Peptidyl-tRNA hydrolase YaeJ - Escherichia coli (strain K12)

Contribute

Send feedback

Read comments (?) or add your own

P40711 (ARFB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 87. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

text xml rdf/xml gff fasta

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Peptidyl-tRNA hydrolase YaeJ
Short name=PTH
EC=3.1.1.29

Alternative name(s):
Alternative ribosome-rescue factor B

Gene names

Name:	yaeJ
Ordered Locus Names:	b0191, JW0187

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	140 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Rescues stalled ribosomes. Can hydrolyze peptidyl-tRNA on ribosomes stalled by both non-stop mRNAs and mRNAs that contain rare codon clusters. May function as a complementary rescue system when the stalled ribosome can not be rescued by the SsrA(tmRNA)-SmpB quality control system or the alternative ribosome-rescue factor A. Ref.8 Ref.9
Catalytic activity	N-substituted aminoacyl-tRNA + H₂O = N-substituted amino acid + tRNA. Ref.8 Ref.9
Subunit structure	Associated with 70S ribosomes and polysomes.
Subcellular location	Cytoplasm Probable.
Domain	The unstructured C-terminal region is required for ribosome binding and peptidyl-tRNA hydrolase activity. Ref.8 Ref.9
Sequence similarities	Belongs to the prokaryotic/mitochondrial release factor family.

Ontologies

Keywords
Biological process	Translation regulation
Cellular component	Cytoplasm
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	rescue of stalled ribosome Inferred from direct assay Ref.9 Ref.8. Source: EcoCyc
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	aminoacyl-tRNA hydrolase activity Inferred from direct assay Ref.9 Ref.8. Source: EcoCyc ribosome binding Inferred from direct assay Ref.8. Source: EcoCyc translation release factor 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 – 140

140

Peptidyl-tRNA hydrolase YaeJ

PRO_0000166858

Experimental info

Mutagenesis

26 – 27

GG → VA: Strong decrease in activity. Ref.8 Ref.9

Mutagenesis

27 – 28

GQ → AE: Strong decrease in activity. Ref.8 Ref.9

Mutagenesis

G → A: Decrease in activity. Ref.8 Ref.9

Mutagenesis

Q → E: Decrease in activity. Ref.9

Secondary structure

140

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P40711 [UniParc].

Last modified November 1, 1995. Version 2.
Checksum: 8F161ADD8C07EBCB
Show »

FASTA

140

15,623

        10         20         30         40         50         60 
MIVISRHVAI PDGELEITAI RAQGAGGQHV NKTSTAIHLR FDIRASSLPE YYKERLLAAS 

        70         80         90        100        110        120 
HHLISSDGVI VIKAQEYRSQ ELNREAALAR LVAMIKELTT EKKARRPTRP TRASKERRLA 

       130        140 
SKAQKSSVKA MRGKVRSGRE

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Identification of cutC and cutF (nlpE) genes involved in copper tolerance in Escherichia coli." Gupta S.D., Lee B.T.O., Camakaris J., Wu H.C. J. Bacteriol. 177:4207-4215(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
[2]	Yamamoto Y. Submitted (DEC-1995) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"Systematic sequencing of the Escherichia coli genome: analysis of the 4.0 - 6.0 min (189,987 - 281,416bp) region." Takemoto K., Mori H., Murayama N., Kataoka K., Yano M., Itoh T., Yamamoto Y., Inokuchi H., Miki T., Hatada E., Fukuda R., Ichihara S., Mizuno T., Makino K., Nakata A., Yura T., Sampei G., Mizobuchi K. Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"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.
[5]	"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.
[6]	"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], SEQUENCE REVISION TO 36. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[7]	"Overproduction of NlpE, a new outer membrane lipoprotein, suppresses the toxicity of periplasmic LacZ by activation of the Cpx signal transduction pathway." Snyder W.B., Davis L.J., Danese P.N., Cosma C.L., Silhavy T.J. J. Bacteriol. 177:4216-4223(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 17-140. Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
[8]	"Escherichia coli YaeJ protein mediates a novel ribosome-rescue pathway distinct from SsrA- and ArfA-mediated pathways." Chadani Y., Ono K., Kutsukake K., Abo T. Mol. Microbiol. 80:772-785(2011) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, INTERACTION WITH RIBOSOMES, DOMAIN, MUTAGENESIS OF GLY-27. Strain: K12.
[9]	"YaeJ is a novel ribosome-associated protein in Escherichia coli that can hydrolyze peptidyl-tRNA on stalled ribosomes." Handa Y., Inaho N., Nameki N. Nucleic Acids Res. 39:1739-1748(2011) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, INTERACTION WITH RIBOSOMES, DOMAIN, MUTAGENESIS OF 26-GLY-GLY-27; 27-GLY-GLN-28; GLY-27 AND GLN-28. Strain: K12.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

L38619 Genomic DNA. Translation: AAA82971.1.
D49445 Genomic DNA. Translation: BAA08432.1.
U70214 Genomic DNA. Translation: AAB08619.1.
U00096 Genomic DNA. Translation: AAC73302.1.
AP009048 Genomic DNA. Translation: BAA77867.2.
U18345 Genomic DNA. Translation: AAA86092.1.

PIR

G64743.

RefSeq

NP_414733.1. NC_000913.2.
YP_488494.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
4DH9	X-ray	3.20	Y	1-140	[»]

ProteinModelPortal

P40711.

SMR

P40711. Positions 2-133.

ModBase

Search...

Protein-protein interaction databases

IntAct

P40711. 8 interactions.

STRING

511145.b0191.

Proteomic databases

PaxDb

P40711.

PRIDE

P40711.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73302; AAC73302; b0191.
BAA77867; BAA77867; BAA77867.

GeneID

12934377.
946046.

KEGG

ecj:Y75_p0188.
eco:b0191.

PATRIC

32115495. VBIEscCol129921_0199.

Organism-specific databases

EchoBASE

EB2258.

EcoGene

EG12354. yaeJ.

Phylogenomic databases

eggNOG

COG1186.

HOGENOM

HOG000244440.

K15034.

OMA

VLIIKAQ.

ProtClustDB

PRK09256.

Enzyme and pathway databases

BioCyc

EcoCyc:EG12354-MONOMER.
ECOL316407:JW0187-MONOMER.
MetaCyc:EG12354-MONOMER.

Gene expression databases

Genevestigator

P40711.

Family and domain databases

InterPro

IPR000352. Pep_chain_release_fac_I_II.
[Graphical view]

Pfam

PF00472. RF-1. 1 hit.
[Graphical view]

PROSITE

PS00745. RF_PROK_I. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

ARFB_ECOLI

Accession

Primary (citable) accession number: P40711

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	November 1, 1995
Last modified:	May 1, 2013
This is version 87 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents