RegulonDB RegulonDB 10.9: Gene Form
   

rplD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rplB rplC rplD rplW TSS_3818 TSS_3818 TSS_3817 TSS_3817 TSS_3816 (cluster) TSS_3816 (cluster) TSS_3815 TSS_3815 TSS_3814 TSS_3814 TSS_3813 TSS_3813 TSS_3812 TSS_3812 TSS_3811 (cluster) TSS_3811 (cluster) TSS_3810 TSS_3810 TSS_3809 (cluster) TSS_3809 (cluster) TSS_3808 TSS_3808 TSS_3807 (cluster) TSS_3807 (cluster)

Gene      
Name: rplD    Texpresso search in the literature
Synonym(s): ECK3306, EG10867, b3319, eryA
Genome position(nucleotides): 3451681 <-- 3452286 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.97
External database links:  
ASAP:
ABE-0010858
CGSC:
260
ECHOBASE:
EB0860
ECOLIHUB:
rplD
OU-MICROARRAY:
b3319
STRING:
511145.b3319
COLOMBOS: rplD


Product      
Name: 50S ribosomal subunit protein L4
Synonym(s): EryA, RplD
Sequence: Get amino acid sequence Fasta Format
Cellular location: ribosome,cytosol
Molecular weight: 22.086
Isoelectric point: 10.438
Motif(s):
 
Type Positions Sequence
131 -> 131 T
67 -> 103 RARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRG
134 -> 134 L
160 -> 160 A
167 -> 167 V

 

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
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.1 - translation attenuation and efficiency
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.1 - operon
  6 - cell structure --> 6.6 - ribosomes
Gene Ontology Terms (GO)  
cellular_component GO:0042788 - polysomal ribosome
GO:0005829 - cytosol
GO:0005840 - ribosome
GO:0015934 - large ribosomal subunit
GO:0022625 - cytosolic large ribosomal subunit
molecular_function GO:0003735 - structural constituent of ribosome
GO:0005515 - protein binding
GO:0030371 - translation repressor activity
GO:0003723 - RNA binding
GO:0019843 - rRNA binding
GO:0048027 - mRNA 5'-UTR binding
GO:0060698 - endoribonuclease inhibitor activity
GO:0001070 - RNA-binding transcription regulator activity
biological_process GO:0006353 - DNA-templated transcription, termination
GO:0006412 - translation
GO:0006417 - regulation of translation
GO:0031555 - transcriptional attenuation
GO:0045892 - negative regulation of transcription, DNA-templated
GO:0042255 - ribosome assembly
GO:0017148 - negative regulation of translation
GO:0046677 - response to antibiotic
GO:0060702 - negative regulation of endoribonuclease activity
GO:2000766 - negative regulation of cytoplasmic translation
Note(s): Note(s): ...[more].
Reference(s): [1] Dunkle JA., et al., 2010
[2] Fu Y., et al., 2013
[3] Gagnon MG., et al., 2010
[4] Gomes C., et al., 2019
[5] Kostopoulou ON., et al., 2012
[6] Pichkur EB., et al., 2020
[7] Singh D., et al., 2020
External database links:  
DIP:
DIP-35791N
DISPROT:
DP00600
ECOCYC:
EG10867-MONOMER
ECOLIWIKI:
b3319
INTERPRO:
IPR002136
INTERPRO:
IPR023574
INTERPRO:
IPR013005
MINT:
P60723
MODBASE:
P60723
PANTHER:
PTHR10746
PDB:
2J28
PDB:
2RDO
PDB:
3BBX
PDB:
3J5L
PDB:
3J7Z
PDB:
3J8G
PDB:
3J9Y
PDB:
3J9Z
PDB:
3JA1
PDB:
3JBU
PDB:
3JBV
PDB:
3JCD
PDB:
3JCE
PDB:
3JCJ
PDB:
3JCN
PDB:
4CSU
PDB:
4U1U
PDB:
4U1V
PDB:
4U20
PDB:
4U24
PDB:
4U25
PDB:
4U26
PDB:
4U27
PDB:
4UY8
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:
5ADY
PDB:
5AFI
PDB:
5AKA
PDB:
5GAD
PDB:
5GAE
PDB:
5GAF
PDB:
5GAG
PDB:
5GAH
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:
5MGP
PDB:
5NCO
PDB:
5NP6
PDB:
5NWY
PDB:
5O2R
PDB:
5U4I
PDB:
5U9F
PDB:
5U9G
PDB:
5UYK
PDB:
5UYL
PDB:
5UYM
PDB:
5UYN
PDB:
5UYP
PDB:
5UYQ
PDB:
5WDT
PDB:
5WE4
PDB:
5WE6
PDB:
5WFK
PDB:
6BU8
PDB:
6BY1
PDB:
6C4I
PDB:
6ENF
PDB:
6ENJ
PDB:
6ENU
PDB:
6GBZ
PDB:
6GC0
PDB:
6GC4
PDB:
6GC6
PDB:
6GC7
PDB:
6GC8
PDB:
6GWT
PDB:
6GXM
PDB:
6GXN
PDB:
6GXO
PDB:
6GXP
PDB:
6H4N
PDB:
6H58
PDB:
6HRM
PDB:
6I0Y
PDB:
6I7V
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:
6QUL
PDB:
6S0K
PDB:
6SZS
PDB:
6TBV
PDB:
6TC3
PFAM:
PF00573
PRIDE:
P60723
PRODB:
PRO_000023812
REFSEQ:
NP_417778
SMR:
P60723
UNIPROT:
P60723


