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Protein

Ribosome-associated inhibitor A

Gene

raiA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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
  • ribosome binding Source: GO_Central
  • rRNA binding Source: UniProtKB-KW

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

Keywordsi

Molecular functionRNA-binding, rRNA-binding
Biological processStress response, Translation regulation

Enzyme and pathway databases

BioCyciEcoCyc:EG11151-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
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

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)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved4 Publications
ChainiPRO_00001692612 – 113Ribosome-associated inhibitor AAdd BLAST112

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei66N6-acetyllysine1 Publication1

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiP0AD49
PRIDEiP0AD49

2D gel databases

SWISS-2DPAGEP0AD49

PTM databases

iPTMnetiP0AD49

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, 36 interactors
DIPiDIP-36014N
IntActiP0AD49, 7 interactors
STRINGi316385.ECDH10B_2764

Structurei

Secondary structure

1113
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 10Combined sources7
Helixi14 – 26Combined sources13
Turni28 – 30Combined sources3
Beta strandi38 – 44Combined sources7
Beta strandi47 – 56Combined sources10
Beta strandi59 – 65Combined sources7
Helixi70 – 89Combined sources20
Helixi98 – 101Combined sources4
Beta strandi109 – 111Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
5V8IX-ray3.251y/2y1-113[»]
6CFKX-ray2.701y/2y1-113[»]
6FKRX-ray3.201z/2z2-98[»]
ProteinModelPortaliP0AD49
SMRiP0AD49
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AD49

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni23 – 26Interaction with 16S rRNA1 Publication4
Regioni83 – 91Interaction with 16S rRNA1 Publication9

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4108WPH Bacteria
COG1544 LUCA
HOGENOMiHOG000264774
InParanoidiP0AD49
KOiK05809
OMAiTPAIRSH
PhylomeDBiP0AD49

Family and domain databases

CDDicd00552 RaiA, 1 hit
Gene3Di3.30.160.100, 1 hit
InterProiView protein in InterPro
IPR036567 RHF-like
IPR003489 RHF/RaiA
PfamiView protein in Pfam
PF02482 Ribosomal_S30AE, 1 hit
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
GeneIDi32213723
947129
KEGGiecj:JW2578
eco:b2597
PATRICifig|1411691.4.peg.4141

Similar proteinsi

Entry informationi

Entry nameiYFIA_ECOLI
AccessioniPrimary (citable) accession number: P0AD49
Secondary accession number(s): P11285
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: January 23, 2007
Last modified: May 23, 2018
This is version 105 of the entry and version 2 of the sequence. See 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

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