RegulonDB RegulonDB 11.1: Gene Form
   

rpsA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rpsA cmk ihfB IHF IHF IHF IHF IHF IHF RseX DksA-ppGpp DksA-ppGpp DksA-ppGpp DksA-ppGpp anti-terminator anti-anti-terminator terminator anti-terminator anti-anti-terminator ycaIp8 ycaIp8 ycaIp6 ycaIp6 TSS_1188 TSS_1188 ihfBp2 ihfBp2 ihfBp ihfBp TSS_1187 (cluster) TSS_1187 (cluster) TSS_1186 (cluster) TSS_1186 (cluster) TSS_1185 (cluster) TSS_1185 (cluster) TSS_1184 TSS_1184 TSS_1183 TSS_1183 TSS_1182 (cluster) TSS_1182 (cluster) TSS_1181 TSS_1181 TSS_1180 TSS_1180 TSS_1179 (cluster) TSS_1179 (cluster) rpsAp3 rpsAp3 TSS_1178 TSS_1178 rpsAp1 rpsAp1

Gene      
Name: rpsA    Texpresso search in the literature
Synonym(s): ECK0902, EG10900, b0911, ssyF
Genome position(nucleotides): 961995 --> 963668
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 51.19


Product      
Name: 30S ribosomal subunit protein S1
Synonym(s): RpsA, SsyF
Sequence: Get amino acid sequence Fasta Format
Cellular location: ribosome,cytosol,membrane
Molecular weight: 61.158
Isoelectric point: 4.609
Motif(s):
 
Type Positions Sequence Comment
19 -> 78 RPGSIVRGVVVAIDKDVVLVDAGLKSESAIPAEQFKNAQGELEIQVGDEVDVALDAVEDG
21 -> 87 GSIVRGVVVAIDKDVVLVDAGLKSESAIPAEQFKNAQGELEIQVGDEVDVALDAVEDGFGETLLSRE UniProt: S1 motif 1.
104 -> 171 DAETVTGVINGKVKGGFTVELNGIRAFLPGSLVDVRPVRDTLHLEGKELEFKVIKLDQKRNNVVVSRR
105 -> 171 AETVTGVINGKVKGGFTVELNGIRAFLPGSLVDVRPVRDTLHLEGKELEFKVIKLDQKRNNVVVSRR UniProt: S1 motif 2.
125 -> 125 N UniProt: In Ref. 1; AA sequence..

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.2 - translation
  2 - information transfer --> 2.3 - protein related --> 2.3.8 - ribosomal proteins
  6 - cell structure --> 6.6 - ribosomes
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005840 - ribosome
GO:0016020 - membrane
GO:0022627 - cytosolic small ribosomal subunit
molecular_function GO:0003676 - nucleic acid binding
GO:0003735 - structural constituent of ribosome
GO:0003723 - RNA binding
GO:0003727 - single-stranded RNA binding
GO:0003729 - mRNA binding
biological_process GO:2000767 - positive regulation of cytoplasmic translation
GO:0006412 - translation
GO:0000028 - ribosomal small subunit assembly
GO:2000766 - negative regulation of cytoplasmic translation
GO:0002181 - cytoplasmic translation
GO:0010501 - RNA secondary structure unwinding
Note(s): Note(s): ...[more].
Reference(s): [1] Cifuentes-Goches JC., et al., 2019
[2] Doi H., et al., 2014
[3] Duval M., et al., 2017
[4] Failmezger J., et al., 2016
[5] Giraud P., et al., 2015
[6] Hughes D. 2016
[7] Kurata T., et al., 2018
[8] Lauber MA., et al., 2012
[9] Mallik S., et al., 2018
[10] Nafissi M., et al., 2012
[11] Osterberg R., et al., 1978
[12] Pan JY., et al., 2011
[13] Raneri M., et al., 2015
[14] Rodriguez-Moya M., et al., 2015
[15] Stefanopoulou M., et al., 2011
[16] Yong AL., et al., 2015
External database links:  
ALPHAFOLD:
 P0AG67
DIP:
 DIP-35884N
ECOCYC:
 EG10900-MONOMER
ECOLIWIKI:
 b0911
INTERPRO:
 IPR000110
INTERPRO:
 IPR003029
INTERPRO:
 IPR012340
INTERPRO:
 IPR035104
INTERPRO:
 IPR022967
MINT:
 P0AG67
MODBASE:
 P0AG67
PANTHER:
 PTHR10724:SF7
PDB:
 6ZTJ
PDB:
 2KHJ
PDB:
 2BH8
PDB:
 2KHI
PDB:
 6H58
PDB:
 4Q7J
PDB:
 4R71
PDB:
 5XQ5
PDB:
 6BU8
PDB:
 6H4N
PFAM:
 PF00575
PRIDE:
 P0AG67
PRODB:
 PRO_000023854
PROSITE:
 PS50126
REFSEQ:
 NP_415431
SMART:
 SM00316
SMR:
 P0AG67
UNIPROT:
 P0AG67


