RegulonDB RegulonDB 11.1: Gene Form
   

rtcB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rtcR rtcB rtcA glpR IHF IHF rtcBp rtcBp rtcAp2 rtcAp2 rtcAp6 rtcAp6 rtcAp1 rtcAp1

Gene      
Name: rtcB    Texpresso search in the literature
Synonym(s): ECK3407, G7751, b3421, yhgL
Genome position(nucleotides): 3556853 <-- 3558079
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 50.94
External database links:  
ASAP:
 ABE-0011170
ECHOBASE:
 EB2774
ECOLIHUB:
 rtcB
OU-MICROARRAY:
 b3421
STRING:
 511145.b3421
COLOMBOS: rtcB


Shine dalgarno      
Sequence: acaacgaaaaGAGAAAaacaaAAT


Product      
Name: RNA-splicing ligase
Synonym(s): RNA ligase, RtcB, YhgL
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 45.222
Isoelectric point: 6.287
Motif(s):
 
Type Positions Sequence Comment
29 -> 408 QLINTAKMPFIFKHIAVMPDVHLGKGSTIGSVIPTKGAIIPAAVGVDIGCGMNALRTALTAEDLPENLAELRQAIETAVPHGRTTGRCKRDKGAWENPPVNVDAKWAELEAGYQWLTQKYPRFLNTNNYKHLGTLGTGNHFIEICLDESDQVWIMLHSGSRGIGNAIGTYFIDLAQKEMQETLETLPSRDLAYFMEGTEYFDDYLKAVAWAQLFASLNRDAMMENVVTALQSITQKTVRQPQTLAMEEINCHHNYVQKEQHFGEEIYVTRKGAVSARAGQYGIIPGSMGAKSFIVRGLGNEESFCSCSHGAGRVMSRTKAKKLFSVEDQIRATAHVECRKDAEVIDEIPMAYKDIDAVMAAQSDLVEVIYTLRQVVCVKG
75 -> 75 D UniProt: Almost no guanylation activity. Can ligate pre-guanylated nucleotide substrates..
78 -> 78 C UniProt: No activity..
84 -> 84 R UniProt: In Ref. 1; AAA58219..
167 -> 167 N UniProt: Retains approximately half of overall wild-type activity. Shows increased nucleotide guanylation activity..

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related
  2 - information transfer --> 2.2 - RNA related
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0046872 - metal ion binding
GO:0016874 - ligase activity
GO:0008452 - RNA ligase activity
GO:0000166 - nucleotide binding
GO:0005525 - GTP binding
GO:0003909 - DNA ligase activity
GO:0030145 - manganese ion binding
biological_process GO:0006266 - DNA ligation
GO:0006281 - DNA repair
GO:0006974 - cellular response to DNA damage stimulus
GO:0006396 - RNA processing
GO:0008033 - tRNA processing
GO:0042245 - RNA repair
Note(s): Note(s): ...[more].
Reference(s): [1] Peach SE., et al., 2015
External database links:  
ALPHAFOLD:
 P46850
ECOCYC:
 G7751-MONOMER
ECOLIWIKI:
 b3421
INTERPRO:
 IPR001233
INTERPRO:
 IPR036025
MODBASE:
 P46850
PFAM:
 PF01139
PRIDE:
 P46850
PRODB:
 PRO_000023892
PROSITE:
 PS01288
REFSEQ:
 NP_417879
SMR:
 P46850
UNIPROT:
 P46850


Operon      
Name: rtcBA         
Operon arrangement:
Transcription unit        Promoter
rtcBA


Transcriptional Regulation      
Display Regulation             
Activated by: RtcR, IHF


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 rtcAp1 3556880 reverse nd [COMP-AINF] [2]
  promoter rtcAp6 3556948 reverse nd [COMP-AINF] [2]
  promoter rtcAp2 3557002 reverse nd [COMP-AINF] [2]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Peach SE., York K., Hesselberth JR., 2015, Global analysis of RNA cleavage by 5'-hydroxyl RNA sequencing., Nucleic Acids Res 43(17):e108

 [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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