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Protein

RNase E specificity factor CsrD

Gene

csrD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: 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 - Biological processi

  • ncRNA catabolic process Source: EcoCyc
  • 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 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10018. csrD.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei10 – 3021HelicalSequence AnalysisAdd
BLAST
Transmembranei135 – 15521HelicalSequence AnalysisAdd
BLAST

GO - Cellular componenti

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 (PubMed:16980588). 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 (PubMed:19332833).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

Interactioni

Protein-protein interaction databases

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

Structurei

3D structure databases

ProteinModelPortaliP13518.
SMRiP13518. Positions 210-634.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini254 – 387134GGDEFPROSITE-ProRule annotationAdd
BLAST
Domaini396 – 644249EALPROSITE-ProRule annotationAdd
BLAST

Region

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

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili194 – 22431Sequence AnalysisAdd
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.PROSITE-ProRule annotation
Contains 1 GGDEF domain.PROSITE-ProRule annotation

Keywords - Domaini

Coiled coil, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiCOG2199.
HOGENOMiHOG000270419.
InParanoidiP13518.
KOiK18765.
OMAiCQYIGRL.
OrthoDBiEOG64V28B.
PhylomeDBiP13518.

Family and domain databases

Gene3Di3.20.20.450. 1 hit.
InterProiIPR001633. EAL_dom.
IPR000160. GGDEF_dom.
IPR029787. Nucleotide_cyclase.
[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

        10         20         30         40         50
MRLTTKFSAF VTLLTGLTIF VTLLGCSLSF YNAIQYKFSH RVQAVATAID
60 70 80 90 100
THLVSNDFSV LRPQITELMM SADIVRVDLL HGDKQVYTLA RNGSYRPVGS
110 120 130 140 150
SDLFRELSVP LIKHPGMSLR LVYQDPMGNY FHSLMTTAPL TGAIGFIIVM
160 170 180 190 200
LFLAVRWLQR QLAGQELLET RATRILNGER GSNVLGTIYE WPPRTSSALD
210 220 230 240 250
TLLREIQNAR EQHSRLDTLI RSYAAQDVKT GLNNRLFFDN QLATLLEDQE
260 270 280 290 300
KVGTHGIVMM IRLPDFNMLS DTWGHSQVEE QFFTLTNLLS TFMMRYPGAL
310 320 330 340 350
LARYHRSDFA ALLPHRTLKE AESIAGQLIK AVDTLPNNKM LDRDDMIHIG
360 370 380 390 400
ICAWRSGQDT EQVMEHAESA TRNAGLQGGN SWAIYDDSLP EKGRGNVRWR
410 420 430 440 450
TLIEQMLSRG GPRLYQKPAV TREGQVHHRE LMCRIFDGNE EVSSAEYMPM
460 470 480 490 500
VLQFGLSEEY DRLQISRLIP LLRYWPEENL AIQVTVESLI RPRFQRWLRD
510 520 530 540 550
TLMQCEKSQR KRIIIELAEA DVGQHISRLQ PVIRLVNALG VRVAVNQAGL
560 570 580 590 600
TLVSTSWIKE LNVELLKLHP GLVRNIEKRT ENQLLVQSLV EACSGTSTQV
610 620 630 640
YATGVRSRSE WQTLIQRGVT GGQGDFFASS QPLDTNVKKY SQRYSV
Length:646
Mass (Da):73,339
Last modified:November 1, 1995 - v2
Checksum:i0387E011BC4D06B8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.
WP_001241469.1. NZ_CP010445.1.

Genome annotation databases

EnsemblBacteriaiAAC76284; AAC76284; b3252.
BAE77294; BAE77294; BAE77294.
GeneIDi947702.
KEGGieco:b3252.
PATRICi32121930. VBIEscCol129921_3349.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.
WP_001241469.1. NZ_CP010445.1.

3D structure databases

ProteinModelPortaliP13518.
SMRiP13518. Positions 210-634.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

Proteomic databases

PaxDbiP13518.
PRIDEiP13518.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76284; AAC76284; b3252.
BAE77294; BAE77294; BAE77294.
GeneIDi947702.
KEGGieco:b3252.
PATRICi32121930. VBIEscCol129921_3349.

Organism-specific databases

EchoBASEiEB0018.
EcoGeneiEG10018. csrD.

Phylogenomic databases

eggNOGiCOG2199.
HOGENOMiHOG000270419.
InParanoidiP13518.
KOiK18765.
OMAiCQYIGRL.
OrthoDBiEOG64V28B.
PhylomeDBiP13518.

Enzyme and pathway databases

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

Miscellaneous databases

PROiP13518.

Family and domain databases

Gene3Di3.20.20.450. 1 hit.
InterProiIPR001633. EAL_dom.
IPR000160. GGDEF_dom.
IPR029787. Nucleotide_cyclase.
[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]
ProtoNetiSearch...

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: July 22, 2015
This is version 121 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.Curated

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.