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P0AD49 (RAIA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 78. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ribosome-associated inhibitor A
Alternative name(s):
Protein Y
SpotY
Short name=pY
Gene names
Name:raiA
Synonyms:yfiA
Ordered Locus Names:b2597, JW2578
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length113 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

During stationary phase, prevents 70S dimer formation, probably in order to regulate translation efficiency during transition between the exponential and the stationary phases. In addition, during environmental stress such as cold shock or excessive cell density at stationary phase, stabilizes the 70S ribosome against dissociation, inhibits translation initiation and increase translation accuracy. When normal growth conditions are restored, is quickly released from the ribosome. Inhibits translation initiation by blocking the A-site (aminoacyl-tRNA site) and P-site (peptidyl-tRNA site) of the ribosome. Counteracts miscoding (translation errors) particularly efficiently at magnesium concentrations close to those observed in vivo but less efficiently at higher concentrations. Counteraction of miscoding was shown to be stronger than inhibition of translation, suggesting that the former activity could be the main function of RaiA in vivo. Ref.7 Ref.9 Ref.12 Ref.13 Ref.14 Ref.18

Subunit structure

Associates mainly with 70S ribosomes. Localized at the surface of the 30S ribosomal subunit, at the interface with the 50S subunit. Binds across the channel in the 30S subunit where tRNAs and mRNA interact during protein biosynthesis. Can also associate with 100S ribosomes. Ref.7

Induction

By environmental stress or during stationary phase. Ref.9 Ref.12

Miscellaneous

During stress, ribosome stabilization by RaiA could serve to protect from degradation the interface between the ribosomal subunits, the key residues lining the A- and P-sites in the small subunit and possibly and the 3' end of the 16S rRNA.

Sequence similarities

Belongs to the Hpf/RaiA ribosome-associated protein family. RaiA subfamily.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

frrP0A8054EBI-1129692,EBI-1114349

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.7 Ref.8 Ref.9 Ref.10
Chain2 – 113112Ribosome-associated inhibitor A
PRO_0000169261

Regions

Region23 – 264Interaction with rRNA Potential
Region83 – 919Interaction with rRNA Potential

Amino acid modifications

Modified residue661N6-acetyllysine Ref.15

Secondary structure

.................. 113
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P0AD49 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 562901F819836A87

FASTA11312,785
        10         20         30         40         50         60 
MTMNITSKQM EITPAIRQHV ADRLAKLEKW QTHLINPHII LSKEPQGFVA DATINTPNGV 

