RegulonDB RegulonDB 11.1: Gene Form
   

crp gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yhfK crp yhfA Fis Fis Fis Fis CRP Fis Fis Cra CRP Fis ppGpp terminator TSS_3961 (cluster) TSS_3961 (cluster) TSS_3960 (cluster) TSS_3960 (cluster) TSS_3959 TSS_3959 TSS_3958 TSS_3958 TSS_3957 (cluster) TSS_3957 (cluster) TSS_3956 TSS_3956 crpp2 crpp2 crpp3 crpp3 crpp1 crpp1 TSS_3954 TSS_3954 yhfAp yhfAp TSS_3953 (cluster) TSS_3953 (cluster)

Gene      
Name: crp    Texpresso search in the literature
Synonym(s): ECK3345, EG10164, b3357, cap, csm, gurB
Genome position(nucleotides): 3486120 --> 3486752
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.45
External database links:  
ASAP:
 ABE-0010970
CGSC:
 906
ECHOBASE:
 EB0162
ECOLIHUB:
 crp
OU-MICROARRAY:
 b3357
STRING:
 511145.b3357
COLOMBOS: crp


Product      
Name: DNA-binding transcriptional dual regulator CRP
Synonym(s): Cap, Crp, Csm, GurB
Sequence: Get amino acid sequence Fasta Format
Regulator Family: CRP
Cellular location: cytosol
Molecular weight: 23.64
Isoelectric point: 8.463
Motif(s):
 
Type Positions Sequence Comment
2 -> 210 VLGKPQTDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGTR UniProt: cAMP-activated global transcriptional regulator CRP.
20 -> 22 HIH UniProt: Activating region 2 (AR2); probably contacts the N-terminus of RpoA; Sequence Annotation Type: region of interest.
22 -> 22 H UniProt: Decreased transcription activation at class II promoters, decreased interaction with RNAP, binds DNA..
23 -> 109 KYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQV
29 -> 29 T UniProt: In Ref. 4; BAE77933..

 
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 --> 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 --> 3.3.4 - global
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0032993 - protein-DNA complex
molecular_function GO:0003680 - minor groove of adenine-thymine-rich DNA binding
GO:0003677 - DNA binding
GO:0005515 - protein binding
GO:0003700 - DNA-binding transcription factor activity
GO:0000166 - nucleotide binding
GO:0043565 - sequence-specific DNA binding
GO:0030552 - cAMP binding
GO:0042802 - identical protein binding
GO:0008301 - DNA binding, bending
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
GO:0045892 - negative regulation of transcription, DNA-templated
GO:0045893 - positive regulation of transcription, DNA-templated
GO:0045013 - carbon catabolite repression of transcription
Evidence: [COMP-AINF-FN-FROM-SEQ] Automated inference of function from sequence
[EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[EXP-IMP] Inferred from mutant phenotype
Reference(s): [1] Beatty CM., et al., 2003
[2] Belyaeva TA., et al., 2000
[3] Hanamura A., et al., 1992
[4] Korner H., et al., 2003
[5] Ramseier TM., et al., 1995
[6] Wade JT., et al., 2001
[7] Wickstrum JR., et al., 2005
[8] Williams RM., et al., 1996
[9] Zheng D., et al., 2004
External database links:  
ALPHAFOLD:
 P0ACJ8
DIP:
 DIP-29232N
ECOCYC:
 PD00257
ECOLIWIKI:
 b3357
INTERPRO:
 IPR000595
INTERPRO:
 IPR036388
INTERPRO:
 IPR036390
INTERPRO:
 IPR012318
INTERPRO:
 IPR014710
INTERPRO:
 IPR018335
INTERPRO:
 IPR018488
INTERPRO:
 IPR018490
MINT:
 P0ACJ8
MODBASE:
 P0ACJ8
PDB:
 1CGP
PDB:
 1G6N
PDB:
 1HW5
PDB:
 1I5Z
PDB:
 1I6X
PDB:
 1J59
PDB:
 1LB2
PDB:
 1O3Q
PDB:
 1O3R
PDB:
 1O3S
PDB:
 1O3T
PDB:
 1RUN
PDB:
 1RUO
PDB:
 1ZRC
PDB:
 1ZRD
PDB:
 1ZRE
PDB:
 1ZRF
PDB:
 2CGP
PDB:
 2GAP
PDB:
 2GZW
PDB:
 2WC2
PDB:
 3FWE
PDB:
 3HIF
PDB:
 3IYD
PDB:
 3KCC
PDB:
 3N4M
PDB:
 3QOP
PDB:
 3RDI
PDB:
 3ROU
PDB:
 3RPQ
PDB:
 3RYP
PDB:
 3RYR
PDB:
 4BH9
PDB:
 4BHP
PDB:
 4FT8
PDB:
 4HZF
PDB:
 4I01
PDB:
 4I02
PDB:
 4I09
PDB:
 4I0A
PDB:
 4I0B
PDB:
 4R8H
PDB:
 5CIZ
PFAM:
 PF00027
PFAM:
 PF13545
PRIDE:
 P0ACJ8
PRINTS:
 PR00034
PRODB:
 PRO_000022333
PROSITE:
 PS50042
PROSITE:
 PS00889
PROSITE:
 PS00888
PROSITE:
 PS00042
PROSITE:
 PS51063
REFSEQ:
 NP_417816
SMART:
 SM00100
SMART:
 SM00419
SMR:
 P0ACJ8
UNIPROT:
 P0ACJ8


