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P76204

- YDIV_ECOLI

UniProt

P76204 - YDIV_ECOLI

Protein

Putative anti-FlhC(2)FlhD(4) factor YdiV

Gene

ydiV

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 99 (01 Oct 2014)
      Sequence version 1 (01 Feb 1997)
      Previous versions | rss
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    Functioni

    Upon overexpression acts as a novel anti-FlhC2FlhD4 factor, decreasing its DNA-binding activity, able to negatively regulate expression of flagellar class II operons including FliC.

    GO - Molecular functioni

    1. transcription factor binding Source: EcoCyc

    GO - Biological processi

    1. negative regulation of bacterial-type flagellum-dependent cell motility Source: EcoCyc
    2. negative regulation of sequence-specific DNA binding transcription factor activity Source: EcoCyc
    3. negative regulation of transcription regulatory region DNA binding Source: EcoCyc
    4. transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Molecular functioni

    Repressor

    Keywords - Biological processi

    Transcription, Transcription regulation

    Enzyme and pathway databases

    BioCyciEcoCyc:G6925-MONOMER.
    ECOL316407:JW1697-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Putative anti-FlhC(2)FlhD(4) factor YdiV
    Alternative name(s):
    c-di-GMP regulator CdgR
    Gene namesi
    Name:ydiV
    Synonyms:cdgR
    Ordered Locus Names:b1707, JW1697
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG13981. ydiV.

    Pathology & Biotechi

    Disruption phenotypei

    A double sdiA/ydiV deletion mutant leads to decreased cAMP levels which inhibits quorum sensing system 2. Repressed by glucose. Unlike the case in Salmonella typhimurium, disruption has no effect on motility or FliC levels.2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 237237Putative anti-FlhC(2)FlhD(4) factor YdiVPRO_0000168997Add
    BLAST

    Expressioni

    Inductioni

    Induced by extracellular autoinducer AI-1 (Vibrio fischeri autoinducer oxoC6), in an SdiA-dependent fashion. Repressed by glucose. Induced at pH 5.0 in an RpoS-dependent fashion. Very poorly expressed in both rich and nutrient-poor medium due to inefficient translation (at protein level).3 Publications

    Gene expression databases

    GenevestigatoriP76204.

    Interactioni

    Protein-protein interaction databases

    DIPiDIP-11763N.
    IntActiP76204. 5 interactions.
    STRINGi511145.b1707.

    Structurei

    Secondary structure

    1
    237
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Turni4 – 85
    Beta strandi9 – 1911
    Beta strandi25 – 3612
    Beta strandi39 – 435
    Helixi45 – 517
    Helixi54 – 7017
    Helixi72 – 776
    Beta strandi81 – 855
    Helixi88 – 969
    Beta strandi97 – 1015
    Helixi102 – 1054
    Beta strandi110 – 1145
    Helixi121 – 1266
    Helixi128 – 1369
    Beta strandi139 – 1446
    Beta strandi146 – 1494
    Helixi152 – 1554
    Beta strandi160 – 1645
    Helixi166 – 1749
    Helixi176 – 1783
    Helixi179 – 18911
    Turni190 – 1923
    Beta strandi194 – 1985
    Helixi204 – 2107
    Helixi211 – 2133
    Beta strandi216 – 2183
    Helixi228 – 2347

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3TLQX-ray1.91A/B1-237[»]
    4ES4X-ray2.90A/C/E/G1-237[»]
    ProteinModelPortaliP76204.
    SMRiP76204. Positions 2-237.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini1 – 237237EALAdd
    BLAST

    Sequence similaritiesi

    Belongs to the YdiV family.Curated
    Contains 1 EAL domain.Curated

    Phylogenomic databases

    eggNOGiCOG2200.
    HOGENOMiHOG000120996.
    OMAiSFEPFMR.
    OrthoDBiEOG6V4GB5.

