RegulonDB RegulonDB 10.10: Gene Form
   

radD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

radD rsuA rplY DksA-ppGpp DksA-ppGpp terminator terminator rplVp rplVp rplYp6 rplYp6 rplYp5 rplYp5 rplYp3 rplYp3 radDp radDp TSS_2479 TSS_2479 rsuAp3 rsuAp3 rsuAp2 rsuAp2

Gene      
Name: radD    Texpresso search in the literature
Synonym(s): ECK2178, EG12045, b2184, yejH, yejI, yejJ
Genome position(nucleotides): 2280632 --> 2282392 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.15
External database links:  
ASAP:
 ABE-0007228
ECHOBASE:
 EB1979
ECOLIHUB:
 yejH
MIM:
 610651
MIM:
 616390
OU-MICROARRAY:
 b2184
STRING:
 511145.b2184
COLOMBOS: radD


Product      
Name: putative DNA repair helicase RadD
Synonym(s): RadD, YejH, YejI, YejJ
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 66.413
Isoelectric point: 7.775
Motif(s):
 
Type Positions Sequence
241 -> 386 IISQIMEFAATRKGVMIFAATVEHAKEIVGLLPAEDAALITGDTPGAERDVLIENFKAQRFRYLVNVAVLTTGFDAPHVDLIAILRPTESVSLYQQIVGRGLRLAPGKTDCLILDYAGNPHDLYAPEVGTPKGKSDNVPVQVFCPA
18 -> 171 NHFRRHKTPAVIVLPTGAGKSLVIAELARLARGRVLVLAHVKELVAQNHAKYQALGLEADIFAAGLKRKESHGKVVFGSVQSVARNLDAFQGEFSLLIVDECHRIGDDEESQYQQILTHLTKVNPHLRLLGLTATPFRLGKGWIYQFHYHGMVR
34 -> 38 GAGKS
187 -> 365 LRYMIKHGYLTPPERLDMPVVQYDFSRLQAQSNGLFSEADLNRELKKQQRITPHIISQIMEFAATRKGVMIFAATVEHAKEIVGLLPAEDAALITGDTPGAERDVLIENFKAQRFRYLVNVAVLTTGFDAPHVDLIAILRPTESVSLYQQIVGRGLRLAPGKTDCLILDYAGNPHDLYA
314 -> 322 FDAPHVDLI

 
Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.6 - protection
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003678 - DNA helicase activity
GO:0004386 - helicase activity
GO:0003697 - single-stranded DNA binding
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0016887 - ATP hydrolysis activity
GO:0046872 - metal ion binding
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0008270 - zinc ion binding
biological_process GO:0051301 - cell division
GO:0006281 - DNA repair
GO:0006412 - translation
GO:0006974 - cellular response to DNA damage stimulus
GO:0009410 - response to xenobiotic stimulus
GO:0032508 - DNA duplex unwinding
GO:0006302 - double-strand break repair
GO:0010212 - response to ionizing radiation
GO:0006301 - postreplication repair
Note(s): Note(s): ...[more].
Reference(s): [1] Cooper DL., et al., 2015
[2] Kumar A., et al., 2016
External database links:  
ECOCYC:
 EG12045-MONOMER
ECOLIWIKI:
 b2184
INTERPRO:
 IPR014001
INTERPRO:
 IPR027417
INTERPRO:
 IPR011332
INTERPRO:
 IPR006935
INTERPRO:
 IPR001650
MODBASE:
 P33919
PDB:
 6JDE
PFAM:
 PF04851
PFAM:
 PF00271
PRIDE:
 P33919
PROSITE:
 PS51194
PROSITE:
 PS51192
REFSEQ:
 NP_416689
SMART:
 SM00487
SMART:
 SM00490
SMR:
 P33919
UNIPROT:
 P33919


Operon      
Name: radD         
Operon arrangement:
Transcription unit        Promoter
radD


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 rsuAp2 2280545 reverse nd [ICWHO] [3]
  promoter rsuAp3 2280548 reverse nd [ICWHO] [3]
  promoter TSS_2479 2280608 forward nd [RS-EPT-CBR] [4]
  promoter rplYp3 2282433 forward nd [ICWHO] [3]
  promoter rplYp5 2282437 forward nd [ICWHO] [3]
  promoter rplYp6 2282438 forward nd [ICWHO] [3]


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] Cooper DL., Boyle DC., Lovett ST., 2015, Genetic analysis of Escherichia coli RadA: functional motifs and genetic interactions., Mol Microbiol 95(5):769-79

 [2] Kumar A., Beloglazova N., Bundalovic-Torma C., Phanse S., Deineko V., Gagarinova A., Musso G., Vlasblom J., Lemak S., Hooshyar M., Minic Z., Wagih O., Mosca R., Aloy P., Golshani A., Parkinson J., Emili A., Yakunin AF., Babu M., 2016, Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli., Cell Rep 14(3):648-61

 [3] 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

 [4] 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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