RegulonDB RegulonDB 11.1: Gene Form
   

rimM gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

trmD rimM rpsP TSS_2951 TSS_2951 TSS_2950 TSS_2950 TSS_2949 TSS_2949 TSS_2948 TSS_2948 rplSp1 rplSp1

Gene      
Name: rimM    Texpresso search in the literature
Synonym(s): ECK2605, EG11153, b2608, yfjA
Genome position(nucleotides): 2745370 <-- 2745918
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.0
External database links:  
ASAP:
 ABE-0008579
ECHOBASE:
 EB1142
ECOLIHUB:
 rimM
OU-MICROARRAY:
 b2608
STRING:
 511145.b2608
COLOMBOS: rimM


Product      
Name: ribosome maturation factor RimM
Synonym(s): 21K, RimM, YfjA
Sequence: Get amino acid sequence Fasta Format
Cellular location: ribosome,cytosol
Molecular weight: 20.605
Isoelectric point: 4.38
Motif(s):
 
Type Positions Sequence Comment
16 -> 97 LGKMGSSYGIRGWLRVFSSTEDAESIFDYQPWFIQKAGQWQQVQLESWKHHNQDMIIKLKGVDDRDAANLLTNCEIVVDSSQ
103 -> 182 EGDYYWKDLMGCQVVTTEGYDLGKVVDMMETGSNDVLVIKANLKDAFGIKERLVPFLDGQVIKKVDLTTRSIEVDWDPGF UniProt: PRC barrel.
104 -> 177 GDYYWKDLMGCQVVTTEGYDLGKVVDMMETGSNDVLVIKANLKDAFGIKERLVPFLDGQVIKKVDLTTRSIEVD
106 -> 107 YY UniProt: 3-fold decreased growth rate; loss of association with 30S ribosomal subunit; loss of interaction with S19..

 
Classification:
Multifun Terms (GenProtEC)  
  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
molecular_function GO:0005515 - protein binding
GO:0043022 - ribosome binding
GO:0003723 - RNA binding
GO:0019843 - rRNA binding
biological_process GO:0042254 - ribosome biogenesis
GO:0006364 - rRNA processing
GO:0042274 - ribosomal small subunit biogenesis
GO:0030490 - maturation of SSU-rRNA
GO:0000028 - ribosomal small subunit assembly
Note(s): Note(s): ...[more].
Evidence: [EXP] Inferred from experiment
Reference(s): [1] Bylund GO., et al., 1998
[2] Clatterbuck Soper SF., et al., 2013
[3] Jain C. 2018
[4] Suzuki S., et al., 2007
[5] Thurlow B., et al., 2016
External database links:  
ALPHAFOLD:
 P0A7X6
ECOCYC:
 EG11153-MONOMER
ECOLIWIKI:
 b2608
INTERPRO:
 IPR011033
INTERPRO:
 IPR009000
INTERPRO:
 IPR027275
INTERPRO:
 IPR036976
INTERPRO:
 IPR002676
INTERPRO:
 IPR011961
PFAM:
 PF01782
PFAM:
 PF05239
PRIDE:
 P0A7X6
PRODB:
 PRO_000023762
REFSEQ:
 NP_417099
SMR:
 P0A7X6
UNIPROT:
 P0A7X6


Operon      
Name: rpsP-rimM-trmD-rplS         
Operon arrangement:
Transcription unit        Promoter
rpsP-rimM-trmD-rplS


Transcriptional Regulation      
Display Regulation             
Repressed by: FNR


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 rplSp1 2744642 reverse nd [COMP-AINF] [6]
  promoter TSS_2948 2744644 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_2949 2744647 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_2950 2744657 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_2951 2744665 reverse nd [RS-EPT-CBR] [7]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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


Reference(s)    

 [1] Bylund GO., Wipemo LC., Lundberg LA., Wikstrom PM., 1998, RimM and RbfA are essential for efficient processing of 16S rRNA in Escherichia coli., J Bacteriol 180(1):73-82

 [2] Clatterbuck Soper SF., Dator RP., Limbach PA., Woodson SA., 2013, In vivo X-ray footprinting of pre-30S ribosomes reveals chaperone-dependent remodeling of late assembly intermediates., Mol Cell 52(4):506-16

 [3] Jain C., 2018, Role of ribosome assembly in Escherichia coli ribosomal RNA degradation., Nucleic Acids Res 46(20):11048-11060

 [4] Suzuki S., Tatsuguchi A., Matsumoto E., Kawazoe M., Kaminishi T., Shirouzu M., Muto Y., Takemoto C., Yokoyama S., 2007, Structural characterization of the ribosome maturation protein, RimM., J Bacteriol 189(17):6397-406

 [5] Thurlow B., Davis JH., Leong V., Moraes TF., Williamson JR., Ortega J., 2016, Binding properties of YjeQ (RsgA), RbfA, RimM and Era to assembly intermediates of the 30S subunit., Nucleic Acids Res 44(20):9918-9932

 [6] 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

 [7] 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