P0AE39 (YPDB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Transcriptional regulatory protein YpdB

Gene names

Name:	ypdB
Ordered Locus Names:	b2381, JW2378

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	244 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Member of the two-component regulatory system YpdA/YpdB involved in carbon control network. Regulates expression of yhjX by binding to its promoter region. Ref.4
Subcellular location	Cytoplasm By similarity.
Post-translational modification	Phosphorylated by YpdA By similarity.
Sequence similarities	Contains 1 HTH LytTR-type DNA-binding domain. Contains 1 response regulatory domain.

Ontologies

Keywords
Biological process	Transcription Transcription regulation Two-component regulatory system
Cellular component	Cytoplasm
Ligand	DNA-binding
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	intracellular signal transduction Inferred from electronic annotation. Source: GOC regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW phosphorelay response regulator activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 244	244	Transcriptional regulatory protein YpdB		PRO_0000081381
Regions
	Domain	1 – 116	116	Response regulatory
	Domain	139 – 244	106	HTH LytTR-type
Amino acid modifications
	Modified residue	53	1	4-aspartylphosphate Probable
Experimental info
	Mutagenesis	53	1	D → E: Strong induction of yhjX. Ref.4
	Mutagenesis	53	1	D → N: Prevents yhjX induction. Ref.4

Sequences

	Sequence		Length	Mass (Da)
	P0AE39 [UniParc]. Last modified December 6, 2005. Version 1. Checksum: 679EA97A44F1260B	FASTA	244	28,721
	10 20 30 40 50 60 MKVIIVEDEF LAQQELSWLI KEHSQMEIVG TFDDGLDVLK FLQHNRVDAI FLDINIPSLD 70 80 90 100 110 120 GVLLAQNISQ FAHKPFIVFI TAWKEHAVEA FELEAFDYIL KPYQESRITG MLQKLEAAWQ 130 140 150 160 170 180 QQQTSSTPAA TVTRENDTIN LVKDERIIVT PINDIYYAEA HEKMTFVYTR RESYVMPMNI 190 200 210 220 230 240 TEFCSKLPPS HFFRCHRSFC VNLNKIREIE PWFNNTYILR LKDLDFEVPV SRSKVKEFRQ LMHL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features." Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T. , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T. DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"Identification of a target gene and activating stimulus for the YpdA/YpdB histidine kinase/response regulator system in Escherichia coli." Fried L., Behr S., Jung K. J. Bacteriol. 195:807-815(2013) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, DNA-BINDING, MUTAGENESIS OF ASP-53. Strain: K12 / MG1655 / ATCC 47076.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U00096 Genomic DNA. Translation: AAC75440.1. AP009048 Genomic DNA. Translation: BAA16251.1.
PIR	B65012.
RefSeq	NP_416882.1. NC_000913.2. YP_490623.1. NC_007779.1.
3D structure databases
ProteinModelPortal	P0AE39.
SMR	P0AE39. Positions 1-122, 148-242.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-48228N.
IntAct	P0AE39. 1 interaction.
STRING	511145.b2381.
Proteomic databases
PaxDb	P0AE39.
PRIDE	P0AE39.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAC75440; AAC75440; b2381. BAA16251; BAA16251; BAA16251.
GeneID	12931566. 947395.
KEGG	ecj:Y75_p2348. eco:b2381.
PATRIC	32120141. VBIEscCol129921_2479.
Organism-specific databases
EchoBASE	EB3901.
EcoGene	EG14149. ypdB.
Phylogenomic databases
eggNOG	COG3279.
HOGENOM	HOG000242207.
KO	K02477.
OMA	YQESRII.
ProtClustDB	CLSK880375.
Enzyme and pathway databases
BioCyc	EcoCyc:G7244-MONOMER. ECOL316407:JW2378-MONOMER.
Gene expression databases
Genevestigator	P0AE39.
Family and domain databases
InterPro	IPR011006. CheY-like_superfamily. IPR007492. LytTR_DNA-bd_dom. IPR001789. Sig_transdc_resp-reg_receiver. [Graphical view]
Pfam	PF04397. LytTR. 1 hit. PF00072. Response_reg. 1 hit. [Graphical view]
SMART	SM00850. LytTR. 1 hit. SM00448. REC. 1 hit. [Graphical view]
SUPFAM	SSF52172. CheY_like. 1 hit.
PROSITE	PS50930. HTH_LYTTR. 1 hit. PS50110. RESPONSE_REGULATORY. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

YPDB_ECOLI

Accession

Primary (citable) accession number: P0AE39
Secondary accession number(s): P77742

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 6, 2005
Last sequence update:	December 6, 2005
Last modified:	May 1, 2013
This is version 68 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program