RegulonDB RegulonDB 11.1: Gene Form
   

rsd gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

thiC nudC rsd Cis-reg; riboswitch rsdp1 rsdp1 rsdp2 rsdp2 nudCp2 nudCp2 nudCp5 nudCp5 TSS_4819 TSS_4819 TSS_4818 (cluster) TSS_4818 (cluster) TSS_4817 TSS_4817 thiCp thiCp

Gene      
Name: rsd    Texpresso search in the literature
Synonym(s): ECK3987, EG11738, b3995, yjaE
Genome position(nucleotides): 4196332 <-- 4196808
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.06
External database links:  
ASAP:
 ABE-0013059
ECHOBASE:
 EB1689
ECOLIHUB:
 rsd
OU-MICROARRAY:
 b3995
STRING:
 511145.b3995
COLOMBOS: rsd


Product      
Name: regulator of sigma D
Synonym(s): Rsd, YjaE, regulator of sigma;70 (sigma;D), stationary phase protein
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 18.243
Isoelectric point: 5.931
Motif(s):
 
Type Positions Sequence Comment
1 -> 147 MLNQLDNLTERVRGSNKLVDRWLHVRKHLLVAYYNLVGIKPGKESYMRLNEKALDDFCQSLVDYLSAGHFSIYERILHKLEGNGQLARAAKIWPQLEANTQQIMDYYDSSLETAIDHDNYLEFQQVLSDIGEALEARFVLEDKLILL
59 -> 71 QSLVDYLSAGHFS UniProt: Interaction with RpoD; Sequence Annotation Type: region of interest.
101 -> 108 QQIMDYYD UniProt: Interaction with RpoD; Sequence Annotation Type: region of interest.

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.1 - sigma factors, anti-sigmafactors
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.3 - stimulon
Gene Ontology Terms (GO)  
cellular_component GO:1903865 - sigma factor antagonist complex
GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0005515 - protein binding
GO:0016989 - sigma factor antagonist activity
GO:0001000 - bacterial-type RNA polymerase core enzyme binding
biological_process GO:0030813 - positive regulation of nucleotide catabolic process
GO:0010922 - positive regulation of phosphatase activity
GO:0006355 - regulation of transcription, DNA-templated
GO:0045892 - negative regulation of transcription, DNA-templated
GO:0010468 - regulation of gene expression
GO:0015968 - stringent response
GO:1903507 - negative regulation of nucleic acid-templated transcription
Note(s): Note(s): ...[more].
Evidence: [EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity
[EXP-IGI] Inferred from genetic interaction
Reference(s): [1] Azam TA., et al., 2000
[2] Hofmann N., et al., 2011
[3] Jishage M., et al., 1998
[4] Jishage M., et al., 2002
[5] Lee JW., et al., 2018
[6] Neira JL., et al., 2018
External database links:  
ALPHAFOLD:
 P0AFX4
DIP:
 DIP-10800N
ECOCYC:
 EG11738-MONOMER
ECOLIWIKI:
 b3995
INTERPRO:
 IPR023785
INTERPRO:
 IPR038309
INTERPRO:
 IPR007448
PDB:
 4XWJ
PDB:
 2P7V
PFAM:
 PF04353
PRIDE:
 P0AFX4
PRODB:
 PRO_000023876
REFSEQ:
 NP_418423
SMR:
 P0AFX4
UNIPROT:
 P0AFX4


Operon      
Name: rsd         
Operon arrangement:
Transcription unit        Promoter
rsd
rsd


Transcriptional Regulation      
Display Regulation             
Activated by: SlyA, McbR, RcdA, SdiA
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_4817 4196300 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_4818 (cluster) 4196683 forward nd [RS-EPT-CBR] [7]
  promoter TSS_4819 4196698 forward nd [RS-EPT-CBR] [7]
  promoter nudCp5 4196714 forward nd [COMP-AINF] [8]
  promoter nudCp2 4196719 forward nd [COMP-AINF] [8]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Azam TA., Hiraga S., Ishihama A., 2000, Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid., Genes Cells 5(8):613-26

 [2] Hofmann N., Wurm R., Wagner R., 2011, The E. coli anti-sigma factor Rsd: studies on the specificity and regulation of its expression., PLoS One 6(5):e19235

 [3] Jishage M., Ishihama A., 1998, A stationary phase protein in Escherichia coli with binding activity to the major sigma subunit of RNA polymerase., Proc Natl Acad Sci U S A 95(9):4953-8

 [4] Jishage M., Kvint K., Shingler V., Nystrom T., 2002, Regulation of sigma factor competition by the alarmone ppGpp., Genes Dev 16(10):1260-70

 [5] Lee JW., Park YH., Seok YJ., 2018, Rsd balances (p)ppGpp level by stimulating the hydrolase activity of SpoT during carbon source downshift in Escherichia coli., Proc Natl Acad Sci U S A 115(29):E6845-E6854

 [6] Neira JL., Hornos F., Cozza C., Camara-Artigas A., Abian O., Velazquez-Campoy A., 2018, The histidine phosphocarrier protein, HPr, binds to the highly thermostable regulator of sigma D protein, Rsd, and its isolated helical fragments., Arch Biochem Biophys 639:26-37

 [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.

 [8] 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

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