P0AAR3 (YBAK_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase ybaK

Gene names

Name:	ybaK
Ordered Locus Names:	b0481, JW0470

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	159 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Functions in trans to edit the amino acid from incorrectly charged Cys-tRNA(Pro). May compensate for the lack of Cys-tRNA(Pro) editing by ProRS. Additionally serves as a general deacylase with weak activity against Cys-tRNA(Cys) and Gly-tRNA(Gly), as well as, at higher concentrations, some other correctly charged tRNAs. Unlike some of its orthologs it is not able to remove the amino acid moiety from incorrectly charged Ala-tRNA(Pro).
Subcellular location	Cytoplasm By similarity.
Disruption phenotype	Non-essential gene. Ref.8
Miscellaneous	Has been suggested to be potentially involved in suppression of transcription of ushA.
Sequence similarities	Belongs to the prolyl-tRNA editing family. ProX subfamily.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Cytoplasm
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	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	aminoacyl-tRNA editing activity Inferred from direct assay Ref.8. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 159

159

Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase ybaK

PRO_0000168620

Secondary structure

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159

Helix Strand Turn

Details...

Helix

3 – 10

8

Beta strand

16 – 19

4

Helix

32 – 37

6

Turn

41 – 43

3

Beta strand

44 – 52

9

Beta strand

55 – 65

11

Beta strand

68 – 70

3

Helix

72 – 79

8

Beta strand

84 – 86

3

Helix

89 – 96

8

Beta strand

105 – 107

3

Beta strand

114 – 117

4

Helix

118 – 122

5

Beta strand

126 – 132

7

Beta strand

135 – 139

5

Helix

141 – 148

8

Beta strand

151 – 153

3

Sequences

	Sequence		Length	Mass (Da)
	P0AAR3 [UniParc]. Last modified October 11, 2005. Version 1. Checksum: 45CD6A2226F2AA01	FASTA	159	17,093
	10 20 30 40 50 60 MTPAVKLLEK NKISFQIHTY EHDPAETNFG DEVVKKLGLN PDQVYKTLLV AVNGDMKHLA 70 80 90 100 110 120 VAVTPVAGQL DLKKVAKALG AKKVEMADPM VAQRSTGYLV GGISPLGQKK RLPTIIDAPA 130 140 150 QEFATIYVSG GKRGLDIELA AGDLAKILDA KFADIARRD

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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.
[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]	"Nucleotide sequence and transcriptional analysis of the E. coli ushA gene, encoding periplasmic UDP-sugar hydrolase (5'-nucleotidase): regulation of the ushA gene, and the signal sequence of its encoded protein product." Burns D.M., Beacham I.R. Nucleic Acids Res. 14:4325-4342(1986) [PubMed: 3012467] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 149-159.
[5]	Jimenez S., Bairoch A. Unpublished observations (AUG-1994) Cited for: IDENTIFICATION.
[6]	"Enrichment of low abundance proteins of Escherichia coli by hydroxyapatite chromatography." Fountoulakis M., Takacs M.-F., Berndt P., Langen H., Takacs B. Electrophoresis 20:2181-2195(1999) [PubMed: 10493123] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY. Strain: B / BL21.
[7]	"Trans-editing of mischarged tRNAs." Ahel I., Korencic D., Ibba M., Soll D. Proc. Natl. Acad. Sci. U.S.A. 100:15422-15427(2003) [PubMed: 14663147] [Abstract] Cited for: LACK OF EDITING ACTIVITY ON MISCHARGED ALA-TRNA(PRO).
[8]	"The bacterial YbaK protein is a Cys-tRNAPro and Cys-tRNA Cys deacylase." Ruan B., Soll D. J. Biol. Chem. 280:25887-25891(2005) [PubMed: 15886196] [Abstract] Cited for: CHARACTERIZATION OF GENERAL DEACYLASE ACTIVITY, DISRUPTION PHENOTYPE.
[9]	"Crystal structure of trans editing enzyme ProX from E.coli." RIKEN structural genomics initiative (RSGI) Submitted (FEB-2009) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (1.58 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U82664 Genomic DNA. Translation: AAB40235.1.
U00096 Genomic DNA. Translation: AAC73583.1.
AP009048 Genomic DNA. Translation: BAE76260.1.
X03895 Genomic DNA. No translation available.

PIR

H64778.

RefSeq

NP_415014.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2DXA	X-ray	1.58	A	1-159	[»]

ProteinModelPortal

P0AAR3.

SMR

P0AAR3. Positions 1-158.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-48133N.

IntAct

P0AAR3. 17 interactions.

MINT

MINT-1228144.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000003221; EBESCP00000003221; EBESCG00000002646.
EBESCT00000016125; EBESCP00000015416; EBESCG00000015185.

GeneID

947083.

GenomeReviews

Gene locus JW0470 in contig AP009048_GR.
Gene locus b0481 in contig U00096_GR.

KEGG

ecj:JW0470.
eco:b0481.

PATRIC

32116119. VBIEscCol129921_0501.

Organism-specific databases

EchoBASE

EB2348.

EcoGene

EG12454. ybaK.

Phylogenomic databases

eggNOG

COG2606.

GeneTree

EBGT00050000011115.

HOGENOM

HBG727700.

OMA

VSPLGQK.

PhylomeDB

P0AAR3.

ProtClustDB

PRK10670.

Enzyme and pathway databases

BioCyc

EcoCyc:EG12454-MONOMER.

Gene expression databases

Genevestigator

P0AAR3.

Family and domain databases

InterPro

IPR004369. Prolyl-tRNA_editing_YbaK/EbsC.
IPR007214. YbaK/aa-tRNA-synth-assoc-dom.
[Graphical view]

Gene3D

G3DSA:3.90.960.10. YbaK/aa-tRNA-synth-assoc-reg. 1 hit.

Pfam

PF04073. YbaK. 1 hit.
[Graphical view]

SUPFAM

SSF55826. YbaK/aa-tRNA-synth-assoc-reg. 1 hit.

TIGRFAMs

TIGR00011. YbaK_EbsC. 1 hit.

ProtoNet

Search...

Entry information

Entry name

YBAK_ECOLI

Accession

Primary (citable) accession number: P0AAR3
Secondary accession number(s): P37175, P77281, Q2MBU6

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 11, 2005
Last sequence update:	October 11, 2005
Last modified:	January 25, 2012
This is version 57 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program