Operon      
Name: rpsJ-rplCDWB-rpsS-rplV-rpsC-rplP-rpmC-rpsQ         
Operon arrangement:
Transcription unit        Promoter
rpsJ-rplCDWB-rpsS-rplV-rpsC-rplP-rpmC-rpsQ


Transcriptional Regulation      
Display Regulation             
Activated by: FNR
Repressed by: ArcA


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_3807 (cluster) 3450543 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [8]
  promoter TSS_3808 3451410 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_3809 (cluster) 3451437 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [8]
  promoter TSS_3810 3451529 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_3811 (cluster) 3451535 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [8]
  promoter TSS_3812 3451962 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_3813 3451965 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_3814 3451991 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_3815 3451997 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_3816 (cluster) 3452000 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [8]
  promoter TSS_3817 3452125 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_3818 3452609 reverse nd [RS-EPT-CBR] [8]


Evidence    

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



Reference(s)    

 [1] Dunkle JA., Xiong L., Mankin AS., Cate JH., 2010, Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action., Proc Natl Acad Sci U S A 107(40):17152-7

 [2] Fu Y., Deiorio-Haggar K., Anthony J., Meyer MM., 2013, Most RNAs regulating ribosomal protein biosynthesis in Escherichia coli are narrowly distributed to Gammaproteobacteria., Nucleic Acids Res 41(6):3491-503

 [3] Gagnon MG., Boutorine YI., Steinberg SV., 2010, Recurrent RNA motifs as probes for studying RNA-protein interactions in the ribosome., Nucleic Acids Res 38(10):3441-53

 [4] Gomes C., Ruiz-Roldan L., Mateu J., Ochoa TJ., Ruiz J., 2019, Azithromycin resistance levels and mechanisms in Escherichia coli., Sci Rep 9(1):6089

 [5] Kostopoulou ON., Petropoulos AD., Dinos GP., Choli-Papadopoulou T., Kalpaxis DL., 2012, Investigating the entire course of telithromycin binding to Escherichia coli ribosomes., Nucleic Acids Res 40(11):5078-87

 [6] Pichkur EB., Paleskava A., Tereshchenkov AG., Kasatsky P., Komarova E., Shiriaev D., Bogdanov A., Dontsova OA., Osterman I., Sergiev PV., Polikanov YS., Myasnikov AG., Konevega AL., 2020, Insights into the improved macrolide inhibitory activity from the high-resolution cryo-EM structure of dirithromycin bound to the E. coli 70S ribosome., RNA

 [7] Singh D., Murashko ON., Lin-Chao S., 2020, Posttranscriptional Regulation of tnaA by Protein-RNA Interaction Mediated by Ribosomal Protein L4 in Escherichia coli., J Bacteriol 202(10)

 [8] 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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