RegulonDB RegulonDB 11.1: Gene Form
   

hrpA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

hrpA ydcF azoR ArcA SoxS Rob MarA anti-terminator terminator terminator ydcFp4 ydcFp4 TSS_1802 TSS_1802 TSS_1801 TSS_1801 ydcFp3 ydcFp3 azoRp8 azoRp8 azoRp6 azoRp6 azoRp azoRp azoRp1 azoRp1 TSS_1800 TSS_1800

Gene      
Name: hrpA    Texpresso search in the literature
Synonym(s): ECK1406, G6732, b1413
Genome position(nucleotides): 1483061 --> 1486963
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.45
External database links:  
ASAP:
 ABE-0004718
ECHOBASE:
 EB2772
ECOLIHUB:
 hrpA
OU-MICROARRAY:
 b1413
STRING:
 511145.b1413
COLOMBOS: hrpA


Product      
Name: ATP-dependent 3'→5' RNA helicase HrpA
Synonym(s): HrpA
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 149.027
Isoelectric point: 8.024
Motif(s):
 
Type Positions Sequence Comment
85 -> 233 DILEAIRDHQVVIVAGETGSGKTTQLPKICMELGRGIKGLIGHTQPRRLAARTVANRIAEELKTEPGGCIGYKVRFSDHVSDNTMVKLMTDGILLAEIQQDRLLMQYDTIIIDEAHERSLNIDFLLGYLKELLPRRPDLKIIITSATID
87 -> 250 LEAIRDHQVVIVAGETGSGKTTQLPKICMELGRGIKGLIGHTQPRRLAARTVANRIAEELKTEPGGCIGYKVRFSDHVSDNTMVKLMTDGILLAEIQQDRLLMQYDTIIIDEAHERSLNIDFLLGYLKELLPRRPDLKIIITSATIDPERFSRHFNNAPIIEVS UniProt: Helicase ATP-binding.
100 -> 107 GETGSGKT UniProt: ATP.
106 -> 106 K K → A: ssRNA-stimulated ATPase activity is reduced
152 -> 152 G UniProt: In Ref. 1; BAA07685..

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.3 - RNA modification
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003676 - nucleic acid binding
GO:0004386 - helicase activity
GO:0016787 - hydrolase activity
GO:0016887 - ATP hydrolysis activity
GO:0003723 - RNA binding
GO:0000166 - nucleotide binding
GO:0003724 - RNA helicase activity
GO:0005524 - ATP binding
GO:0034458 - 3'-5' RNA helicase activity
biological_process GO:0009451 - RNA modification
GO:0006397 - mRNA processing
GO:0000462 - maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
Note(s): Note(s): ...[more].
Reference(s): [1] Price MN., et al., 2018
External database links:  
ALPHAFOLD:
 P43329
DIP:
 DIP-9937N
ECOCYC:
 G6732-MONOMER
ECOLIWIKI:
 b1413
INTERPRO:
 IPR027417
INTERPRO:
 IPR001650
INTERPRO:
 IPR024590
INTERPRO:
 IPR003593
INTERPRO:
 IPR007502
INTERPRO:
 IPR010222
INTERPRO:
 IPR011545
INTERPRO:
 IPR011709
INTERPRO:
 IPR014001
MODBASE:
 P43329
PDB:
 7AKP
PDB:
 6ZWX
PDB:
 6ZWW
PFAM:
 PF11898
PFAM:
 PF07717
PFAM:
 PF04408
PFAM:
 PF00271
PFAM:
 PF00270
PRIDE:
 P43329
PRODB:
 PRO_000022922
PROSITE:
 PS51192
PROSITE:
 PS51194
REFSEQ:
 NP_415931
SMART:
 SM00490
SMART:
 SM00487
SMART:
 SM00382
SMART:
 SM00847
SMR:
 P43329
UNIPROT:
 P43329


Operon      
Name: hrpA         
Operon arrangement:
Transcription unit        Promoter
hrpA


RNA cis-regulatory element    
Attenuation: Translational


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_1800 1482829 forward nd [RS-EPT-CBR] [2]
  promoter azoRp1 1482873 reverse nd [COMP-AINF] [3]
  promoter azoRp6 1482927 reverse nd [COMP-AINF] [3]
  promoter azoRp8 1482991 reverse nd [COMP-AINF] [3]
  promoter ydcFp3 1487202 forward nd [COMP-AINF] [3]
  promoter TSS_1801 1487204 forward nd [RS-EPT-CBR] [2]
  promoter TSS_1802 1487218 forward nd [RS-EPT-CBR] [2]
  promoter ydcFp4 1487231 forward nd [COMP-AINF] [3]


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] Price MN., Wetmore KM., Waters RJ., Callaghan M., Ray J., Liu H., Kuehl JV., Melnyk RA., Lamson JS., Suh Y., Carlson HK., Esquivel Z., Sadeeshkumar H., Chakraborty R., Zane GM., Rubin BE., Wall JD., Visel A., Bristow J., Blow MJ., Arkin AP., Deutschbauer AM., 2018, Mutant phenotypes for thousands of bacterial genes of unknown function., Nature 557(7706):503-509

 [2] 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.

 [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

RegulonDB