RegulonDB RegulonDB 11.1: Gene Form
   

rpmB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yicR rpmB rpmG DksA-ppGpp DksA-ppGpp terminator anti-terminator anti-anti-terminator rpmBp rpmBp TSS_4218 (cluster) TSS_4218 (cluster) TSS_4217 (cluster) TSS_4217 (cluster) TSS_4216 TSS_4216 TSS_4215 TSS_4215 TSS_4214 (cluster) TSS_4214 (cluster) TSS_4213 (cluster) TSS_4213 (cluster) mutMp2 mutMp2

Gene      
Name: rpmB    Texpresso search in the literature
Synonym(s): ECK3627, EG10886, b3637
Genome position(nucleotides): 3811438 <-- 3811674
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.16
External database links:  
ASAP:
ABE-0011885
CGSC:
240
ECHOBASE:
EB0879
ECOLIHUB:
rpmB
OU-MICROARRAY:
b3637
STRING:
511145.b3637
COLOMBOS: rpmB


Product      
Name: 50S ribosomal subunit protein L28
Synonym(s): RpmB
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol,ribosome
Molecular weight: 9.006
Isoelectric point: 11.959
Motif(s):
 
Type Positions Sequence Comment
2 -> 78 SRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDKKGIDTVLAELRARGEKY UniProt: 50S ribosomal protein L28.
3 -> 62 RVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDKK

 

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:0005829 - cytosol
GO:0005840 - ribosome
GO:0022625 - cytosolic large ribosomal subunit
molecular_function GO:0003735 - structural constituent of ribosome
GO:0005515 - protein binding
GO:0003723 - RNA binding
GO:0019843 - rRNA binding
biological_process GO:0006412 - translation
GO:0000027 - ribosomal large subunit assembly
GO:0002181 - cytoplasmic translation
Note(s): Note(s): ...[more].
Reference(s): [1] Ballesta JP., et al., 1976
[2] Butler PD., et al., 1985
[3] Butler PD., et al., 1984
[4] Coleman SH., et al., 1993
[5] Dabbs ER. 1979
[6] Dabbs ER., et al., 1983
[7] Dzionara M., et al., 1977
[8] Herold M., et al., 1987
[9] Isono K., et al., 1980
[10] Kitakawa M., et al., 1980
[11] Lee JS., et al., 1981
[12] Markey F., et al., 1976
[13] Michalski CJ., et al., 1975
[14] Morrison CA., et al., 1977
[15] Mustoe AM., et al., 2018
[16] Parker KK., et al., 1983
[17] Romero DP., et al., 1990
[18] Sander G., et al., 1975
[19] Spierer P., et al., 1979
[20] Wittmann-Liebold B., et al., 1977
External database links:  
ALPHAFOLD:
P0A7M2
DIP:
DIP-35745N
ECOCYC:
EG10886-MONOMER
ECOLIWIKI:
b3637
INTERPRO:
IPR037147
INTERPRO:
IPR001383
INTERPRO:
IPR026569
INTERPRO:
IPR034704
PANTHER:
PTHR13528
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:
4V50
PDB:
4V52
PDB:
4V53
PDB:
4V54
PDB:
4V55
PDB:
4V56
PDB:
4V57
PDB:
4V5H
PDB:
4V5Y
PDB:
4V64
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:
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:
6GC8
PDB:
6GWT
PDB:
6GXM
PDB:
6GXN
PDB:
6GXO
PDB:
6GXP
PDB:
6H4N
PDB:
6H58
PDB:
6HRM
PDB:
6I0Y
PDB:
6I7V
PDB:
6O9K
PDB:
6OFX
PDB:
6OG7
PDB:
6ORE
PDB:
6ORL
PDB:
6OST
PDB:
6OT3
PDB:
6OUO
PDB:
6Q97
PDB:
6Q98
PDB:
6Q9A
PDB:
6QDW
PDB:
6QUL
PDB:
6S0K
PDB:
6SZS
PDB:
6TBV
PDB:
6TC3
PDB:
6VWL
PDB:
6VWM
PDB:
6VWN
PDB:
6WD6
PDB:
6WDB
PDB:
6WDC
PDB:
6WDD
PDB:
6WDE
PDB:
6WDF
PDB:
6WDG
PDB:
6WDH
PDB:
6WDI
PDB:
6WDJ
PDB:
6WDK
PDB:
6WDL
PDB:
6WDM
PDB:
6WNT
PDB:
6WNV
PDB:
6WNW
PDB:
6XZ7
PDB:
6XZA
PDB:
6XZB
PDB:
6Y69
PDB:
6YS3
PDB:
6YSR
PDB:
6YSS
PDB:
6YSU
PDB:
6ZTJ
PDB:
6ZTL
PDB:
6ZTM
PDB:
6ZTN
PDB:
6ZTO
PDB:
6ZTP
PDB:
6ZU1
PDB:
7BV8
PDB:
7JSS
PDB:
7JSW
PDB:
7JSZ
PDB:
7JT1
PDB:
7JT2
PDB:
7JT3
PFAM:
PF00830
PRIDE:
P0A7M2
PRODB:
PRO_000023833
REFSEQ:
NP_418094
SMR:
P0A7M2
UNIPROT:
P0A7M2


Operon      
Name: yicR-rpmBG-mutM         
Operon arrangement:
Transcription unit        Promoter
mutM
rpmBG
rpmBG-mutM
yicR-rpmBG
yicR-rpmBG-mutM
mutM


