RegulonDB RegulonDB 10.10: Gene Form
   

deaD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

deaD mtr nlpI yrbN TyrR TyrR TrpR TrpR anti-anti-terminator anti-terminator terminator TSS_3438 TSS_3438 TSS_3437 TSS_3437 TSS_3436 TSS_3436 yrbNp yrbNp TSS_3435 TSS_3435 deaDp1 deaDp1 TSS_3434 TSS_3434 TSS_3433 TSS_3433 TSS_3432 TSS_3432 mtrp1 mtrp1 mtrp2 mtrp2

Gene      
Name: deaD    Texpresso search in the literature
Synonym(s): ECK3150, EG10215, b3162, csdA, mssB, rhlD
Genome position(nucleotides): 3305971 <-- 3307860 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 55.56
External database links:  
ASAP:
 ABE-0010392
CGSC:
 33472
ECHOBASE:
 EB0211
ECOLIHUB:
 deaD
MIM:
 268305
MIM:
 608546
OU-MICROARRAY:
 b3162
STRING:
 511145.b3162
COLOMBOS: deaD


Product      
Name: ATP-dependent RNA helicase DeaD
Synonym(s): CsdA, DEAD-box RNA helicase, DeaD, MssB, RhlD
Sequence: Get amino acid sequence Fasta Format
Cellular location: ribosome,cytosol
Molecular weight: 70.546
Isoelectric point: 9.136
Motif(s):
 
Type Positions Sequence
568 -> 629 GGERRGGGRGFGGERREGGRNFSGERREGGRGDGRRFSGERREGRAPRRDDSTGRRRFGGDA
6 -> 34 TTFADLGLKAPILEALNDLGYEKPSPIQA
31 -> 195 PIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLQNLDPELKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDVETIMAQIPEGHQTALFSATMPEAIR
444 -> 444 A
489 -> 558 YRIEVGRDDGVEVRHIVGAIANEGDISSRYIGNIKLFASHSTIELPKGMPGEVLQHFTRTRILNKPMNMQ

 
Classification:
Multifun Terms (GenProtEC)  
  6 - cell structure --> 6.6 - ribosomes
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0005840 - ribosome
molecular_function GO:0003676 - nucleic acid binding
GO:0004386 - helicase activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0016817 - hydrolase activity, acting on acid anhydrides
GO:0016887 - ATP hydrolysis activity
GO:0003723 - RNA binding
GO:0000166 - nucleotide binding
GO:0003724 - RNA helicase activity
GO:0005524 - ATP binding
GO:0042803 - protein homodimerization activity
GO:0033592 - RNA strand annealing activity
biological_process GO:0006401 - RNA catabolic process
GO:0000027 - ribosomal large subunit assembly
GO:0009314 - response to radiation
GO:0045727 - positive regulation of translation
GO:0048255 - mRNA stabilization
GO:0070417 - cellular response to cold
External database links:  
DIP:
 DIP-35752N
ECOCYC:
 EG10215-MONOMER
ECOLIWIKI:
 b3162
INTERPRO:
 IPR012677
INTERPRO:
 IPR034415
INTERPRO:
 IPR028618
INTERPRO:
 IPR000629
INTERPRO:
 IPR001650
INTERPRO:
 IPR005580
INTERPRO:
 IPR011545
INTERPRO:
 IPR014001
INTERPRO:
 IPR014014
INTERPRO:
 IPR021046
INTERPRO:
 IPR027417
PDB:
 5B88
PDB:
 5GJU
PDB:
 5GI4
PFAM:
 PF12343
PFAM:
 PF03880
PFAM:
 PF00271
PFAM:
 PF00270
PRIDE:
 P0A9P6
PRODB:
 PRO_000022422
PROSITE:
 PS51194
PROSITE:
 PS51195
PROSITE:
 PS51192
PROSITE:
 PS00039
REFSEQ:
 NP_417631
SMART:
 SM00490
SMART:
 SM00487
SMR:
 P0A9P6
SWISSMODEL:
 P0A9P6
UNIPROT:
 P0A9P6


Operon      
Name: yrbN-deaD         
Operon arrangement:
Transcription unit        Promoter
yrbN-deaD
yrbN-deaD
deaD


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_3432 3307002 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3433 3307564 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3434 3307652 reverse nd [RS-EPT-CBR] [1]
  promoter deaDp1 3307909 reverse nd [ICWHO] [2]
  promoter TSS_3435 3308055 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3436 3308214 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3437 3308694 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3438 3308871 reverse nd [RS-EPT-CBR] [1]


Evidence    

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

 [ICWHO] Inferred computationally without human oversight


Reference(s)    

 [1] 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.

 [2] 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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