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Protein

Ribosome-associated inhibitor A

Gene

raiA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

During stationary phase prevents 70S dimer formation, probably in order to regulate translation efficiency during transition between the exponential and the stationary phases (PubMed:16324148). During environmental stress such as cold shock or excessive cell density at stationary phase, stabilizes the 70S ribosome against dissociation, inhibits translation elongation and increases translation accuracy (PubMed:11375931, PubMed:15219834). When normal growth conditions are restored, is quickly released from the ribosome (PubMed:11375931). Has been suggested to inhibit translation elongation by blocking the A-site (aminoacyl-tRNA site) (PubMed:11375931). Has also been suggested to inhibit translation initiation by blocking the A-site and P-site (peptidyl-tRNA site) of the ribosome (PubMed:15502846, PubMed:23420694). At 15 degrees Celsius binds 30S subunits and stimulates their association with 50S subunits into idle 70S ribosomes (PubMed:23420694). Crystallization with T.thermophilus 70S ribosomes shows it binds in the channel between the head and body of the 30S subunit, where mRNA, tRNAs, initiation factors IF1 and IF3 and elongation factor G would bind; this protein's extended tail follows the mRNA channel and probably prevents RMF binding, which would prevent ribosome dimerization (PubMed:22605777). This protein also stabilizes the 30S head relative to the rest of the ribosome, which may also prevent dimerization (PubMed:22605777). Counteracts miscoding (translation errors) particularly efficiently at magnesium concentrations close to those observed in vivo but less efficiently at higher concentrations (PubMed:15219834). Counteraction of miscoding was shown to be stronger than inhibition of translation, suggesting that the former activity could be the main function of this protein in vivo (PubMed:15219834).8 Publications

GO - Molecular functioni

  • ribosomal small subunit binding Source: EcoCyc

GO - Biological processi

  • negative regulation of translational elongation Source: EcoCyc
  • negative regulation of translational initiation Source: EcoCyc
  • primary metabolic process Source: InterPro
  • response to cold Source: EcoCyc
Complete GO annotation...

Keywords - Biological processi

Stress response, Translation regulation

Keywords - Ligandi

RNA-binding, rRNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11151-MONOMER.
ECOL316407:JW2578-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribosome-associated inhibitor A1 Publication
Alternative name(s):
Protein Y1 Publication
Short name:
pY1 Publication
Ribosome associated factor Y1 Publication
Spot Y1 Publication
Gene namesi
Name:raiA1 Publication
Synonyms:yfiACurated
Ordered Locus Names:b2597, JW2578
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11151. raiA.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
  • cytosolic small ribosomal subunit Source: EcoliWiki
Complete GO annotation...

Pathology & Biotechi

Disruption phenotypei

Non-essential gene, increased formation of inactive 100S ribosomes in stationary phase, which persist longer than in wild-type. Double hpr-yfiA deletion mutants form 90S ribosomes (PubMed:16324148). A quadruple yfiA-hpf-rmf-sra knockout strain is significantly outcompeted by wild-type after 4 days growth (PubMed:17277072). No visible effect on viability or growth rate at 37 or 10 degrees Celsius, slight effect on bulk translation and timing of expression of some cold-shock proteins (PubMed:23420694).3 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved4 Publications
Chaini2 – 113112Ribosome-associated inhibitor APRO_0000169261Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei66 – 661N6-acetyllysine1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

EPDiP0AD49.
PaxDbiP0AD49.
PRIDEiP0AD49.

2D gel databases

SWISS-2DPAGEP0AD49.

