RegulonDB RegulonDB 10.9: Gene Form
   

rpsD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rpoA rpsD rpsK TSS_3659 TSS_3659 TSS_3658 TSS_3658 TSS_3657 TSS_3657 TSS_3656 TSS_3656 TSS_3655 TSS_3655 TSS_3654 TSS_3654 TSS_3653 TSS_3653 TSS_3652 TSS_3652 TSS_3651 TSS_3651 TSS_3650 TSS_3650 TSS_3649 TSS_3649 TSS_3648 TSS_3648 TSS_3647 TSS_3647 TSS_3646 TSS_3646 TSS_3645 TSS_3645 TSS_3644 TSS_3644 TSS_3643 TSS_3643 TSS_3642 TSS_3642 TSS_3641 TSS_3641 TSS_3640 TSS_3640 TSS_3639 (cluster) TSS_3639 (cluster) TSS_3638 TSS_3638 TSS_3637 (cluster) TSS_3637 (cluster) TSS_3636 (cluster) TSS_3636 (cluster) TSS_3635 TSS_3635 TSS_3634 TSS_3634 TSS_3633 (cluster) TSS_3633 (cluster) TSS_3632 TSS_3632 TSS_3631 TSS_3631 TSS_3630 TSS_3630 TSS_3629 (cluster) TSS_3629 (cluster) TSS_3628 (cluster) TSS_3628 (cluster) TSS_3627 (cluster) TSS_3627 (cluster) TSS_3626 (cluster) TSS_3626 (cluster) TSS_3625 TSS_3625 TSS_3624 (cluster) TSS_3624 (cluster) TSS_3623 TSS_3623 TSS_3622 (cluster) TSS_3622 (cluster) TSS_3621 TSS_3621 TSS_3620 TSS_3620 TSS_3619 TSS_3619 TSS_3618 TSS_3618 TSS_3617 TSS_3617 TSS_3616 TSS_3616 TSS_3615 TSS_3615

Gene      
Name: rpsD    Texpresso search in the literature
Synonym(s): ECK3283, EG10903, b3296, ramA, sud(2), sud2
Genome position(nucleotides): 3441055 <-- 3441675 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
50.72
External database links:  
ASAP:
ABE-0010805
CGSC:
227
ECHOBASE:
EB0896
ECOLIHUB:
rpsD
OU-MICROARRAY:
b3296
STRING:
511145.b3296
COLOMBOS: rpsD


Product      
Name: 30S ribosomal subunit protein S4
Synonym(s): RamA, RpsD
Sequence: Get amino acid sequence Fasta Format
Cellular location: ribosome,cytosol
Molecular weight: 23.469
Isoelectric point: 10.657
Motif(s):
 
Type Positions Sequence
3 -> 95 RYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQKVRRIYGVLERQFRNYYKEAARLKGNTGENLLALLE
91 -> 91 L
96 -> 156 GRLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK
138 -> 144 SPNDVVS
170 -> 206 WLEVDAGKMEGTFKRKPERSDLSADINEHLIVELYSK

 