    Family and domain databases

    Gene3Di3.20.20.450. 1 hit.
    InterProiIPR001633. Diguanylate_PEstase_EAL_dom.
    [Graphical view]
    PfamiPF00563. EAL. 1 hit.
    [Graphical view]
    SUPFAMiSSF141868. SSF141868. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P76204-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKIFLENLYH SDCYFLPIRD NQQVLVGVEL ITHFSSEDGT VRIPTSRVIA    50
    QLTEEQHWQL FSEQLELLKS CQHFFIQHKL FAWLNLTPQV ATLLLERDNY 100
    AGELLKYPFI ELLINENYPH LNEGKDNRGL LSLSQVYPLV LGNLGAGNST 150
    MKAVFDGLFT RVMLDKSFIQ QQITHRSFEP FIRAIQAQIS PCCNCIIAGG 200
    IDTAEILAQI TPFDFHALQG CLWPAVPINQ ITTLVQR 237
    Length:237
    Mass (Da):27,046
    Last modified:February 1, 1997 - v1
    Checksum:i5684FCD246D7C16F
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U00096 Genomic DNA. Translation: AAC74777.1.
    AP009048 Genomic DNA. Translation: BAE76505.1.
    PIRiC64929.
    RefSeqiNP_416222.1. NC_000913.3.
    YP_489969.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74777; AAC74777; b1707.
    BAE76505; BAE76505; BAE76505.
    GeneIDi12931305.
    946217.
    KEGGiecj:Y75_p1682.
    eco:b1707.
    PATRICi32118720. VBIEscCol129921_1778.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U00096 Genomic DNA. Translation: AAC74777.1 .
    AP009048 Genomic DNA. Translation: BAE76505.1 .
    PIRi C64929.
    RefSeqi NP_416222.1. NC_000913.3.
    YP_489969.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3TLQ X-ray 1.91 A/B 1-237 [» ]
    4ES4 X-ray 2.90 A/C/E/G 1-237 [» ]
    ProteinModelPortali P76204.
    SMRi P76204. Positions 2-237.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-11763N.
    IntActi P76204. 5 interactions.
    STRINGi 511145.b1707.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC74777 ; AAC74777 ; b1707 .
    BAE76505 ; BAE76505 ; BAE76505 .
    GeneIDi 12931305.
    946217.
    KEGGi ecj:Y75_p1682.
    eco:b1707.
    PATRICi 32118720. VBIEscCol129921_1778.

    Organism-specific databases

    EchoBASEi EB3738.
    EcoGenei EG13981. ydiV.

    Phylogenomic databases

    eggNOGi COG2200.
    HOGENOMi HOG000120996.
    OMAi SFEPFMR.
    OrthoDBi EOG6V4GB5.

    Enzyme and pathway databases

    BioCyci EcoCyc:G6925-MONOMER.
    ECOL316407:JW1697-MONOMER.

    Miscellaneous databases

    PROi P76204.

    Gene expression databases

    Genevestigatori P76204.

    Family and domain databases

    Gene3Di 3.20.20.450. 1 hit.
    InterProi IPR001633. Diguanylate_PEstase_EAL_dom.
    [Graphical view ]
    Pfami PF00563. EAL. 1 hit.
    [Graphical view ]
    SUPFAMi SSF141868. SSF141868. 1 hit.
    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. "Cyclic-di-GMP-mediated signalling within the sigma network of Escherichia coli."
      Weber H., Pesavento C., Possling A., Tischendorf G., Hengge R.
      Mol. Microbiol. 62:1014-1034(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION, RPOS-DEPENDENCE.
      Strain: K12 / MC4100.
    4. "An EAL domain protein and cyclic AMP contribute to the interaction between the two quorum sensing systems in Escherichia coli."
      Zhou X., Meng X., Sun B.
      Cell Res. 18:937-948(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION BY AI-1 IN AN SDIA-DEPENDENT FASHION, REPRESSION BY GLUCOSE, DISRUPTION PHENOTYPE.
      Strain: K12 / W3110 / ZK126.
    5. "Functional and expressional analyses of the anti-FlhD4C2 factor gene ydiV in Escherichia coli."
      Wada T., Hatamoto Y., Kutsukake K.
      Microbiology 158:1533-1542(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: POSSIBLE FUNCTION, INTERACTION WITH FLHC(2)FLHD(4), INDUCTION, DISRUPTION PHENOTYPE.
      Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.

    Entry informationi

    Entry nameiYDIV_ECOLI
    AccessioniPrimary (citable) accession number: P76204
    Secondary accession number(s): Q2MB51
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: February 1, 1997
    Last modified: October 1, 2014
    This is version 99 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

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

    External Data

    Dasty 3