RegulonDB RegulonDB 11.1: Gene Form
   

raiA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

bamD raiA unknown raiZ pheL CRP Cis-reg; leader anti-anti-terminator terminator TSS_2939 TSS_2939 pheLp pheLp TSS_2938 (cluster) TSS_2938 (cluster) TSS_2937 TSS_2937 TSS_2936 (cluster) TSS_2936 (cluster) TSS_2935 TSS_2935 TSS_2934 (cluster) TSS_2934 (cluster) TSS_2933 TSS_2933 TSS_2932 TSS_2932 TSS_2931 (cluster) TSS_2931 (cluster) raiAp raiAp TSS_2930 TSS_2930 TSS_2929 TSS_2929 TSS_2928 TSS_2928 TSS_2927 TSS_2927 TSS_2926 TSS_2926 TSS_2925 TSS_2925 TSS_2924 TSS_2924 TSS_2923 TSS_2923 TSS_2922 TSS_2922 TSS_2921 (cluster) TSS_2921 (cluster) TSS_2920 (cluster) TSS_2920 (cluster) TSS_2919 TSS_2919 TSS_2918 TSS_2918

Gene      
Name: raiA    Texpresso search in the literature
Synonym(s): ECK2594, EG11151, b2597, pY, urf1, yfiA
Genome position(nucleotides): 2737154 --> 2737495
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 46.2
External database links:  
ASAP:
 ABE-0008540
ECHOBASE:
 EB1140
ECOLIHUB:
 raiA
OU-MICROARRAY:
 b2597
STRING:
 511145.b2597
COLOMBOS: raiA


Product      
Name: ribosome-associated inhibitor A
Synonym(s): RaiA, Urf1, YfiA, pY, stationary phase translation inhibitor and ribosome stability factor
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 12.785
Isoelectric point: 6.678
Motif(s):
 
Type Positions Sequence Comment
2 -> 113 TMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQGFVADATINTPNGVLVASGKHEDMYTAINELINKLERQLNKLQHKGEARRAATSVKDANFVEEVEEE UniProt: Ribosome-associated inhibitor A.
4 -> 91 NITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQGFVADATINTPNGVLVASGKHEDMYTAINELINKLERQLNKLQHK
23 -> 26 RLAK UniProt: Interaction with 16S rRNA; Sequence Annotation Type: region of interest.
83 -> 91 RQLNKLQHK UniProt: Interaction with 16S rRNA; Sequence Annotation Type: region of interest.
91 -> 113 KGEARRAATSVKDANFVEEVEEE UniProt: Disordered; Sequence Annotation Type: region of interest.

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.2 - translation
  6 - cell structure --> 6.6 - ribosomes
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0022627 - cytosolic small ribosomal subunit
molecular_function GO:0005515 - protein binding
GO:0043022 - ribosome binding
GO:0003723 - RNA binding
GO:0019843 - rRNA binding
GO:0043024 - ribosomal small subunit binding
biological_process GO:0006417 - regulation of translation
GO:0044238 - primary metabolic process
GO:0045947 - negative regulation of translational initiation
GO:0009409 - response to cold
GO:0022611 - dormancy process
GO:0045900 - negative regulation of translational elongation
Note(s): Note(s): ...[more].
Evidence: [EXP] Inferred from experiment
[EXP-IDA] Inferred from direct assay
Reference(s): [1] Agafonov DE., et al., 1999
[2] Agafonov DE., et al., 2001
[3] Bubunenko M., et al., 2007
[4] Di Pietro F., et al., 2013
[5] Ferdosh S., et al., 2021
[6] Vila-Sanjurjo A., et al., 2004
External database links:  
ALPHAFOLD:
 P0AD49
DIP:
 DIP-36014N
ECOCYC:
 EG11151-MONOMER
ECOLIWIKI:
 b2597
INTERPRO:
 IPR036567
INTERPRO:
 IPR003489
PDB:
 5V8I
PDB:
 6CFK
PDB:
 6FKR
PDB:
 6XHX
PDB:
 5FDV
PDB:
 5FDU
PDB:
 4Y4O
PDB:
 4V8I
PDB:
 4V4G
PDB:
 1N3G
PDB:
 1L4S
PFAM:
 PF02482
PRIDE:
 P0AD49
PRODB:
 PRO_000023676
REFSEQ:
 NP_417088
SMR:
 P0AD49
UNIPROT:
 P0AD49


