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P13518

- CSRD_ECOLI

UniProt

P13518 - CSRD_ECOLI

Protein

RNase E specificity factor CsrD

Gene

csrD

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 115 (01 Oct 2014)
      Sequence version 2 (01 Nov 1995)
      Previous versions | rss
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    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

    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

    GO - Cellular componenti

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

    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

    Gene expression databases

    GenevestigatoriP13518.

    Interactioni

    Protein-protein interaction databases

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

    Structurei

    3D structure databases

    ProteinModelPortaliP13518.
    ModBaseiSearch...
    MobiDBiSearch...

    Transmembrane

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

    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.
    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

    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: October 1, 2014
    This is version 115 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