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 mutMp2 3811277 reverse The σ factor was determined
Read more >
[COMP-AINF], [COMP-AINF-POSITIONAL-IDENTIFICATION], [COMP-AINF-SIMILAR-TO-CONSENSUS] [21], [22]
  promoter TSS_4213 (cluster) 3811691 reverse nd [RS-EPT-CBR] [23]
  promoter TSS_4214 (cluster) 3811696 reverse nd [RS-EPT-CBR] [23]
  promoter TSS_4215 3811699 reverse nd [RS-EPT-CBR] [23]
  promoter TSS_4216 3811705 reverse nd [RS-EPT-CBR] [23]
  promoter TSS_4217 (cluster) 3811805 reverse nd [RS-EPT-CBR] [23]
  promoter TSS_4218 (cluster) 3811816 reverse nd [RS-EPT-CBR] [23]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

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



Reference(s)    

 [1] Ballesta JP., Waring MJ., Vazquez D., 1976, Specific release of ribosomal proteins by nucleic acid-intercalating agents., Nucleic Acids Res 3(5):1307-22

 [2] Butler PD., Wild DG., 1985, The location of a mutation affecting ribosomal protein synthesis by Escherichia coli., J Gen Microbiol 131(1):135-44

 [3] Butler PD., Wild DG., 1984, Ribosomal protein synthesis by a mutant of Escherichia coli., Eur J Biochem 144(3):649-54

 [4] Coleman SH., Maguire BA., Wild DG., 1993, Ribosome assembly in three strains of Escherichia coli with mutations in the rpmB,G operon., J Gen Microbiol 139(4):707-16

 [5] Dabbs ER., 1979, Selection for Escherichia coli mutants with proteins missing from the ribosome., J Bacteriol 140(2):734-7

 [6] Dabbs ER., Hasenbank R., Kastner B., Rak KH., Wartusch B., Stoffler G., 1983, Immunological studies of Escherichia coli mutants lacking one or two ribosomal proteins., Mol Gen Genet 192(3):301-8

 [7] Dzionara M., Robinson SM., Wittmann-Liebold B., 1977, Prediction for secondary structures of ten proteins from the 50S subunit of the Escherichia coli ribosome., J Supramol Struct 7(2):191-204

 [8] Herold M., Nierhaus KH., 1987, Incorporation of six additional proteins to complete the assembly map of the 50 S subunit from Escherichia coli ribosomes., J Biol Chem 262(18):8826-33

 [9] Isono K., Schnier J., Kitakawa M., 1980, Genetic fine structure of the pyrE region containing the genes for ribosomal proteins L28 and L33 in Escherichia coli., Mol Gen Genet 179(2):311-7

 [10] Kitakawa M., Blumenthal L., Isono K., 1980, Isolation and characterization of specialized transducing lambda phages carrying ribosomal protein genes of Escherichia coli., Mol Gen Genet 180(2):343-9

 [11] Lee JS., An G., Friesen JD., Isono K., 1981, Cloning and the nucleotide sequence of the genes for Escherichia coli ribosomal proteins L28 (rpmB) and L33 (rpmG)., Mol Gen Genet 184(2):218-23

 [12] Markey F., Sims PF., Wild DG., 1976, The composition of an unusual precursor of 50 S ribosomes in a mutant of Escherichia coli., Biochem J 158(2):451-6

 [13] Michalski CJ., Sells BH., 1975, Molecular morphology of ribosomes. Iodination of Escherichia coli ribosomal proteins with solid-state lactoperoxidase., Eur J Biochem 52(2):385-9

 [14] Morrison CA., Tischendorf G., Stoffler G., Garrett RA., 1977, Accessibility of proteins in 50S ribosomal subunits of Escherichia coli to antibodies: an ultracentrifugation study., Mol Gen Genet 151(3):245-52

 [15] Mustoe AM., Busan S., Rice GM., Hajdin CE., Peterson BK., Ruda VM., Kubica N., Nutiu R., Baryza JL., Weeks KM., 2018, Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing., Cell 173(1):181-195.e18

 [16] Parker KK., Wickstrom E., 1983, Crosslinking of Escherichia coli 50S ribosomal subunits with chlorambucilyl oligoprolyl phenylalanyl-tRNA molecular rulers., Nucleic Acids Res 11(2):515-24

 [17] Romero DP., Arredondo JA., Traut RR., 1990, Identification of a region of Escherichia coli ribosomal protein L2 required for the assembly of L16 into the 50 S ribosomal subunit., J Biol Chem 265(30):18185-91

 [18] Sander G., Marsh RC., Voigt J., Parmeggiani A., 1975, A comparative study of the 50S ribosomal subunit and several 50S subparticles in EF-T-and EF-G-dependent activities., Biochemistry 14(9):1805-14

 [19] Spierer P., Wang CC., Marsh TL., Zimmermann RA., 1979, Cooperative interactions among protein and RNA components of the 50S ribosomal subunit of Escherichia coli., Nucleic Acids Res 6(4):1669-82

 [20] Wittmann-Liebold B., Marzinzig E., 1977, Primary structure of protein L28 from the large subunit of Escherichia coli ribosomes., FEBS Lett 81(1):214-7

 [21] 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

 [22] Zhao K., Liu M., Burgess RR., 2005, The global transcriptional response of Escherichia coli to induced sigma 32 protein involves sigma 32 regulon activation followed by inactivation and degradation of sigma 32 in vivo., J Biol Chem 280(18):17758-68

 [23] 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.


RegulonDB