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Protein

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

Gene

ydiV

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

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

  • transcription factor binding Source: EcoCyc

GO - Biological processi

  • negative regulation of bacterial-type flagellum-dependent cell motility Source: EcoCyc
  • negative regulation of sequence-specific DNA binding transcription factor activity Source: EcoCyc
  • negative regulation of transcription regulatory region DNA binding Source: EcoCyc
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

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 Componenti: Chromosome UP000000625 Componenti: 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

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 – 85Combined sources
Beta strandi9 – 1911Combined sources
Beta strandi25 – 3612Combined sources
Beta strandi39 – 435Combined sources
Helixi45 – 517Combined sources
Helixi54 – 7017Combined sources
Helixi72 – 776Combined sources
Beta strandi81 – 855Combined sources
Helixi88 – 969Combined sources
Beta strandi97 – 1015Combined sources
Helixi102 – 1054Combined sources
Beta strandi110 – 1145Combined sources
Helixi121 – 1266Combined sources
Helixi128 – 1369Combined sources
Beta strandi139 – 1446Combined sources
Beta strandi146 – 1494Combined sources
Helixi152 – 1554Combined sources
Beta strandi160 – 1645Combined sources
Helixi166 – 1749Combined sources
Helixi176 – 1783Combined sources
Helixi179 – 18911Combined sources
Turni190 – 1923Combined sources
Beta strandi194 – 1985Combined sources
Helixi204 – 2107Combined sources
Helixi211 – 2133Combined sources
Beta strandi216 – 2183Combined sources
Helixi228 – 2347Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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. 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

        10         20         30         40         50
MKIFLENLYH SDCYFLPIRD NQQVLVGVEL ITHFSSEDGT VRIPTSRVIA
60 70 80 90 100
QLTEEQHWQL FSEQLELLKS CQHFFIQHKL FAWLNLTPQV ATLLLERDNY
110 120 130 140 150
AGELLKYPFI ELLINENYPH LNEGKDNRGL LSLSQVYPLV LGNLGAGNST
160 170 180 190 200
MKAVFDGLFT RVMLDKSFIQ QQITHRSFEP FIRAIQAQIS PCCNCIIAGG
210 220 230
IDTAEILAQI TPFDFHALQG CLWPAVPINQ ITTLVQR
Length:237
Mass (Da):27,046
Last modified:February 1, 1997 - v1
Checksum:i5684FCD246D7C16F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74777.1.
AP009048 Genomic DNA. Translation: BAE76505.1.
PIRiC64929.
RefSeqiNP_416222.1. NC_000913.3.

Genome annotation databases

EnsemblBacteriaiAAC74777; AAC74777; b1707.
BAE76505; BAE76505; BAE76505.
GeneIDi946217.
KEGGiecj:Y75_p1682.
eco:b1707.
PATRICi32118720. VBIEscCol129921_1778.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74777.1.
AP009048 Genomic DNA. Translation: BAE76505.1.
PIRiC64929.
RefSeqiNP_416222.1. NC_000913.3.

3D structure databases

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

Protein-protein interaction databases

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

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74777; AAC74777; b1707.
BAE76505; BAE76505; BAE76505.
GeneIDi946217.
KEGGiecj:Y75_p1682.
eco:b1707.
PATRICi32118720. VBIEscCol129921_1778.

Organism-specific databases

EchoBASEiEB3738.
EcoGeneiEG13981. ydiV.

Phylogenomic databases

eggNOGiCOG2200.
HOGENOMiHOG000120996.
OMAiSFEPFMR.
OrthoDBiEOG6V4GB5.

Enzyme and pathway databases

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

Miscellaneous databases

PROiP76204.

Family and domain databases

Gene3Di3.20.20.450. 1 hit.
InterProiIPR001633. EAL_dom.
[Graphical view]
PfamiPF00563. EAL. 1 hit.
[Graphical view]
SUPFAMiSSF141868. SSF141868. 1 hit.
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. "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: June 24, 2015
This is version 104 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

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.