Operon      
Name: crp         
Operon arrangement:
Transcription unit        Promoter
crp
crp
crp


Transcriptional Regulation      
Display Regulation             
Activated by: CRP, Cra
Repressed by: CRP, Fis


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_3953 (cluster) 3485846 reverse nd [RS-EPT-CBR] [10]
  promoter TSS_3954 3485952 reverse nd [RS-EPT-CBR] [10]
  promoter TSS_3956 3486049 forward nd [RS-EPT-CBR] [10]
  promoter TSS_3957 (cluster) 3486051 forward nd [RS-EPT-CBR] [10]
  promoter TSS_3958 3486110 forward nd [RS-EPT-CBR] [10]
  promoter TSS_3959 3486595 forward nd [RS-EPT-CBR] [10]
  promoter TSS_3960 (cluster) 3486615 forward nd [RS-EPT-CBR] [10]
  promoter TSS_3961 (cluster) 3486621 forward nd [RS-EPT-CBR] [10]


Evidence    

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


Reference(s)    

 [1] Beatty CM., Browning DF., Busby SJ., Wolfe AJ., 2003, Cyclic AMP receptor protein-dependent activation of the Escherichia coli acsP2 promoter by a synergistic class III mechanism., J Bacteriol 185(17):5148-57

 [2] Belyaeva TA., Wade JT., Webster CL., Howard VJ., Thomas MS., Hyde EI., Busby SJ., 2000, Transcription activation at the Escherichia coli melAB promoter: the role of MelR and the cyclic AMP receptor protein., Mol Microbiol 36(1):211-22

 [3] Hanamura A., Aiba H., 1992, A new aspect of transcriptional control of the Escherichia coli crp gene: positive autoregulation., Mol Microbiol 6(17):2489-97

 [4] Korner H., Sofia HJ., Zumft WG., 2003, Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: exploiting the metabolic spectrum by controlling alternative gene programs., FEMS Microbiol Rev 27(5):559-92

 [5] Ramseier TM., Saier MH., 1995, cAMP-cAMP receptor protein complex: five binding sites in the control region of the Escherichia coli mannitol operon., Microbiology 141 ( Pt 8):1901-7

 [6] Wade JT., Belyaeva TA., Hyde EI., Busby SJ., 2001, A simple mechanism for co-dependence on two activators at an Escherichia coli promoter., EMBO J 20(24):7160-7

 [7] Wickstrum JR., Santangelo TJ., Egan SM., 2005, Cyclic AMP receptor protein and RhaR synergistically activate transcription from the L-rhamnose-responsive rhaSR promoter in Escherichia coli., J Bacteriol 187(19):6708-18

 [8] Williams RM., Rhodius VA., Bell AI., Kolb A., Busby SJ., 1996, Orientation of functional activating regions in the Escherichia coli CRP protein during transcription activation at class II promoters., Nucleic Acids Res 24(6):1112-8

 [9] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [10] 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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