RegulonDB RegulonDB 11.1: Gene Form
   

grcA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ung eamB grcA Fis CpxR Fis ArcA FNR ArcA FNR CRP Fis PdhR ungp ungp TSS_2888 TSS_2888 TSS_2887 TSS_2887 grcAp1 grcAp1 TSS_2886 (cluster) TSS_2886 (cluster) TSS_2885 (cluster) TSS_2885 (cluster) grcAp2 grcAp2 TSS_2884 (cluster) TSS_2884 (cluster) TSS_2883 TSS_2883 TSS_2882 TSS_2882 TSS_2881 TSS_2881 TSS_2880 TSS_2880 TSS_2879 (cluster) TSS_2879 (cluster) TSS_2878 (cluster) TSS_2878 (cluster) TSS_2877 TSS_2877 TSS_2876 TSS_2876 TSS_2875 TSS_2875

Gene      
Name: grcA    Texpresso search in the literature
Synonym(s): ECK2577, EG11784, b2579, yfiD
Genome position(nucleotides): 2716066 <-- 2716449
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 47.92
External database links:  
ASAP:
 ABE-0008489
ECHOBASE:
 EB1732
ECOLIHUB:
 yfiD
OU-MICROARRAY:
 b2579
STRING:
 511145.b2579
COLOMBOS: grcA


Product      
Name: stress-induced alternate pyruvate formate-lyase subunit
Synonym(s): GrcA, YfiD
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 14.284
Isoelectric point: 4.825
Motif(s):
 
Type Positions Sequence Comment
5 -> 127 IQITKAANDDLLNSFWLLDSEKGEARCIVAKAGYAEDEVVAVSKLGDIEYREVPVEVKPEVRVEGGQHLNVNVLRRETLEDAVKHPEKYPQLTIRVSGYAVRFNSLTPEQQRDVIARTFTESL UniProt: Glycine radical.
16 -> 108 LNSFWLLDSEKGEARCIVAKAGYAEDEVVAVSKLGDIEYREVPVEVKPEVRVEGGQHLNVNVLRRETLEDAVKHPEKYPQLTIRVSGYAVRFN

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.7 - anaerobic respiration
  5 - cell processes --> 5.5 - adaptations --> 5.5.4 - pH
  5 - cell processes --> 5.5 - adaptations --> 5.5.6 - other (mechanical, nutritional, oxidative stress)
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003824 - catalytic activity
GO:0005515 - protein binding
GO:0008861 - formate C-acetyltransferase activity
biological_process GO:0006950 - response to stress
GO:0006567 - threonine catabolic process
Note(s): Note(s): ...[more].
Evidence: [EXP] Inferred from experiment
[EXP-IMP] Inferred from mutant phenotype
Reference(s): [1] Amitai S., et al., 2009
[2] Andorfer MC., et al., 2021
[3] Wagner AF., et al., 2001
External database links:  
ALPHAFOLD:
 P68066
DIP:
 DIP-47913N
ECOCYC:
 EG11784-MONOMER
ECOLIWIKI:
 b2579
INTERPRO:
 IPR011140
INTERPRO:
 IPR019777
INTERPRO:
 IPR001150
MODBASE:
 P68066
PDB:
 6OWR
PFAM:
 PF01228
PRIDE:
 P68066
PRODB:
 PRO_000022835
PROSITE:
 PS51149
PROSITE:
 PS00850
REFSEQ:
 NP_417074
SMR:
 P68066
SWISSMODEL:
 P68066
UNIPROT:
 P68066


Operon      
Name: grcA         
Operon arrangement:
Transcription unit        Promoter
grcA
grcA


Transcriptional Regulation      
Display Regulation             
Activated by: CRP, FNR, ArcA, Fis
Repressed by: FNR, Fur, PdhR


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_2875 2716280 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2876 2716282 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2877 2716291 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2878 (cluster) 2716431 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2879 (cluster) 2716446 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2880 2716470 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2881 2716473 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2882 2716478 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2883 2716482 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2884 (cluster) 2716501 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2885 (cluster) 2716511 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2886 (cluster) 2716522 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2887 2716686 forward nd [RS-EPT-CBR] [4]
  promoter TSS_2888 2716730 forward nd [RS-EPT-CBR] [4]


Evidence    

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


Reference(s)    

 [1] Amitai S., Kolodkin-Gal I., Hananya-Meltabashi M., Sacher A., Engelberg-Kulka H., 2009, Escherichia coli MazF leads to the simultaneous selective synthesis of both "death proteins" and "survival proteins"., PLoS Genet 5(3):e1000390

 [2] Andorfer MC., Backman LRF., Li PL., Ulrich EC., Drennan CL., 2021, Rescuing activity of oxygen-damaged pyruvate formate-lyase by a spare part protein., J Biol Chem 297(6):101423

 [3] Wagner AF., Schultz S., Bomke J., Pils T., Lehmann WD., Knappe J., 2001, YfiD of Escherichia coli and Y06I of bacteriophage T4 as autonomous glycyl radical cofactors reconstituting the catalytic center of oxygen-fragmented pyruvate formate-lyase., Biochem Biophys Res Commun 285(2):456-62

 [4] 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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