RegulonDB RegulonDB 11.1: Gene Form
   

rtcA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

malT rtcB rtcA rtcAp2 rtcAp2 rtcAp6 rtcAp6 rtcAp1 rtcAp1 TSS_4026 TSS_4026 TSS_4025 TSS_4025 TSS_4024 TSS_4024 TSS_4023 TSS_4023 TSS_4022 TSS_4022 TSS_4021 TSS_4021 TSS_4020 TSS_4020 TSS_4019 TSS_4019 TSS_4018 (cluster) TSS_4018 (cluster) TSS_4017 TSS_4017

Gene      
Name: rtcA    Texpresso search in the literature
Synonym(s): ECK3406, G7750, b3419, b3420, b4475, yhgJ, yhgK
Genome position(nucleotides): 3555833 <-- 3556849
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 59.69
External database links:  
ASAP:
 ABE-0174104
ECHOBASE:
 EB2773
ECOLIHUB:
 rtcA
OU-MICROARRAY:
 b3420
STRING:
 511145.b4475
COLOMBOS: rtcA


Product      
Name: RNA 3'-terminal phosphate cyclase
Synonym(s): RtcA, YhgJ, YhgK
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 35.903
Isoelectric point: 7.263
Motif(s):
 
Type Positions Sequence Comment
12 -> 325 GEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGGTDNPSAPPADFIRRVLEPLLAKIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFNTLQLGERGNIVQMRGEVLLAGVPRHVAEREIATLAGSFSLHEQNIHNLPRDQGPGNTVSLEVESENITERFFVVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQLVLPMALAGAGEFTVAHPSCHLLTNIAVVERFLPVRFS
103 -> 103 Q UniProt: No effect on RNA cyclase activity and RtcA adenylation..
128 -> 128 S UniProt: No effect on RNA cyclase activity and RtcA adenylation..
130 -> 130 P UniProt: 33% of wild-type RNA cyclase activity and 13% of wild-type RtcA adenylation..
134 -> 134 F UniProt: 3% of wild-type RNA cyclase activity and 2% of wild-type RtcA adenylation..

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.3 - RNA modification
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003824 - catalytic activity
GO:0016874 - ligase activity
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0003963 - RNA-3'-phosphate cyclase activity
biological_process GO:0006396 - RNA processing
Note(s): Note(s): ...[more].
External database links:  
ALPHAFOLD:
 P46849
ECOCYC:
 G7750-MONOMER
ECOLIWIKI:
 b4475
INTERPRO:
 IPR036553
INTERPRO:
 IPR037136
INTERPRO:
 IPR023797
INTERPRO:
 IPR020719
INTERPRO:
 IPR017770
INTERPRO:
 IPR013792
INTERPRO:
 IPR013791
INTERPRO:
 IPR000228
MODBASE:
 P46849
PANTHER:
 PTHR11096
PANTHER:
 PTHR11096:SF0
PDB:
 1QMI
PDB:
 3TUX
PDB:
 3TUT
PDB:
 3TV1
PDB:
 3TW3
PDB:
 3KGD
PDB:
 1QMH
PFAM:
 PF01137
PFAM:
 PF05189
PRIDE:
 P46849
PROSITE:
 PS01287
REFSEQ:
 YP_026219
SMR:
 P46849
UNIPROT:
 P46849


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 TSS_4017 3553091 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4018 (cluster) 3553664 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4019 3553757 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4020 3553836 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4021 3553843 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4022 3554481 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4023 3554746 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4024 3555139 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4025 3555545 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4026 3555555 forward nd [RS-EPT-CBR] [1]
  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    

 [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] 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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