P75989 (YCGE_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
HTH-type transcriptional repressor YcgE

Gene names

Name:	ycgE
Ordered Locus Names:	b1162, JW1149

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	243 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Controls the expression of 6 small proteins that may play a role in biofilm maturation. Binds to and represses the operator of the ycgZ-ymgA-ariR-ymgC operon, it also regulates yliL and ynaK. Binding is antagonized by YcgF upon blue-light (470 nm) irradiation. Blue light may increase the affinity of YcgF for YcgE, allowing it to be released from its operator. Ref.4
Subunit structure	The N-terminal MerR-like domain of this protein interacts with YcgF. Ref.5
Induction	Expression is strongly activated (7-fold at 16 degrees Celsius compared to 37 degrees) at low temperature. Ref.4 Ref.5
Disruption phenotype	3- to 20-fold derepression of the genes for 6 small proteins including the ycgZ-ymgA-ariR-ymgC operon. While the YcgE/F system is induced at low temperatures under blue-light irradiation it is not essential for growth under these conditions. When both lon and ycgE are disrupted levels of OmpF decrease, leading to lower drug susceptibility, with a greater effect at 26 degrees than at 37 degrees Celsius. The mechanism is not yet understood. Ref.4 Ref.5
Sequence similarities	Contains 1 HTH merR-type DNA-binding domain.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Ligand	DNA-binding
Molecular function	Repressor
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW nucleotide binding Inferred from electronic annotation. Source: InterPro sequence-specific DNA binding transcription factor activity Inferred from direct assay Ref.5. Source: EcoCyc
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
hipA	P23874	1	EBI-560582,EBI-560590
lpdA	P0A9P0	1	EBI-560582,EBI-542856

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 243	243	HTH-type transcriptional repressor YcgE		PRO_0000098165
Regions
	Domain	3 – 72	70	HTH merR-type
	DNA binding	6 – 25	20	H-T-H motif Potential

Sequences

	Sequence		Length	Mass (Da)
	P75989 [UniParc]. Last modified February 1, 1997. Version 1. Checksum: E8E5AD376A18EB84	FASTA	243	28,265
	10 20 30 40 50 60 MAYYSIGDVA ERCGINPVTL RAWQRRYGLL KPQRSEGGHR LFDEEDIQRI EEIKRWISNG 70 80 90 100 110 120 VPVGKVKALL ETTSQDTEDD WSRLQEEMMS ILRMANPAKL RARIISLGRE YPVDQLINHV 130 140 150 160 170 180 YLPVRQRLVL DHNTSRIMSS MFDGALIEYA ATSLFEMRRK PGKEAILMAW NVEERARLWL 190 200 210 220 230 240 EAWRLSLSGW HISVLADPIE SPRPELFPTQ TLIVWTGMAP TRRQNELLQH WGEQGYKVIF HAP

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. , Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M., Horiuchi T. DNA Res. 3:137-155(1996) [PubMed: 8905232] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[2]	"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: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"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: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"Combined inactivation of lon and ycgE decreases multidrug susceptibility by reducing the amount of OmpF porin in Escherichia coli." Duval V., Nicoloff H., Levy S.B. Antimicrob. Agents Chemother. 53:4944-4948(2009) [PubMed: 19721064] [Abstract] Cited for: ROLE IN REGULATION OF OMPF IN ASSOCIATION WITH LON, DISRUPTION PHENOTYPE. Strain: K12 / AG100.
[5]	"The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli." Tschowri N., Busse S., Hengge R. Genes Dev. 23:522-534(2009) [PubMed: 19240136] [Abstract] Cited for: INTERACTION WITH YCGF, DNA-BINDING, INDUCTION, DISRUPTION PHENOTYPE. Strain: K12 / MC4100.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U00096 Genomic DNA. Translation: AAC74246.1. AP009048 Genomic DNA. Translation: BAA35997.1.
PIR	G64861.
RefSeq	NP_415680.1. NC_000913.2.
3D structure databases
ProteinModelPortal	P75989.
SMR	P75989. Positions 3-73.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-11552N.
IntAct	P75989. 39 interactions.
MINT	MINT-1244002.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	EBESCT00000000225; EBESCP00000000225; EBESCG00000000184. EBESCT00000017210; EBESCP00000016501; EBESCG00000016269.
GeneID	945735.
GenomeReviews	Gene locus JW1149 in contig AP009048_GR. Gene locus b1162 in contig U00096_GR.
KEGG	ecj:JW1149. eco:b1162.
PATRIC	32117561. VBIEscCol129921_1203.
Organism-specific databases
EchoBASE	EB3645.
EcoGene	EG13886. ycgE.
Phylogenomic databases
eggNOG	COG0789.
GeneTree	EBGT00050000010907.
HOGENOM	HBG417247.
OMA	DRTRLWL.
ProtClustDB	CLSK2301693.
Enzyme and pathway databases
BioCyc	EcoCyc:G6602-MONOMER.
Gene expression databases
Genevestigator	P75989.
Family and domain databases
InterPro	IPR009061. DNA-bd_dom_put. IPR000551. Tscrpt_reg_HTH_MerR. [Graphical view]
Pfam	PF00376. MerR. 1 hit. [Graphical view]
SMART	SM00422. HTH_MERR. 1 hit. [Graphical view]
SUPFAM	SSF46955. Putativ_DNA_bind. 1 hit.
PROSITE	PS00552. HTH_MERR_1. 1 hit. PS50937. HTH_MERR_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

YCGE_ECOLI

Accession

Primary (citable) accession number: P75989
Secondary accession number(s): Q9R7N5

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1998
Last sequence update:	February 1, 1997
Last modified:	January 25, 2012
This is version 96 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program