Expressioni

Inductioni

During stationary phase (at protein level) (PubMed:11168583, PubMed:11375931). Also by cold stress, remains ribosome-associated for the 4 hours tested, then disappears when cells are warmed (at protein level) (PubMed:11375931, PubMed:23420694).3 Publications

Interactioni

Subunit structurei

Associates mainly with 70S ribosomes (PubMed:11168583, PubMed:11375931). Localized at the surface of the 30S ribosomal subunit, at the interface with the 50S subunit (PubMed:10535924, PubMed:15502846, PubMed:22605777). Binds across the channel in the 30S subunit where tRNAs and mRNA interact during protein biosynthesis (PubMed:15502846, PubMed:22605777). Can also associate with 100S ribosomes, which are inactive dimers of 70S ribosomes (PubMed:11168583). Contacts modifed methylated residues of 16S rRNA (in complex with T.thermophilus ribosome, 2/3 residues are also modified in E.coli) (PubMed:25775268).7 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
frrP0A8054EBI-1129692,EBI-1114349

Protein-protein interaction databases

BioGridi4261618. 11 interactions.
DIPiDIP-36014N.
IntActiP0AD49. 7 interactions.
MINTiMINT-1260187.
STRINGi511145.b2597.

Structurei

Secondary structure

1
113
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 107Combined sources
Helixi14 – 2613Combined sources
Turni28 – 303Combined sources
Beta strandi38 – 447Combined sources
Beta strandi47 – 5610Combined sources
Beta strandi59 – 657Combined sources
Helixi70 – 8920Combined sources
Helixi98 – 1014Combined sources
Beta strandi109 – 1113Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1L4SNMR-A2-113[»]
1N3GNMR-A1-113[»]
4V4GX-ray11.50a2-91[»]
4V8IX-ray2.70AY/CY1-113[»]
4Y4OX-ray2.301y/2y1-113[»]
5FDUX-ray2.901x/2x2-98[»]
5FDVX-ray2.801x/2x2-98[»]
ProteinModelPortaliP0AD49.
SMRiP0AD49. Positions 1-113.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AD49.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni23 – 264Interaction with 16S rRNA1 Publication
Regioni83 – 919Interaction with 16S rRNA1 Publication

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4108WPH. Bacteria.
COG1544. LUCA.
HOGENOMiHOG000264774.
InParanoidiP0AD49.
KOiK05809.
OMAiTPAIRSH.
OrthoDBiEOG618R0J.
PhylomeDBiP0AD49.

Family and domain databases

Gene3Di3.30.160.100. 1 hit.
InterProiIPR003489. Ribosomal_S30Ae/sigma54_mod.
[Graphical view]
PfamiPF02482. Ribosomal_S30AE. 1 hit.
[Graphical view]
SUPFAMiSSF69754. SSF69754. 1 hit.
TIGRFAMsiTIGR00741. yfiA. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0AD49-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTMNITSKQM EITPAIRQHV ADRLAKLEKW QTHLINPHII LSKEPQGFVA
60 70 80 90 100
DATINTPNGV LVASGKHEDM YTAINELINK LERQLNKLQH KGEARRAATS
110
VKDANFVEEV EEE
Length:113
Mass (Da):12,785
Last modified:January 23, 2007 - v2
Checksum:i562901F819836A87
GO

Mass spectrometryi

Molecular mass is 12640 Da from positions 2 - 113. Determined by MALDI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiA30275. Q5ECPA.
RefSeqiNP_417088.1. NC_000913.3.
WP_000178456.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75646; AAC75646; b2597.
BAA16481; BAA16481; BAA16481.
GeneIDi947129.
KEGGiecj:JW2578.
eco:b2597.
PATRICi32120595. VBIEscCol129921_2696.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiA30275. Q5ECPA.
RefSeqiNP_417088.1. NC_000913.3.
WP_000178456.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1L4SNMR-A2-113[»]
1N3GNMR-A1-113[»]
4V4GX-ray11.50a2-91[»]
4V8IX-ray2.70AY/CY1-113[»]
4Y4OX-ray2.301y/2y1-113[»]
5FDUX-ray2.901x/2x2-98[»]
5FDVX-ray2.801x/2x2-98[»]
ProteinModelPortaliP0AD49.
SMRiP0AD49. Positions 1-113.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261618. 11 interactions.
DIPiDIP-36014N.
IntActiP0AD49. 7 interactions.
MINTiMINT-1260187.
STRINGi511145.b2597.

