RegulonDB RegulonDB 10.8: Gene Form
   

rutR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

putA rutA rutR NtrC NtrC PhoP RutR ArcA terminator anti-terminator anti-anti-terminator rutRp rutRp rutRp2 rutRp2 rutAp rutAp

Gene      
Name: rutR    Texpresso search in the literature
Synonym(s): ECK1004, EG12301, b1013, ycdC
Genome position(nucleotides): 1074242 --> 1074880 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
51.33
External database links:  
ASAP:
ABE-0003422
ECHOBASE:
EB2207
OU-MICROARRAY:
b1013
PortEco:
rutR
STRING:
511145.b1013
COLOMBOS: rutR


Product      
Name: DNA-binding transcriptional dual regulator RutR
Synonym(s): RutR, YcdC
Sequence: Get amino acid sequence Fasta Format
Regulator Family: TetR/AcrR
Cellular location: cytosol
Molecular weight: 23.688
Isoelectric point: 9.311
Motif(s):
 
Type Positions Sequence
17 -> 77 SAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIW
70 -> 212 LRQILDIWLAPLKAFREDFAPLAAIKEYIRLKLEVSRDYPQASRLFCMEMLAGAPLLMDELTGDLKALIDEKSALIAGWVKSGKLAPIDPQHLIFMIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGIRPR
23 -> 69 ILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAV
39 -> 58 TRLEQIAELAGVSKTNLLYY

 

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 --> 3.1.2.3 - repressor
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.1 - operon
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0005515 - protein binding
GO:0003700 - DNA-binding transcription factor activity
GO:0000976 - transcription regulatory region sequence-specific DNA binding
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0045892 - negative regulation of transcription, DNA-templated
GO:0045893 - positive regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [AIFS] Automated inference of function from sequence
[APPH] Assay of protein purified to homogeneity
[HIFS] Human inference of function from sequence
[IMP] Inferred from mutant phenotype
Reference(s): [1] Loh KD., et al., 2006
[2] Perez-Rueda E., et al., 2004
[3] Shimada T., et al., 2007
External database links:  
ECOCYC:
PD01352
ECOLIWIKI:
b1013
INTERPRO:
IPR001647
INTERPRO:
IPR036271
INTERPRO:
IPR019915
INTERPRO:
IPR013573
INTERPRO:
IPR009057
MODBASE:
P0ACU2
PANTHER:
PTHR30328
PDB:
4JYK
PDB:
4X1E
PDB:
3LOC
PDB:
4XK4
PFAM:
PF08362
PFAM:
PF00440
PRIDE:
P0ACU2
PRINTS:
PR00455
PRODB:
PRO_000023899
PROSITE:
PS50977
REFSEQ:
NP_415533
SMR:
P0ACU2
UNIPROT:
P0ACU2


Operon      
Name: rutR         
Operon arrangement:
Transcription unit        Promoter
rutR
rutR


Transcriptional Regulation      
Display Regulation             
Repressed by: RutR


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


Reference(s)    

 [1] Loh KD., Gyaneshwar P., Markenscoff Papadimitriou E., Fong R., Kim KS., Parales R., Zhou Z., Inwood W., Kustu S., 2006, A previously undescribed pathway for pyrimidine catabolism., Proc Natl Acad Sci U S A 103(13):5114-9

 [2] Perez-Rueda E., Collado-Vides J., Segovia L., 2004, Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea., Comput Biol Chem 28(5-6):341-50

 [3] Shimada T., Hirao K., Kori A., Yamamoto K., Ishihama A., 2007, RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines., Mol Microbiol 66(3):744-57


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