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:0005829 - cytosol
GO:0005840 - ribosome
GO:0015935 - small ribosomal subunit
GO:0022627 - cytosolic small ribosomal subunit
molecular_function GO:0000900 - translation repressor activity, mRNA regulatory element binding
GO:0003735 - structural constituent of ribosome
GO:0005515 - protein binding
GO:0003723 - RNA binding
GO:0019843 - rRNA binding
GO:0048027 - mRNA 5'-UTR binding
biological_process GO:0006353 - DNA-templated transcription, termination
GO:0006412 - translation
GO:0006417 - regulation of translation
GO:0031564 - transcription antitermination
GO:0045947 - negative regulation of translational initiation
GO:0046677 - response to antibiotic
GO:0000028 - ribosomal small subunit assembly
GO:0045903 - positive regulation of translational fidelity
GO:1990145 - maintenance of translational fidelity
Note(s): Note(s): ...[more].
Reference(s): [1] Al-Majdoub ZM., et al., 2014
[2] Bedwell D., et al., 1985
[3] Bjornsson A., et al., 1993
[4] Daya-Grosjean L., et al., 1974
[5] Mayerle M., et al., 2013
[6] Schulte C., et al., 1974
[7] Ungewickell E., et al., 1975
[8] Vallabhaneni H., et al., 2009
External database links:  
DIP:
DIP-35794N
ECOCYC:
EG10903-MONOMER
ECOLIWIKI:
b3296
INTERPRO:
IPR002942
INTERPRO:
IPR036986
INTERPRO:
IPR022801
INTERPRO:
IPR001912
INTERPRO:
IPR005709
INTERPRO:
IPR018079
MINT:
P0A7V8
PANTHER:
PTHR11831:SF4
PANTHER:
PTHR11831
PDB:
1EG0
PDB:
1M5G
PDB:
2YKR
PDB:
3J9Y
PDB:
3J9Z
PDB:
3JA1
PDB:
3JBU
PDB:
3JBV
PDB:
3JCD
PDB:
3JCE
PDB:
3JCJ
PDB:
3JCN
PDB:
4A2I
PDB:
4ADV
PDB:
4U1U
PDB:
4U1V
PDB:
4U20
PDB:
4U24
PDB:
4U25
PDB:
4U26
PDB:
4U27
PDB:
4V47
PDB:
4V48
PDB:
4V4H
PDB:
4V4Q
PDB:
4V4V
PDB:
4V4W
PDB:
4V50
PDB:
4V52
PDB:
4V53
PDB:
4V54
PDB:
4V55
PDB:
4V56
PDB:
4V57
PDB:
4V5B
PDB:
4V5H
PDB:
4V5Y
PDB:
4V64
PDB:
4V65
PDB:
4V66
PDB:
4V69
PDB:
4V6C
PDB:
4V6D
PDB:
4V6E
PDB:
4V6K
PDB:
4V6L
PDB:
4V6M
PDB:
4V6N
PDB:
4V6O
PDB:
4V6P
PDB:
4V6Q
PDB:
4V6R
PDB:
4V6S
PDB:
4V6T
PDB:
4V6V
PDB:
4V6Y
PDB:
4V6Z
PDB:
4V70
PDB:
4V71
PDB:
4V72
PDB:
4V73
PDB:
4V74
PDB:
4V75
PDB:
4V76
PDB:
4V77
PDB:
4V78
PDB:
4V79
PDB:
4V7A
PDB:
4V7B
PDB:
4V7C
PDB:
4V7D
PDB:
4V7I
PDB:
4V7S
PDB:
4V7T
PDB:
4V7U
PDB:
4V7V
PDB:
4V85
PDB:
4V89
PDB:
4V9C
PDB:
4V9D
PDB:
4V9O
PDB:
4V9P
PDB:
4WF1
PDB:
4WOI
PDB:
4WWW
PDB:
4YBB
PDB:
5AFI
PDB:
5H5U
PDB:
5IQR
PDB:
5IT8
PDB:
5J5B
PDB:
5J7L
PDB:
5J88
PDB:
5J8A
PDB:
5J91
PDB:
5JC9
PDB:
5JTE
PDB:
5JU8
PDB:
5KCR
PDB:
5KCS
PDB:
5KPS
PDB:
5KPV
PDB:
5KPW
PDB:
5KPX
PDB:
5L3P
PDB:
5LZA
PDB:
5LZB
PDB:
5LZC
PDB:
5LZD
PDB:
5LZE
PDB:
5LZF
PDB:
5MDV
PDB:
5MDW
PDB:
5MDY
PDB:
5MDZ
PDB:
5ME0
PDB:
5ME1
PDB:
5MGP
PDB:
5MY1
PDB:
5NO2
PDB:
5NO3
PDB:
5NO4
PDB:
5NP6
PDB:
5NWY
PDB:
5O2R
PDB:
5U4I
PDB:
5U4J
PDB:
5U9F
PDB:
5U9G
PDB:
5UYK
PDB:
5UYL
PDB:
5UYM
PDB:
5UYN
PDB:
5UYP
PDB:
5UYQ
PDB:
5UZ4
PDB:
5WDT
PDB:
5WE4
PDB:
5WE6
PDB:
5WFK
PDB:
6BU8
PDB:
6BY1
PDB:
6C4I
PDB:
6ENF
PDB:
6ENJ
PDB:
6ENU
PDB:
6GWT
PDB:
6GXM
PDB:
6GXN
PDB:
6GXO
PDB:
6GXP
PDB:
6H4N
PDB:
6H58
PDB:
6HRM
PDB:
6I7V
PDB:
6NQB
PDB:
6O9J
PDB:
6O9K
PDB:
6OFX
PDB:
6OG7
PDB:
6ORE
PDB:
6ORL
PDB:
6OST
PDB:
6OT3
PDB:
6OUO
PDB:
6Q97
PDB:
6Q98
PDB:
6Q9A
PDB:
6SZS
PDB:
6TBV
PDB:
6TC3
PFAM:
PF00163
PFAM:
PF01479
PRIDE:
P0A7V8
PRODB:
PRO_000023857
PROSITE:
PS00632
PROSITE:
PS50889
REFSEQ:
NP_417755
SMART:
SM01390
SMART:
SM00363
SMR:
P0A7V8
UNIPROT:
P0A7V8


