RegulonDB RegulonDB 10.9: Gene Form
   

srmB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

srmB yfiE yfiC nadB TSS_2874 (cluster) TSS_2874 (cluster) srmBp4 srmBp4 yfiCp3 yfiCp3

Gene      
Name: srmB    Texpresso search in the literature
Synonym(s): ECK2574, EG10975, b2576, rbaB, rhlA
Genome position(nucleotides): 2712896 --> 2714230 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 54.76
External database links:  
ASAP:
 ABE-0008478
CGSC:
 32859
ECHOBASE:
 EB0968
ECOLIHUB:
 srmB
OU-MICROARRAY:
 b2576
STRING:
 511145.b2576
COLOMBOS: srmB


Product      
Name: ATP-dependent RNA helicase SrmB
Synonym(s): DEAD-box RNA helicase, RbaB, RhlA, SrmB
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 49.914
Isoelectric point: 9.823
Motif(s):
 
Type Positions Sequence
28 -> 197 TAIQAAAIPPALDGRDVLGSAPTGTGKTAAYLLPALQHLLDFPRKKSGPPRILILTPTRELAMQVSDHARELAKHTHLDIATITGGVAYMNHAEVFSENQDIVVATTGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDIEHIAGETRWRKQTLLFSATLEGDAIQ
236 -> 343 TALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAG
157 -> 160 DEAD
4 -> 32 TTFSELELDESLLEALQDKGFTRPTAIQA
35 -> 209 IPPALDGRDVLGSAPTGTGKTAAYLLPALQHLLDFPRKKSGPPRILILTPTRELAMQVSDHARELAKHTHLDIATITGGVAYMNHAEVFSENQDIVVATTGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDIEHIAGETRWRKQTLLFSATLEGDAIQDFAERLLEDPVE

 
Classification:
Multifun Terms (GenProtEC)  
  6 - cell structure --> 6.6 - ribosomes
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003676 - nucleic acid binding
GO:0004386 - helicase activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0016887 - ATPase activity
GO:0003723 - RNA binding
GO:0008143 - poly(A) binding
GO:0000166 - nucleotide binding
GO:0003724 - RNA helicase activity
GO:0005524 - ATP binding
GO:0008186 - RNA-dependent ATPase activity
GO:0033592 - RNA strand annealing activity
biological_process GO:0031555 - transcriptional attenuation
GO:0042254 - ribosome biogenesis
GO:0000027 - ribosomal large subunit assembly
Note(s): Note(s): ...[more].
Reference(s): [1] Arunasri K., et al., 2013
[2] Iost I., et al., 2019
[3] Rabuck-Gibbons JN., et al., 2020
[4] Sharma H., et al., 2016
External database links:  
DIP:
 DIP-10920N
ECOCYC:
 EG10975-MONOMER
ECOLIWIKI:
 b2576
INTERPRO:
 IPR001650
INTERPRO:
 IPR028621
INTERPRO:
 IPR027417
INTERPRO:
 IPR014014
INTERPRO:
 IPR000629
INTERPRO:
 IPR011545
INTERPRO:
 IPR014001
MODBASE:
 P21507
PDB:
 2YJT
PFAM:
 PF00270
PFAM:
 PF00271
PRIDE:
 P21507
PRODB:
 PRO_000023988
PROSITE:
 PS51194
PROSITE:
 PS51195
PROSITE:
 PS00039
PROSITE:
 PS51192
REFSEQ:
 NP_417071
SMART:
 SM00487
SMART:
 SM00490
SMR:
 P21507
SWISSMODEL:
 P21507
UNIPROT:
 P21507


Operon      
Name: srmB         
Operon arrangement:
Transcription unit        Promoter
srmB


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 yfiCp3 2712805 reverse Similarity to the consensus
Read more > 		[ICWHO] [5]
  promoter srmBp4 2712876 forward Similarity to the consensus
Read more > 		[ICWHO] [5]
  promoter srmBp4 2712876 forward Similarity to the consensus
Read more > 		[ICWHO] [5]
  promoter TSS_2874 (cluster) 2712878 forward For this promoter, there
Read more > 		[RS-EPT-CBR] [6]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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


Reference(s)    

 [1] Arunasri K., Adil M., Venu Charan K., Suvro C., Himabindu Reddy S., Shivaji S., 2013, Effect of simulated microgravity on E. coli K12 MG1655 growth and gene expression., PLoS One 8(3):e57860

 [2] Iost I., Jain C., 2019, A DEAD-box protein regulates ribosome assembly through control of ribosomal protein synthesis., Nucleic Acids Res 47(15):8193-8206

 [3] Rabuck-Gibbons JN., Popova AM., Greene EM., Cervantes CF., Lyumkis D., Williamson JR., 2020, SrmB Rescues Trapped Ribosome Assembly Intermediates., J Mol Biol 432(4):978-990

 [4] Sharma H., Anand B., 2016, Fluorescence bimolecular complementation enables facile detection of ribosome assembly defects in Escherichia coli., RNA Biol 13(9):872-82

 [5] 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

 [6] 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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