Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

RNase E specificity factor CsrD

Gene

csrD

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

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

GO - Biological processi

  • ncRNA catabolic process Source: EcoCyc
  • regulation of RNA metabolic process Source: EcoCyc

Enzyme and pathway databases

BioCyciEcoCyc:EG10018-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10018 csrD

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transmembranei10 – 30HelicalSequence analysisAdd BLAST21
Transmembranei135 – 155HelicalSequence analysisAdd BLAST21

GO - Cellular componenti

  • integral component of membrane Source: UniProtKB-KW
  • plasma membrane Source: EcoCyc

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 DgcC, 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)DescriptionActionsGraphical viewLength
Mutagenesisi584L → A: Decreased transcription of csrB. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001694921 – 646RNase E specificity factor CsrDAdd BLAST646

Proteomic databases

PaxDbiP13518
PRIDEiP13518

Expressioni

Inductioni

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

Interactioni

Protein-protein interaction databases

BioGridi4261943, 11 interactors
DIPiDIP-12292N
IntActiP13518, 1 interactor
STRINGi316385.ECDH10B_3428

Structurei

3D structure databases

ProteinModelPortaliP13518
SMRiP13518
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini254 – 387GGDEFPROSITE-ProRule annotationAdd BLAST134
Domaini396 – 644EALPROSITE-ProRule annotationAdd BLAST249

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni152 – 219HAMP-likeAdd BLAST68

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili194 – 224Sequence analysisAdd BLAST31

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

Keywords - Domaini

Coiled coil, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG41062P1 Bacteria
ENOG410XSQH LUCA
HOGENOMiHOG000270419
InParanoidiP13518
KOiK18765
OMAiCQYIGRL
PhylomeDBiP13518

Family and domain databases

CDDicd01948 EAL, 1 hit
cd01949 GGDEF, 1 hit
Gene3Di3.20.20.450, 1 hit
InterProiView protein in InterPro
IPR001633 EAL_dom
IPR035919 EAL_sf
IPR033423 GAPES4
IPR000160 GGDEF_dom
IPR029787 Nucleotide_cyclase
PfamiView protein in Pfam
PF00563 EAL, 1 hit
PF17157 GAPES4, 1 hit
PF00990 GGDEF, 1 hit
SMARTiView protein in SMART
SM00052 EAL, 1 hit
SM00267 GGDEF, 1 hit
SUPFAMiSSF141868 SSF141868, 1 hit
SSF55073 SSF55073, 1 hit
TIGRFAMsiTIGR00254 GGDEF, 1 hit
PROSITEiView protein in PROSITE
PS50883 EAL, 1 hit
PS50887 GGDEF, 1 hit

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_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC76284; AAC76284; b3252
BAE77294; BAE77294; BAE77294
GeneIDi947702
KEGGiecj:JW3221
eco:b3252
PATRICifig|1411691.4.peg.3477

Similar proteinsi

Entry informationi

Entry nameiCSRD_ECOLI
AccessioniPrimary (citable) accession number: P13518
Secondary accession number(s): Q2M8W2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: November 1, 1995
Last modified: March 28, 2018
This is version 137 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health