2D gel databases

SWISS-2DPAGEP0AD49.

Proteomic databases

EPDiP0AD49.
PaxDbiP0AD49.
PRIDEiP0AD49.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75646; AAC75646; b2597.
BAA16481; BAA16481; BAA16481.
GeneIDi947129.
KEGGiecj:JW2578.
eco:b2597.
PATRICi32120595. VBIEscCol129921_2696.

Organism-specific databases

EchoBASEiEB1140.
EcoGeneiEG11151. raiA.

Phylogenomic databases

eggNOGiENOG4108WPH. Bacteria.
COG1544. LUCA.
HOGENOMiHOG000264774.
InParanoidiP0AD49.
KOiK05809.
OMAiTPAIRSH.
OrthoDBiEOG618R0J.
PhylomeDBiP0AD49.

Enzyme and pathway databases

BioCyciEcoCyc:EG11151-MONOMER.
ECOL316407:JW2578-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0AD49.
PROiP0AD49.

Family and domain databases

Gene3Di3.30.160.100. 1 hit.
InterProiIPR003489. Ribosomal_S30Ae/sigma54_mod.
[Graphical view]
PfamiPF02482. Ribosomal_S30AE. 1 hit.
[Graphical view]
SUPFAMiSSF69754. SSF69754. 1 hit.
TIGRFAMsiTIGR00741. yfiA. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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. 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, MASS SPECTROMETRY.
    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.
    Strain: K12 / MC4100 / AD202.
  10. 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 BY COLD SHOCK, 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 70S RIBOSOME DIMERIZATION, DISRUPTION PHENOTYPE.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  15. "Essentiality of ribosomal and transcription antitermination proteins analyzed by systematic gene replacement in Escherichia coli."
    Bubunenko M., Baker T., Court D.L.
    J. Bacteriol. 189:2844-2853(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISRUPTION PHENOTYPE.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  16. "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.
  17. "Role of the ribosome-associated protein PY in the cold-shock response of Escherichia coli."
    Di Pietro F., Brandi A., Dzeladini N., Fabbretti A., Carzaniga T., Piersimoni L., Pon C.L., Giuliodori A.M.
    MicrobiologyOpen 2:293-307(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INDUCTION BY COLD SHOCK, DISRUPTION PHENOTYPE.
    Strain: MRE-600.
  18. "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.
  19. "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.
  20. "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 BOUND TO THE E.COLI 70S RIBOSOME, FUNCTION IN INHIBITION OF TRANSLATION, BLOCKING OF A-AND P-SITES, SUBUNIT.
    Strain: MRE-600.
  21. "How hibernation factors RMF, HPF, and YfiA turn off protein synthesis."
    Polikanov Y.S., Blaha G.M., Steitz T.A.
    Science 336:915-918(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) BOUND TO THE T.THERMOPHILUS 70S RIBOSOME, FUNCTION, SUBUNIT.
  22. "Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly."
    Polikanov Y.S., Melnikov S.V., Soll D., Steitz T.A.
    Nat. Struct. Mol. Biol. 22:342-344(2015) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) BOUND TO THE T.THERMOPHILUS RIBOSOME, SUBUNIT, RRNA-BINDING.
  23. "Structure of the mammalian antimicrobial peptide Bac7(1-16) bound within the exit tunnel of a bacterial ribosome."
    Seefeldt A.C., Graf M., Perebaskine N., Nguyen F., Arenz S., Mardirossian M., Scocchi M., Wilson D.N., Innis C.A.
    Nucleic Acids Res. 44:2429-2438(2016) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) OF 2-98 BOUND TO THE T.THERMOPHILUS RIBOSOME WITH EUKARYOTIC ANTIMICROBIAL PEPTIDES, SUBUNIT.

Entry informationi

Entry nameiYFIA_ECOLI
AccessioniPrimary (citable) accession number: P0AD49
Secondary accession number(s): P11285
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: January 23, 2007
Last modified: June 8, 2016
This is version 93 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.