Operon      
Name: rpsMKD-rpoA-rplQ         
Operon arrangement:
Transcription unit        Promoter
rpsMKD-rpoA-rplQ
rpsMKD-rpoA-rplQ


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_3615 3440198 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3616 3440200 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3617 3440202 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3618 3440207 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3619 3440256 forward nd [RS-EPT-CBR] [9]
  promoter TSS_3620 3440528 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3621 3440670 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3622 (cluster) 3440696 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [9]
  promoter TSS_3623 3440698 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3624 (cluster) 3441009 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [9]
  promoter TSS_3625 3441034 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3626 (cluster) 3441039 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [9]
  promoter TSS_3627 (cluster) 3441042 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [9]
  promoter TSS_3628 (cluster) 3441047 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [9]
  promoter TSS_3629 (cluster) 3441078 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [9]
  promoter TSS_3630 3441080 forward nd [RS-EPT-CBR] [9]
  promoter TSS_3631 3441085 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3632 3441141 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3633 (cluster) 3441144 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [9]
  promoter TSS_3634 3441149 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3635 3441154 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3636 (cluster) 3441158 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [9]
  promoter TSS_3637 (cluster) 3441166 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [9]
  promoter TSS_3638 3441370 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3639 (cluster) 3441375 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [9]
  promoter TSS_3640 3441422 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3641 3441432 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3642 3441447 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3643 3441449 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3644 3441486 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3645 3441492 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3646 3441494 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3647 3441505 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3648 3441526 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3649 3441571 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3650 3441576 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3651 3441665 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3652 3441693 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3653 3441735 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3654 3441857 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3655 3441871 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3656 3441875 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3657 3441883 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3658 3442063 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3659 3442068 reverse nd [RS-EPT-CBR] [9]


Evidence    

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



Reference(s)    

 [1] Al-Majdoub ZM., Carroll KM., Gaskell SJ., Barber J., 2014, Quantification of the proteins of the bacterial ribosome using QconCAT technology., J Proteome Res 13(3):1211-22

 [2] Bedwell D., Davis G., Gosink M., Post L., Nomura M., Kestler H., Zengel JM., Lindahl L., 1985, Nucleotide sequence of the alpha ribosomal protein operon of Escherichia coli., Nucleic Acids Res 13(11):3891-903

 [3] Bjornsson A., Isaksson LA., 1993, UGA codon context which spans three codons. Reversal by ms2i6A37 in tRNA, mutation in rpsD(S4) or streptomycin., J Mol Biol 232(4):1017-29

 [4] Daya-Grosjean L., Reinbolt J., Pongs O., Garrett RA., 1974, A study of the regions of ribosomal proteins S4, S8, S15 and S20 that interact with 16 S RNA of Escherichia coli., FEBS Lett 44(3):253-6

 [5] Mayerle M., Woodson SA., 2013, Specific contacts between protein S4 and ribosomal RNA are required at multiple stages of ribosome assembly., RNA 19(4):574-85

 [6] Schulte C., Morrison CA., Garrett RA., 1974, Protein-ribonucleic acid interactions in Escherichia coli ribosomes. Solution studies on S4-16S ribonucleic acid and L24-23S ribonucleic acid binding., Biochemistry 13(5):1032-7

 [7] Ungewickell E., Garrett R., Ehresmann C., Stiegler P., Fellner P., 1975, An investigation of the 16-S RNA binding sites of ribosomal proteins S4, S8, S15, and S20 FROM Escherichia coli., Eur J Biochem 51(1):165-80

 [8] Vallabhaneni H., Farabaugh PJ., 2009, Accuracy modulating mutations of the ribosomal protein S4-S5 interface do not necessarily destabilize the rps4-rps5 protein-protein interaction., RNA 15(6):1100-9

 [9] 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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