RegulonDB

Gene
Name:	rpmB
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:

DIP:

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UNIPROT:

Operon

Name:

yicR-rpmBG-mutM

Operon arrangement:

Transcription unit	Promoter
mutM	mutMp
rpmBG	rpmBp
rpmBG-mutM	rpmBp
yicR-rpmBG	yicRp
yicR-rpmBG-mutM	yicRp
mutM

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

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	mutMp2	3811277	reverse	The σ factor was determined by transcription profiling experiments and a bioinformatics approach Zhao K,2005. We assigned a putative transcriptional start site to this promoter based on the observation that the majority of the promoters, whose transcriptional start sites were determined experimentally, present a distance of 6 nucleotides between the transcriptional start site and the -10 box. 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.