GGDEF. 1 hit.
[Graphical view]
SMARTiSM00052. EAL. 1 hit.
SM00267. GGDEF. 1 hit.
[Graphical view]
SUPFAMiSSF141868. SSF141868. 1 hit.
SSF55073. SSF55073. 1 hit.
TIGRFAMsiTIGR00254. GGDEF. 1 hit.
PROSITEiPS50883. EAL. 1 hit.
PS50887. GGDEF. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P13518-1 [UniParc]FASTAAdd to Basket

« Hide

MRLTTKFSAF VTLLTGLTIF VTLLGCSLSF YNAIQYKFSH RVQAVATAID    50
THLVSNDFSV LRPQITELMM SADIVRVDLL HGDKQVYTLA RNGSYRPVGS 100
SDLFRELSVP LIKHPGMSLR LVYQDPMGNY FHSLMTTAPL TGAIGFIIVM 150
LFLAVRWLQR QLAGQELLET RATRILNGER GSNVLGTIYE WPPRTSSALD 200
TLLREIQNAR EQHSRLDTLI RSYAAQDVKT GLNNRLFFDN QLATLLEDQE 250
KVGTHGIVMM IRLPDFNMLS DTWGHSQVEE QFFTLTNLLS TFMMRYPGAL 300
LARYHRSDFA ALLPHRTLKE AESIAGQLIK AVDTLPNNKM LDRDDMIHIG 350
ICAWRSGQDT EQVMEHAESA TRNAGLQGGN SWAIYDDSLP EKGRGNVRWR 400
TLIEQMLSRG GPRLYQKPAV TREGQVHHRE LMCRIFDGNE EVSSAEYMPM 450
VLQFGLSEEY DRLQISRLIP LLRYWPEENL AIQVTVESLI RPRFQRWLRD 500
TLMQCEKSQR KRIIIELAEA DVGQHISRLQ PVIRLVNALG VRVAVNQAGL 550
TLVSTSWIKE LNVELLKLHP GLVRNIEKRT ENQLLVQSLV EACSGTSTQV 600
YATGVRSRSE WQTLIQRGVT GGQGDFFASS QPLDTNVKKY SQRYSV 646
Length:646
Mass (Da):73,339
Last modified:November 1, 1995 - v2
Checksum:i0387E011BC4D06B8
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U18997 Genomic DNA. Translation: AAA58055.1.
U00096 Genomic DNA. Translation: AAC76284.1.
AP009048 Genomic DNA. Translation: BAE77294.1.
M22055 Genomic DNA. Translation: AAA83890.1.
PIRiF65117. QQECE5.
RefSeqiNP_417718.1. NC_000913.3.
YP_491435.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC76284; AAC76284; b3252.
BAE77294; BAE77294; BAE77294.
GeneIDi12932949.
947702.
KEGGiecj:Y75_p3171.
eco:b3252.
PATRICi32121930. VBIEscCol129921_3349.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U18997 Genomic DNA. Translation: AAA58055.1 .
U00096 Genomic DNA. Translation: AAC76284.1 .
AP009048 Genomic DNA. Translation: BAE77294.1 .
M22055 Genomic DNA. Translation: AAA83890.1 .
PIRi F65117. QQECE5.
RefSeqi NP_417718.1. NC_000913.3.
YP_491435.1. NC_007779.1.

3D structure databases

ProteinModelPortali P13518.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-12292N.
IntActi P13518. 1 interaction.
MINTi MINT-1286606.
STRINGi 511145.b3252.

Proteomic databases

PaxDbi P13518.
PRIDEi P13518.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC76284 ; AAC76284 ; b3252 .
BAE77294 ; BAE77294 ; BAE77294 .
GeneIDi 12932949.
947702.
KEGGi ecj:Y75_p3171.
eco:b3252.
PATRICi 32121930. VBIEscCol129921_3349.

Organism-specific databases

EchoBASEi EB0018.
EcoGenei EG10018. csrD.

Phylogenomic databases

eggNOGi COG2199.
HOGENOMi HOG000270419.
OMAi RMDTLIR.
OrthoDBi EOG64V28B.
PhylomeDBi P13518.

Enzyme and pathway databases

BioCyci EcoCyc:EG10018-MONOMER.
ECOL316407:JW3221-MONOMER.

Miscellaneous databases

PROi P13518.

Gene expression databases

Genevestigatori P13518.

Family and domain databases

Gene3Di 3.20.20.450. 1 hit.
InterProi IPR001054. A/G_cyclase.
IPR001633. Diguanylate_PEstase_EAL_dom.
IPR000160. GGDEF_dom.
[Graphical view ]
Pfami PF00563. EAL. 1 hit.
PF00990. GGDEF. 1 hit.
[Graphical view ]
SMARTi SM00052. EAL. 1 hit.
SM00267. GGDEF. 1 hit.
[Graphical view ]
SUPFAMi SSF141868. SSF141868. 1 hit.
SSF55073. SSF55073. 1 hit.
TIGRFAMsi TIGR00254. GGDEF. 1 hit.
PROSITEi PS50883. EAL. 1 hit.
PS50887. GGDEF. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. 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.

Entry informationi

Entry nameiCSRD_ECOLI
AccessioniPrimary (citable) accession number: P13518
Secondary accession number(s): Q2M8W2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: November 1, 1995
Last modified: June 11, 2014
This is version 114 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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