P0A8J4 (YBED_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
UPF0250 protein YbeD

Gene names

Name:	ybeD
Ordered Locus Names:	b0631, JW0626

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

General annotation (Comments)

Sequence similarities

Belongs to the UPF0250 family.

Ontologies

Keywords
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
None. [Check GOA]

Binary interactions

With	Entry	#Exp.	IntAct	Notes
tufA	P0CE47	2	EBI-370708,EBI-301077

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 87

87

UPF0250 protein YbeD HAMAP-Rule MF_00659

PRO_0000209296

Secondary structure

1

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87

Helix Strand Turn

Details...

Beta strand

4 – 6

3

Beta strand

15 – 22

8

Helix

27 – 38

12

Beta strand

39 – 41

3

Beta strand

45 – 48

4

Beta strand

53 – 62

10

Helix

67 – 77

11

Beta strand

80 – 82

3

Beta strand

84 – 86

3

Sequences

	Sequence		Length	Mass (Da)
	P0A8J4 [UniParc]. Last modified June 7, 2005. Version 1. Checksum: 13B14D3B2A6E1F95	FASTA	87	9,827
	10 20 30 40 50 60 MKTKLNELLE FPTPFTYKVM GQALPELVDQ VVEVVQRHAP GDYTPTVKPS SKGNYHSVSI 70 80 TINATHIEQV ETLYEELGKI DIVRMVL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Lipoic acid metabolism in Escherichia coli: sequencing and functional characterization of the lipA and lipB genes." Reed K.E., Cronan J.E. Jr. J. Bacteriol. 175:1325-1336(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[2]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"Sequence of minutes 4-25 of Escherichia coli." Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W. Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"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.
[5]	"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.
[6]	"Structural similarity of YbeD protein from Escherichia coli to allosteric regulatory domains." Kozlov G., Elias D., Semesi A., Yee A., Cygler M., Gehring K. J. Bacteriol. 186:8083-8088(2004) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

L07636 Genomic DNA. Translation: AAA66341.1.
U82598 Genomic DNA. Translation: AAB40831.1.
U00096 Genomic DNA. Translation: AAC73732.1.
AP009048 Genomic DNA. Translation: BAA35274.1.

PIR

E64797.

RefSeq

NP_415164.1. NC_000913.2.
YP_488922.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1RWU	NMR	-	A	1-87	[»]

ProteinModelPortal

P0A8J4.

SMR

P0A8J4. Positions 1-87.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-31839N.

IntAct

P0A8J4. 9 interactions.

MINT

MINT-1273776.

STRING

511145.b0631.

Proteomic databases

PaxDb

P0A8J4.

PRIDE

P0A8J4.

Protocols and materials databases

DNASU

945220.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73732; AAC73732; b0631.
BAA35274; BAA35274; BAA35274.

GeneID

12931685.
945220.

KEGG

ecj:Y75_p0621.
eco:b0631.

PATRIC

32116443. VBIEscCol129921_0661.

Organism-specific databases

EchoBASE

EB1550.

EcoGene

EG11592. ybeD.

Phylogenomic databases

eggNOG

COG2921.

HOGENOM

HOG000265101.

KO

K09158.

OMA

KVMGLAK.

ProtClustDB

PRK04998.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11592-MONOMER.
ECOL316407:JW0626-MONOMER.

Gene expression databases

Genevestigator

P0A8J4.

Family and domain databases

HAMAP

MF_00659. UPF0250.

InterPro

IPR007454. UPF0250.
[Graphical view]

Pfam

PF04359. DUF493. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P0A8J4.

Entry information

Entry name

YBED_ECOLI

Accession

Primary (citable) accession number: P0A8J4
Secondary accession number(s): P30977

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 7, 2005
Last sequence update:	June 7, 2005
Last modified:	May 1, 2013
This is version 69 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program