RegulonDB RegulonDB 11.1: Gene Form
   

rapA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rapA polB rluA terminator rapAp3 rapAp3 rapAp2 rapAp2 TSS_118 TSS_118 rapAp1 rapAp1 TSS_117 TSS_117 TSS_116 TSS_116 rluAp1 rluAp1

Gene      
Name: rapA    Texpresso search in the literature
Synonym(s): ECK0060, EG11083, b0059, hepA, yabA
Genome position(nucleotides): 60358 <-- 63264
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 54.9
External database links:  
ASAP:
 ABE-0000198
CGSC:
 29491
ECHOBASE:
 EB1075
ECOLIHUB:
 hepA
OU-MICROARRAY:
 b0059
STRING:
 511145.b0059
COLOMBOS: rapA


Product      
Name: RNA polymerase-binding ATPase and RNAP recycling factor
Synonym(s): HepA, RNA polymerase (RNAP)-binding ATPase and RNAP recycling factor, RapA, YabA
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 109.769
Isoelectric point: 4.813
Motif(s):
 
Type Positions Sequence Comment
2 -> 968 PFTLGQRWISDTESELGLGTVVAVDARTVTLLFPSTGENRLYARSDSPVTRVMFNPGDTITSHDGWQMQVEEVKEENGLLTYIGTRLDTEESGVALREVFLDSKLVFSKPQDRLFAGQIDRMDRFALRYRARKYSSEQFRMPYSGLRGQRTSLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPETLQHQWLVEMLRRFNLRFALFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWSEDAPSREYQAIEQLAEHVPGVLLLTATPEQLGMESHFARLRLLDPNRFHDFAQFVEEQKNYRPVADAVAMLLAGNKLSNDELNMLGEMIGEQDIEPLLQAANSDSEDAQSARQELVSMLMDRHGTSRVLFRNTRNGVKGFPKRELHTIKLPLPTQYQTAIKVSGIMGARKSAEDRARDMLYPERIYQEFEGDNATWWNFDPRVEWLMGYLTSHRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTAQSVLVRWYHEGLDAFEHTCPTGRTIYDSVYNDLINYLASPDQTEGFDDLIKNCREQHEALKAQLEQGRDRLLEIHSNGGEKAQALAESIEEQDDDTNLIAFAMNLFDIIGINQDDRGDNMIVLTPSDHMLVPDFPGLSEDGITITFDREVALAREDAQFITWEHPLIRNGLDLILSGDTGSSTISLLKNKALPVGTLLVELIYVVEAQAPKQLQLNRFLPPTPVRMLLDKNGNNLAAQVEFETFNRQLNAVNRHTGSKLVNAVQQDVHAILQLGEAQIEKSARALIDAARNEADEKLSAELSRLEALRAVNPNIRDDELTAIESNRQQVMESLDQAGWRLDALRLIVVTHQ UniProt: RNA polymerase-associated protein RapA.
3 -> 53 FTLGQRWISDTESELGLGTVVAVDARTVTLLFPSTGENRLYARSDSPVTRV
11 -> 11 S UniProt: In Ref. 7; AA sequence..
55 -> 118 FNPGDTITSHDGWQMQVEEVKEENGLLTYIGTRLDTEESGVALREVFLDSKLVFSKPQDRLFAG
164 -> 334 DVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPETLQHQWLVEMLRRFNLRFALFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWSEDAPSREYQAIEQLAEHVPGVLLLTATPEQLGMESHFARLRLLDPN UniProt: Helicase ATP-binding.

