P0AD49 (RAIA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	113 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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.

Ontologies

Keywords
Biological process	Stress response Translation regulation
PTM	Acetylation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	negative regulation of translational elongation Inferred from direct assay Ref.12. Source: EcoCyc negative regulation of translational initiation Inferred from direct assay Ref.18. Source: EcoCyc primary metabolic process Inferred from electronic annotation. Source: InterPro response to cold Inferred from expression pattern Ref.12. Source: EcoCyc
Cellular_component	cytosolic small ribosomal subunit Inferred from direct assay Ref.7Ref.18. Source: EcoliWiki
Molecular_function	ribosomal small subunit binding Inferred from direct assay Ref.7. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.7 Ref.8 Ref.9 Ref.10

Chain

2 – 113

112

Ribosome-associated inhibitor A

PRO_0000169261

Regions

Region

23 – 26

4

Interaction with rRNA Potential

Region

83 – 91

9

Interaction with rRNA Potential

Amino acid modifications

Modified residue

66

1

N6-acetyllysine Ref.15

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

113

Helix Strand Turn

Details...

Beta strand

4 – 8

5

Helix

14 – 23

10

Helix

24 – 30

7

Beta strand

35 – 42

8

Beta strand

48 – 56

9

Beta strand

59 – 69

11

Helix

70 – 90

21

Helix

91 – 93

3

Helix

98 – 101

4

Beta strand

109 – 111

3

Sequences

	Sequence		Length	Mass (Da)
	P0AD49 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 562901F819836A87	FASTA	113	12,785
	10 20 30 40 50 60 MTMNITSKQM EITPAIRQHV ADRLAKLEKW QTHLINPHII LSKEPQGFVA DATINTPNGV 70 80 90 100 110 LVASGKHEDM YTAINELINK LERQLNKLQH KGEARRAATS VKDANFVEEV EEE

References

	« Hide 'large scale' referencesShow '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. , 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 277:1453-1474(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, 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.

PIR

Q5ECPA. A30275.

RefSeq

NP_417088.1. NC_000913.2.
YP_490820.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1L4S	NMR	-	A	2-113	[»]
1N3G	NMR	-	A	1-113	[»]
1VOQ	X-ray	11.50	a	2-91	[»]
1VOS	X-ray	11.50	a	2-91	[»]
1VOV	X-ray	11.50	a	2-91	[»]
1VOX	X-ray	11.50	a	2-91	[»]
1VOZ	X-ray	11.50	a	2-91	[»]
3V2C	X-ray	2.70	Y	1-113	[»]
3V2E	X-ray	2.70	Y	1-113	[»]

ProteinModelPortal

P0AD49.

SMR

P0AD49. Positions 1-113.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-36014N.

IntAct

P0AD49. 6 interactions.

MINT

MINT-1260187.

STRING

511145.b2597.

2D gel databases

SWISS-2DPAGE

P0AD49.

Proteomic databases

PaxDb

P0AD49.

PRIDE

P0AD49.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC75646; AAC75646; b2597.
BAA16481; BAA16481; BAA16481.

GeneID

12932624.
947129.

KEGG

ecj:Y75_p2545.
eco:b2597.

PATRIC

32120595. VBIEscCol129921_2696.

Organism-specific databases

EchoBASE

EB1140.

EcoGene

EG11151. raiA.

Phylogenomic databases

eggNOG

COG1544.

HOGENOM

HOG000264774.

KO

K05809.

OMA

INITSKQ.

ProtClustDB

PRK10324.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11151-MONOMER.
ECOL316407:JW2578-MONOMER.

Gene expression databases

Genevestigator

P0AD49.

Family and domain databases

Gene3D

3.30.160.100. 1 hit.

InterPro

IPR003489. Ribosomal_S30Ae/sigma54_mod.
[Graphical view]

Pfam

PF02482. Ribosomal_S30AE. 1 hit.
[Graphical view]

SUPFAM

SSF69754. Ribosomal_S30Ae/sigma54_mod. 1 hit.

TIGRFAMs

TIGR00741. yfiA. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P0AD49.

Entry information

Entry name

RAIA_ECOLI

Accession

Primary (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:	May 1, 2013
This is version 71 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program