raiA:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

RaiA

Synonyms

cold shock protein associated with 30S ribosomal subunit[1], B2597[2][1], YfiA[2][1], Urf1[2][1], RaiA[2][1], pY[2][1] , ECK2594, JW2578, yfiA, b2597

Product description

stationary phase translation inhibitor and ribosome stability factor[2][3]

Protein Y, associated with 30S ribosomal subunit; inhibits 70S dimer formation; stabilizes the ribosomal 70S complex against dissociation at low magnesium ion concentrations; counteracts miscoding under stress conditions [4]

EC number (for enzymes)


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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0005488

binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003489

F

Seeded from EcoCyc (v14.0)

complete

GO:0006417

regulation of translation

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0810

P

Seeded from EcoCyc (v14.0)

complete

GO:0022627

cytosolic small ribosomal subunit

PMID:10535924[5]

IDA: Inferred from Direct Assay

C

Purified protein Y was incubated with purified 70S ribosomes or purified 30S or 50S subunits. The binding mixture was filtered through Amicon filters that would retain ribosomal particles, but not protein Y (Fig. 3).

complete

GO:0006950

response to stress

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0346

P

Seeded from EcoCyc (v14.0)

complete

GO:0022627

cytosolic small ribosomal subunit

PMID:15502846[6]

IDA: Inferred from Direct Assay

C

X-ray crystal structures of 70S ribosomes with and without YfiA protein. The purified YfiA protein was soaked into the crystals.

complete

GO:0044238

primary metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003489

P

Seeded from EcoCyc (v14.0)

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

30S ribosomal subunit

Binding to 30S subunit shown by biochemical studies.[5]

Binding to 30S subunit shown by X-ray crystal structures of 70S ribosomes with and without YfiA protein. <ref name=PMID:15502846>


Protein

matC

PMID:16606699[7]

Experiment(s):EBI-1143442

Protein

rpmB

PMID:16606699[7]

Experiment(s):EBI-1143442

Protein

yciN

PMID:16606699[7]

Experiment(s):EBI-1143442

Protein

cybC

PMID:16606699[7]

Experiment(s):EBI-1143442

Protein

greB

PMID:16606699[7]

Experiment(s):EBI-1143442
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes

cytoplasm

From EcoCyc[3]


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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MTMNITSKQM EITPAIRQHV ADRLAKLEKW QTHLINPHII LSKEPQGFVA DATINTPNGV
LVASGKHEDM YTAINELINK LERQLNKLQH KGEARRAATS VKDANFVEEV EEE
Length

113

Mol. Wt

12.784 kDa

pI

6.7 (calculated)

Extinction coefficient

6,990 (calc based on 1 Y, 1 W, and 0 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Initiator Methionine

1

Removed

UniProt:P0AD49

Domain

2..95

PF02482 Sigma 54 modulation protein / S30EA ribosomal protein

PMID:19920124[8]

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Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=raiA taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16130518

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947129

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008540

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AD49

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11151

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11151

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947129

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001134

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1140

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 Agafonov, DE et al. (1999) A protein residing at the subunit interface of the bacterial ribosome. Proc. Natl. Acad. Sci. U.S.A. 96 12345-9 PubMed
  6. ↑ Vila-Sanjurjo, A et al. (2004) Structural basis for the control of translation initiation during stress. Nat. Struct. Mol. Biol. 11 1054-9 PubMed
  7. ↑ 7.0 7.1 7.2 7.3 7.4 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  8. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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