 
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
  5 - cell processes --> 5.5 - adaptations
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
molecular_function GO:0140658 - ATP-dependent chromatin remodeler activity
GO:0003676 - nucleic acid binding
GO:0003677 - DNA 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:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0001000 - bacterial-type RNA polymerase core enzyme binding
biological_process GO:0006338 - chromatin remodeling
GO:0006355 - regulation of transcription, DNA-templated
GO:0045893 - positive regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity
Reference(s): [1] Kansara SG., et al., 2011
[2] Kolsto AB., et al., 1993
[3] McKinley BA., et al., 2007
[4] Muzzin O., et al., 1998
[5] Rouby J., et al., 2002
[6] Salmelin C., et al., 2002
[7] Sukhodolets MV., et al., 2001
[8] Sukhodolets MV., et al., 2003
[9] Sukhodolets MV., et al., 1998
[10] Yohannes E., et al., 2005
External database links:  
ALPHAFOLD:
 P60240
DIP:
 DIP-35881N
ECOCYC:
 EG11083-MONOMER
ECOLIWIKI:
 b0059
INTERPRO:
 IPR040765
INTERPRO:
 IPR040766
INTERPRO:
 IPR038718
INTERPRO:
 IPR027417
INTERPRO:
 IPR023949
INTERPRO:
 IPR022737
INTERPRO:
 IPR014001
INTERPRO:
 IPR001650
INTERPRO:
 IPR000330
MODBASE:
 P60240
PDB:
 6BOG
PDB:
 4S20
PFAM:
 PF18337
PFAM:
 PF12137
PFAM:
 PF18339
PFAM:
 PF00271
PFAM:
 PF00176
PRIDE:
 P60240
PRODB:
 PRO_000023677
PROSITE:
 PS51194
PROSITE:
 PS51192
REFSEQ:
 NP_414601
SMART:
 SM00490
SMART:
 SM00487
SMR:
 P60240
UNIPROT:
 P60240


Operon      
Name: rapA-rluA         
Operon arrangement:
Transcription unit        Promoter
rapA-rluA
hepA
rapA


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 rluAp1 60450 reverse nd [COMP-AINF] [11]
  promoter TSS_116 62712 reverse nd [RS-EPT-CBR] [12]
  promoter TSS_117 62992 reverse nd [RS-EPT-CBR] [12]
  promoter TSS_118 63450 reverse nd [RS-EPT-CBR] [12]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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


Reference(s)    

 [1] Kansara SG., Sukhodolets MV., 2011, Oligomerization of the E. coli core RNA polymerase: formation of (α2ββ'ω)2-DNA complexes and regulation of the oligomerization by auxiliary subunits., PLoS One 6(4):e18990

 [2] Kolsto AB., Bork P., Kvaloy K., Lindback T., Gronstadt A., Kristensen T., Sander C., 1993, Prokaryotic members of a new family of putative helicases with similarity to transcription activator SNF2., J Mol Biol 230(2):684-8

 [3] McKinley BA., Sukhodolets MV., 2007, Escherichia coli RNA polymerase-associated SWI/SNF protein RapA: evidence for RNA-directed binding and remodeling activity., Nucleic Acids Res 35(21):7044-60

 [4] Muzzin O., Campbell EA., Xia L., Severinova E., Darst SA., Severinov K., 1998, Disruption of Escherichia coli hepA, an RNA polymerase-associated protein, causes UV sensitivity., J Biol Chem 273(24):15157-61

 [5] Rouby J., Pugniere M., Mani JC., Granier C., Monmouton P., Theulier Saint Germain S., Leonetti JP., 2002, Characterization of monoclonal antibodies against Escherichia coli core RNA polymerase., Biochem J 361(Pt 2):347-54

 [6] Salmelin C., Vilpo J., 2002, Chlorambucil-induced high mutation rate and suicidal gene downregulation in a base excision repair-deficient Escherichia coli strain., Mutat Res 500(1-2):125-34

 [7] Sukhodolets MV., Cabrera JE., Zhi H., Jin DJ., 2001, RapA, a bacterial homolog of SWI2/SNF2, stimulates RNA polymerase recycling in transcription., Genes Dev 15(24):3330-41

 [8] Sukhodolets MV., Garges S., Jin DJ., 2003, Purification and activity assays of RapA, the RNA polymerase-associated homolog of the SWI/SNF protein superfamily., Methods Enzymol 370:283-90

 [9] Sukhodolets MV., Jin DJ., 1998, RapA, a novel RNA polymerase-associated protein, is a bacterial homolog of SWI2/SNF2., J Biol Chem 273(12):7018-23

 [10] Yohannes E., Thurber AE., Wilks JC., Tate DP., Slonczewski JL., 2005, Polyamine stress at high pH in Escherichia coli K-12., BMC Microbiol 5:59

 [11] 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

 [12] 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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