RegulonDB RegulonDB 10.9: Gene Form
   

cra gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

cra ilvH mraZ fruL MraZ MraZ MraZ PdhR terminator anti-terminator anti-anti-terminator mraWp1 mraWp1 mraZp mraZp TSS_156 (cluster) TSS_156 (cluster) TSS_155 (cluster) TSS_155 (cluster) TSS_154 TSS_154 TSS_153 TSS_153 fruRp8 fruRp8 TSS_152 TSS_152

Gene      
Name: cra    Texpresso search in the literature
Synonym(s): ECK0081, EG10338, b0080, fruC, fruR, shl
Genome position(nucleotides): 88028 --> 89032 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
54.93
External database links:  
ASAP:
ABE-0000299
CGSC:
18304
ECHOBASE:
EB0334
ECOLIHUB:
fruR
OU-MICROARRAY:
b0080
STRING:
511145.b0080
COLOMBOS: cra


Product      
Name: DNA-binding transcriptional dual regulator Cra
Synonym(s): Cra, FruC, FruR, Shl
Sequence: Get amino acid sequence Fasta Format
Regulator Family: GalR/LacI
Cellular location: cytosol
Molecular weight: 37.999
Isoelectric point: 6.956
Motif(s):
 
Type Positions Sequence
62 -> 312 RSIGLVIPDLENTSYTRIANYLERQARQRGYQLLIACSEDQPDNEMRCIEHLLQRQVDAIIVSTSLPPEHPFYQRWANDPFPIVALDRALDREHFTSVVGADQDDAEMLAEELRKFPAETVLYLGALPELSVSFLREQGFRTAWKDDPREVHFLYANSYEREAAAQLFEKWLETHPMPQALFTTSFALLQGVMDVTLRRDGKLPSDLAIATFGDNELLDFLQCPVLAVAQRHRDVAERVLEIVLASLDEPR
2 -> 50 KLDEIARLAGVSRTTASYVINGKAKQYRVSDKTVEKVMAVVREHNYHPN
1 -> 58 MKLDEIARLAGVSRTTASYVINGKAKQYRVSDKTVEKVMAVVREHNYHPNAVAAGLRA
3 -> 22 LDEIARLAGVSRTTASYVIN

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.1 - glycolysis
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.2 - activator
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.2 - regulon
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
GO:0042802 - identical protein binding
GO:0000976 - transcription regulatory region sequence-specific DNA binding
GO:0000986 - bacterial-type cis-regulatory region sequence-specific DNA binding
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0009750 - response to fructose
GO:2000142 - regulation of DNA-templated transcription, initiation
Reference(s): [1] Jahreis K., et al., 1991
[2] Leclerc G., et al., 1990
[3] Mikulskis A., et al., 1997
[4] Ramseier TM., et al., 1993
[5] Yura T., et al., 1992
External database links:  
DIP:
DIP-35838N
ECOCYC:
PD00521
ECOLIWIKI:
b0080
INTERPRO:
IPR028082
INTERPRO:
IPR012781
INTERPRO:
IPR010982
INTERPRO:
IPR000843
INTERPRO:
IPR001761
MODBASE:
P0ACP1
PDB:
2IKS
PDB:
1UXD
PDB:
1UXC
PFAM:
PF00532
PFAM:
PF00356
PRIDE:
P0ACP1
PRODB:
PRO_000022702
PROSITE:
PS00356
PROSITE:
PS50932
REFSEQ:
NP_414622
SMART:
SM00354
SMR:
P0ACP1
UNIPROT:
P0ACP1


Operon      
Name: cra         
Operon arrangement:
Transcription unit        Promoter
cra


Transcriptional Regulation      
Display Regulation             
Repressed by: PhoB
Growth Conditions:

[1] 

C: Escherichia coli| poor medium| sodium nitrate 20 mM| 37.0 C| OD650 from 0.5 to 0.7
E: Escherichia coli| cra knockout mutant| poor medium| sodium nitrate 20 mM| 37.0 C| OD650 from 0.5 to 0.7

[2] 

C: Escherichia coli| poor medium| sodium nitrite 2.5 mM| 37.0 C| OD650 from 0.5 to 0.7
E: Escherichia coli| cra knockout mutant| poor medium| sodium nitrite 2.5 mM| 37.0 C| OD650 from 0.5 to 0.7

[3] 

C: Escherichia coli| poor medium| 37.0 C| OD650 from 0.5 to 0.7
E: Escherichia coli| cra knockout mutant| poor medium| 37.0 C| OD650 from 0.5 to 0.7



RNA cis-regulatory element    
Attenuation: Transcriptional


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_152 87478 forward nd [RS-EPT-CBR] [6]
  promoter TSS_153 87969 forward nd [RS-EPT-CBR] [6]
  promoter TSS_154 89040 forward nd [RS-EPT-CBR] [6]
  promoter TSS_155 (cluster) 89360 forward For this promoter, there
Read more >
[RS-EPT-CBR] [6]
  promoter TSS_156 (cluster) 89589 forward For this promoter, there
Read more >
[RS-EPT-CBR] [6]


Evidence    

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



Reference(s)    

 [1] Jahreis K., Postma PW., Lengeler JW., 1991, Nucleotide sequence of the ilvH-fruR gene region of Escherichia coli K12 and Salmonella typhimurium LT2., Mol Gen Genet 226(1-2):332-6

 [2] Leclerc G., Noel G., Drapeau GR., 1990, Molecular cloning, nucleotide sequence, and expression of shl, a new gene in the 2-minute region of the genetic map of Escherichia coli., J Bacteriol 172(8):4696-700

 [3] Mikulskis A., Aristarkhov A., Lin EC., 1997, Regulation of expression of the ethanol dehydrogenase gene (adhE) in Escherichia coli by catabolite repressor activator protein Cra., J Bacteriol 179(22):7129-34

 [4] Ramseier TM., Negre D., Cortay JC., Scarabel M., Cozzone AJ., Saier MH., 1993, In vitro binding of the pleiotropic transcriptional regulatory protein, FruR, to the fru, pps, ace, pts and icd operons of Escherichia coli and Salmonella typhimurium., J Mol Biol 234(1):28-44

 [5] Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K., Mizobuchi K., Nakata A., 1992, Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region., Nucleic Acids Res 20(13):3305-8

 [6] 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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