P76204 (YDIV_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Putative anti-FlhC(2)FlhD(4) factor YdiV

Alternative name(s):
c-di-GMP regulator CdgR

Gene names

Name:	ydiV
Synonyms:	cdgR
Ordered Locus Names:	b1707, JW1697

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	237 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.5
Induction	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). Ref.3 Ref.4 Ref.5
Disruption phenotype	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. Ref.4 Ref.5
Sequence similarities	Belongs to the YdiV family. Contains 1 EAL domain.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Molecular function	Repressor
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	negative regulation of flagellar cell motility Inferred from mutant phenotype Ref.5. Source: EcoCyc negative regulation of sequence-specific DNA binding transcription factor activity Inferred from direct assay Ref.5. Source: EcoCyc negative regulation of transcription regulatory region DNA binding Inferred from direct assay PubMed 23002140. Source: EcoCyc transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 237

237

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

PRO_0000168997

Regions

Domain

1 – 237

237

EAL

Secondary structure

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237

Helix Strand Turn

Details...

Turn

4 – 8

5

Beta strand

9 – 19

11

Beta strand

25 – 36

12

Beta strand

39 – 43

5

Helix

45 – 51

7

Helix

54 – 70

17

Helix

72 – 77

6

Beta strand

81 – 85

5

Helix

88 – 96

9

Beta strand

97 – 101

5

Helix

102 – 105

4

Beta strand

110 – 114

5

Helix

121 – 126

6

Helix

128 – 136

9

Beta strand

139 – 144

6

Beta strand

146 – 149

4

Helix

152 – 155

4

Beta strand

160 – 164

5

Helix

166 – 174

9

Helix

176 – 178

3

Helix

179 – 189

11

Turn

190 – 192

3

Beta strand

194 – 198

5

Helix

204 – 210

7

Helix

211 – 213

3

Beta strand

216 – 218

3

Helix

228 – 234

7

Sequences

	Sequence		Length	Mass (Da)
	P76204 [UniParc]. Last modified February 1, 1997. Version 1. Checksum: 5684FCD246D7C16F	FASTA	237	27,046
	10 20 30 40 50 60 MKIFLENLYH SDCYFLPIRD NQQVLVGVEL ITHFSSEDGT VRIPTSRVIA QLTEEQHWQL 70 80 90 100 110 120 FSEQLELLKS CQHFFIQHKL FAWLNLTPQV ATLLLERDNY AGELLKYPFI ELLINENYPH 130 140 150 160 170 180 LNEGKDNRGL LSLSQVYPLV LGNLGAGNST MKAVFDGLFT RVMLDKSFIQ QQITHRSFEP 190 200 210 220 230 FIRAIQAQIS PCCNCIIAGG IDTAEILAQI TPFDFHALQG CLWPAVPINQ ITTLVQR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] 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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U00096 Genomic DNA. Translation: AAC74777.1.
AP009048 Genomic DNA. Translation: BAE76505.1.

PIR

C64929.

RefSeq

NP_416222.1. NC_000913.2.
YP_489969.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P76204.

SMR

P76204. Positions 2-237.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-11763N.

IntAct

P76204. 5 interactions.

STRING

511145.b1707.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC74777; AAC74777; b1707.
BAE76505; BAE76505; BAE76505.

GeneID

12931305.
946217.

KEGG

ecj:Y75_p1682.
eco:b1707.

PATRIC

32118720. VBIEscCol129921_1778.

Organism-specific databases

EchoBASE

EB3738.

EcoGene

EG13981. ydiV.

Phylogenomic databases

eggNOG

COG2200.

HOGENOM

HOG000120996.

OMA

LAVEMIS.

ProtClustDB

CLSK880169.

Enzyme and pathway databases

BioCyc

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

Gene expression databases

Genevestigator

P76204.

Family and domain databases

Gene3D

3.20.20.450. 1 hit.

InterPro

IPR001633. Diguanylate_PEstase_EAL_dom.
[Graphical view]

Pfam

PF00563. EAL. 1 hit.
[Graphical view]

SUPFAM

SSF141868. SSF141868. 1 hit.

PROSITE

PS50883. EAL. False negative.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

YDIV_ECOLI

Accession

Primary (citable) accession number: P76204
Secondary accession number(s): Q2MB51

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	February 1, 1997
Last modified:	May 1, 2013
This is version 89 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program