Operon      
Name: raiAZ         
Operon arrangement:
Transcription unit        Promoter
raiAZ


Transcriptional Regulation      
Display Regulation             
Activated by: CRP


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_2918 2736248 forward nd [RS-EPT-CBR] [7]
  promoter TSS_2919 2736286 forward nd [RS-EPT-CBR] [7]
  promoter TSS_2920 (cluster) 2736329 forward nd [RS-EPT-CBR] [7]
  promoter TSS_2921 (cluster) 2736345 forward nd [RS-EPT-CBR] [7]
  promoter TSS_2922 2736549 forward nd [RS-EPT-CBR] [7]
  promoter TSS_2923 2736555 forward nd [RS-EPT-CBR] [7]
  promoter TSS_2924 2736559 forward nd [RS-EPT-CBR] [7]
  promoter TSS_2925 2736561 forward nd [RS-EPT-CBR] [7]
  promoter TSS_2926 2736565 forward nd [RS-EPT-CBR] [7]
  promoter TSS_2927 2736586 forward nd [RS-EPT-CBR] [7]
  promoter TSS_2928 2736612 forward nd [RS-EPT-CBR] [7]
  promoter TSS_2929 2736658 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_2930 2737089 forward nd [RS-EPT-CBR] [7]
  promoter TSS_2931 (cluster) 2737123 forward nd [RS-EPT-CBR] [7]
  promoter TSS_2932 2737131 forward nd [RS-EPT-CBR] [7]
  promoter TSS_2933 2737251 forward nd [RS-EPT-CBR] [7]
  promoter TSS_2934 (cluster) 2737256 forward nd [RS-EPT-CBR] [7]
  promoter TSS_2935 2737260 forward nd [RS-EPT-CBR] [7]
  promoter TSS_2936 (cluster) 2737373 forward nd [RS-EPT-CBR] [7]
  promoter TSS_2937 2737381 forward nd [RS-EPT-CBR] [7]
  promoter TSS_2938 (cluster) 2737413 forward nd [RS-EPT-CBR] [7]
  promoter TSS_2939 2737580 forward nd [RS-EPT-CBR] [7]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


Reference(s)    

 [1] Agafonov DE., Kolb VA., Nazimov IV., Spirin AS., 1999, A protein residing at the subunit interface of the bacterial ribosome., Proc Natl Acad Sci U S A 96(22):12345-9

 [2] Agafonov DE., Kolb VA., Spirin AS., 2001, Ribosome-associated protein that inhibits translation at the aminoacyl-tRNA binding stage., EMBO Rep 2(5):399-402

 [3] Bubunenko M., Baker T., Court DL., 2007, Essentiality of ribosomal and transcription antitermination proteins analyzed by systematic gene replacement in Escherichia coli., J Bacteriol 189(7):2844-53

 [4] Di Pietro F., Brandi A., Dzeladini N., Fabbretti A., Carzaniga T., Piersimoni L., Pon CL., Giuliodori AM., 2013, Role of the ribosome-associated protein PY in the cold-shock response of Escherichia coli., Microbiologyopen 2(2):293-307

 [5] Ferdosh S., Banerjee S., Pathak BK., Sengupta J., Barat C., 2021, Hibernating ribosomes exhibit chaperoning activity but can resist unfolded protein-mediated subunit dissociation., FEBS J 288(4):1305-1324

 [6] Vila-Sanjurjo A., Schuwirth BS., Hau CW., Cate JH., 2004, Structural basis for the control of translation initiation during stress., Nat Struct Mol Biol 11(11):1054-9

 [7] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

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