        70         80         90        100        110 
LVASGKHEDM YTAINELINK LERQLNKLQH KGEARRAATS VKDANFVEEV EEE 

« Hide

References

« Hide 'large scale' references
[1]"Nucleotide sequence and transcription of the phenylalanine and tyrosine operons of Escherichia coli K12."
Hudson G.S., Davidson B.E.
J. Mol. Biol. 180:1023-1051(1984) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Identification of two Escherichia coli K12 proteins which are induced in response to pollutant stress."
Faber F., van Giezen M., van Gorcom R.F.M., Harder W.
Submitted (APR-1996) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[3]"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. expand/collapse author list , 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.
[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 277:1453-1462(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]"pheAo mutants of Escherichia coli have a defective pheA attenuator."
Gavini N., Davidson B.E.
J. Biol. Chem. 265:21532-21535(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 77-113.
[7]"A protein residing at the subunit interface of the bacterial ribosome."
Agafonov D.E., Kolb V.A., Nazimov I.V., Spirin A.S.
Proc. Natl. Acad. Sci. U.S.A. 96:12345-12349(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 2-18, FUNCTION IN STABILIZATION OF THE RIBOSOME, INTERACTION WITH THE RIBOSOMAL 30S SUBUNIT.
Strain: MRE-600.
[8]"Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12."
Link A.J., Robison K., Church G.M.
Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 2-13.
Strain: K12 / EMG2.
[9]"Two proteins, YfiA and YhbH, associated with resting ribosomes in stationary phase Escherichia coli."
Maki Y., Yoshida H., Wada A.
Genes Cells 5:965-974(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 2-13, FUNCTION, INTERACTION WITH 70S AND 100S RIBOSOMES, INDUCTION.
[10]Pasquali C., Sanchez J.-C., Ravier F., Golaz O., Hughes G.J., Frutiger S., Paquet N., Wilkins M., Appel R.D., Bairoch A., Hochstrasser D.F.
Submitted (SEP-1994) to UniProtKB
Cited for: PROTEIN SEQUENCE OF 2-12.
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[11]"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] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY.
Strain: B / BL21.
[12]"Ribosome-associated protein that inhibits translation at the aminoacyl-tRNA binding stage."
Agafonov D.E., Kolb V.A., Spirin A.S.
EMBO Rep. 2:399-402(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN BLOCKING OF THE RIBOSOMAL A-SITE, FUNCTION IN INHIBITION OF TRANSLATION, INDUCTION, GENE NAME.
Strain: MRE-600.
[13]"The ribosome-associated inhibitor A reduces translation errors."
Agafonov D.E., Spirin A.S.
Biochem. Biophys. Res. Commun. 320:354-358(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN THE REDUCTION OF TRANSLATION ERRORS.
[14]"Ribosome binding proteins YhbH and YfiA have opposite functions during 100S formation in the stationary phase of Escherichia coli."
Ueta M., Yoshida H., Wada C., Baba T., Mori H., Wada A.
Genes Cells 10:1103-1112(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN THE PREVENTION OF THE 70S RIBOSOME DIMERIZATION.
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[15]"Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli."
Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y.
Mol. Cell. Proteomics 8:215-225(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-66, IDENTIFICATION BY MASS SPECTROMETRY.
Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.
[16]"Solution structure of the ribosome-associated cold shock response protein Yfia of Escherichia coli."
Rak A., Kalinin A., Shcherbakov D., Bayer P.
Biochem. Biophys. Res. Commun. 299:710-714(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR.
[17]"Ribosome-associated factor Y adopts a fold resembling a double-stranded RNA binding domain scaffold."
Ye K., Serganov A., Hu W., Garber M., Patel D.J.
Eur. J. Biochem. 269:5182-5191(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 2-113.
[18]"Structural basis for the control of translation initiation during stress."
Vila-Sanjurjo A., Schuwirth B.S., Hau C.W., Cate J.H.
Nat. Struct. Mol. Biol. 11:1054-1059(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (11.50 ANGSTROMS) OF 2-91, FUNCTION IN INHIBITION OF TRANSLATION, BLOCKING OF A- AND P-SITES.
Strain: MRE-600.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M10431 Genomic DNA. Translation: AAA24328.1.
Z70523 Genomic DNA. Translation: CAA94436.1.
U00096 Genomic DNA. Translation: AAC75646.1.
AP009048 Genomic DNA. Translation: BAA16481.1.
M58024 Genomic DNA. Translation: AAA62782.1.
PIRQ5ECPA. A30275.
RefSeqNP_417088.1. NC_000913.3.
YP_490820.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1L4SNMR-A2-113[»]
1N3GNMR-A1-113[»]
1VOQX-ray11.50a2-91[»]
1VOSX-ray11.50a2-91[»]
1VOVX-ray11.50a2-91[»]
1VOXX-ray11.50a2-91[»]
1VOZX-ray11.50a2-91[»]
3V2CX-ray2.70Y1-113[»]
3V2EX-ray2.70Y1-113[»]
ProteinModelPortalP0AD49.
SMRP0AD49. Positions 1-113.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-36014N.
IntActP0AD49. 7 interactions.
MINTMINT-1260187.
STRING511145.b2597.

2D gel databases

SWISS-2DPAGEP0AD49.

Proteomic databases

PaxDbP0AD49.
PRIDEP0AD49.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC75646; AAC75646; b2597.
BAA16481; BAA16481; BAA16481.
GeneID12932624.
947129.
KEGGecj:Y75_p2545.
eco:b2597.
PATRIC32120595. VBIEscCol129921_2696.

Organism-specific databases

EchoBASEEB1140.
EcoGeneEG11151. raiA.

Phylogenomic databases

eggNOGCOG1544.
HOGENOMHOG000264774.
KOK05809.
OMAINITSKQ.
OrthoDBEOG618R0J.
PhylomeDBP0AD49.

Enzyme and pathway databases

BioCycEcoCyc:EG11151-MONOMER.
ECOL316407:JW2578-MONOMER.

Gene expression databases

GenevestigatorP0AD49.

Family and domain databases

Gene3D3.30.160.100. 1 hit.
InterProIPR003489. Ribosomal_S30Ae/sigma54_mod.
[Graphical view]
PfamPF02482. Ribosomal_S30AE. 1 hit.
[Graphical view]
SUPFAMSSF69754. SSF69754. 1 hit.
TIGRFAMsTIGR00741. yfiA. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP0AD49.
PROP0AD49.

Entry information

Entry nameRAIA_ECOLI
AccessionPrimary (citable) accession number: P0AD49
Secondary accession number(s): P11285
Entry history
Integrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: January 23, 2007
Last modified: June 11, 2014
This is version 78 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

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