Operon      
Name: cmk-rpsA-ihfB         
Operon arrangement:
Transcription unit        Promoter
cmk-rpsA
rpsA-ihfB
rpsA-ihfB
ihfB
ihfB


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_1178 961718 forward nd [RS-EPT-CBR] [17]
  promoter TSS_1179 (cluster) 961893 forward nd [RS-EPT-CBR] [17]
  promoter TSS_1180 961899 forward nd [RS-EPT-CBR] [17]
  promoter TSS_1181 962373 forward nd [RS-EPT-CBR] [17]
  promoter TSS_1182 (cluster) 962813 forward nd [RS-EPT-CBR] [17]
  promoter TSS_1183 962831 forward nd [RS-EPT-CBR] [17]
  promoter TSS_1184 962837 reverse nd [RS-EPT-CBR] [17]
  promoter TSS_1185 (cluster) 963236 forward nd [RS-EPT-CBR] [17]
  promoter TSS_1186 (cluster) 963240 forward nd [RS-EPT-CBR] [17]
  promoter TSS_1187 (cluster) 963362 forward nd [RS-EPT-CBR] [17]
  promoter TSS_1188 964101 forward nd [RS-EPT-CBR] [17]
  promoter ycaIp6 964105 forward nd [COMP-AINF] [18]
  promoter ycaIp8 964108 forward nd [COMP-AINF] [18]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Cifuentes-Goches JC., Hernandez-Ancheyta L., Guarneros G., Oviedo N., Hernandez-Sanchez J., 2019, Domains two and three of Escherichia coli ribosomal S1 protein confers 30S subunits a high affinity for downstream A/U-rich mRNAs., J Biochem 166(1):29-40

 [2] Doi H., Hoshino Y., Nakase K., Usuda Y., 2014, Reduction of hydrogen peroxide stress derived from fatty acid beta-oxidation improves fatty acid utilization in Escherichia coli., Appl Microbiol Biotechnol 98(2):629-39

 [3] Duval M., Marenna A., Chevalier C., Marzi S., 2017, Site-Directed Chemical Probing to map transient RNA/protein interactions., Methods 117:48-58

 [4] Failmezger J., Nitschel R., Sanchez-Kopper A., Kraml M., Siemann-Herzberg M., 2016, Site-Specific Cleavage of Ribosomal RNA in Escherichia coli-Based Cell-Free Protein Synthesis Systems., PLoS One 11(12):e0168764

 [5] Giraud P., Crechet JB., Uzan M., Bontems F., Sizun C., 2015, Resonance assignment of the ribosome binding domain of E. coli ribosomal protein S1., Biomol NMR Assign 9(1):107-11

 [6] Hughes D., 2016, Using the power of genetic suppressors to probe the essential functions of RNase E., Curr Genet 62(1):53-7

 [7] Kurata T., Nakanishi S., Hashimoto M., Taoka M., Isobe T., Kato JI., 2018, Subunit Composition of Ribosome in the yqgF Mutant Is Deficient in pre-16S rRNA Processing of Escherichia coli., J Mol Microbiol Biotechnol 28(4):179-182

 [8] Lauber MA., Rappsilber J., Reilly JP., 2012, Dynamics of ribosomal protein S1 on a bacterial ribosome with cross-linking and mass spectrometry., Mol Cell Proteomics 11(12):1965-76

 [9] Mallik S., Basu S., Hait S., Kundu S., 2018, Translational regulation of ribosomal protein S15 drives characteristic patterns of protein-mRNA epistasis., Proteins 86(8):827-832

 [10] Nafissi M., Chau J., Xu J., Johnson RC., 2012, Robust translation of the nucleoid protein Fis requires a remote upstream AU element and is enhanced by RNA secondary structure., J Bacteriol 194(10):2458-69

 [11] Osterberg R., Sjoberg B., 1978, Small-angle X-ray scattering study of the proteins S1, S8, S15, S16, S20 from Escherichia coli ribosomes., FEBS Lett 93(1):115-9

 [12] Pan JY., Wu H., Liu X., Li PP., Li H., Wang SY., Peng XX., 2011, Complexome of Escherichia coli cytosolic proteins under normal native conditions., Mol Biosyst 7(9):2651-63

 [13] Raneri M., Sciandrone B., Briani F., 2015, A whole-cell assay for specific inhibitors of translation initiation in bacteria., J Biomol Screen 20(5):627-33

 [14] Rodriguez-Moya M., Gonzalez R., 2015, Proteomic analysis of the response of Escherichia coli to short-chain fatty acids., J Proteomics 122:86-99

 [15] Stefanopoulou M., Kokoschka M., Sheldrick WS., Wolters DA., 2011, Cell response of Escherichia coli to cisplatin-induced stress., Proteomics 11(21):4174-88

 [16] Yong AL., Ooh KF., Ong HC., Chai TT., Wong FC., 2015, Investigation of antibacterial mechanism and identification of bacterial protein targets mediated by antibacterial medicinal plant extracts., Food Chem 186:32-6

 [17] 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.

 [18] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

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