RegulonDB RegulonDB 10.10: Gene Form
   

gyrB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

gyrB recF yidB Fis Fis anti-terminator terminator TSS_4265 (cluster) TSS_4265 (cluster) gyrBp gyrBp TSS_4264 TSS_4264 TSS_4263 TSS_4263 TSS_4262 TSS_4262 TSS_4261 TSS_4261 TSS_4260 (cluster) TSS_4260 (cluster) TSS_4259 TSS_4259 yidBp3 yidBp3

Gene      
Name: gyrB    Texpresso search in the literature
Synonym(s): ECK3691, EG10424, acrB, b3699, cou, himB, hisU, hopA, nalC, parA, pcbA, pcpA
Genome position(nucleotides): 3877705 <-- 3880119 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 54.99
External database links:  
ASAP:
 ABE-0012093
CGSC:
 650
ECHOBASE:
 EB0419
ECOLIHUB:
 gyrB
OU-MICROARRAY:
 b3699
STRING:
 511145.b3699
COLOMBOS: gyrB


Product      
Name: DNA gyrase subunit B
Synonym(s): AcrB, Cou, GyrB, HimB, HisU, HopA, NalC, ParA, PcbA, PcpA
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 89.95
Isoelectric point: 5.931
Motif(s):
 
Type Positions Sequence
38 -> 38 H
136 -> 136 R
164 -> 164 G
385 -> 385 A
419 -> 531 ELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQ

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related --> 2.1.1 - DNA replication
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0005694 - chromosome
GO:0009330 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex
molecular_function GO:0003677 - DNA binding
GO:0003916 - DNA topoisomerase activity
GO:0005515 - protein binding
GO:0008094 - ATP-dependent activity, acting on DNA
GO:0016853 - isomerase activity
GO:0046872 - metal ion binding
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0003918 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
GO:0034335 - DNA negative supercoiling activity
biological_process GO:0006261 - DNA-dependent DNA replication
GO:0006351 - transcription, DNA-templated
GO:0009410 - response to xenobiotic stimulus
GO:0046677 - response to antibiotic
GO:0006265 - DNA topological change
Note(s): Note(s): ...[more].
External database links:  
DIP:
 DIP-48005N
ECOCYC:
 EG10424-MONOMER
ECOLIWIKI:
 b3699
INTERPRO:
 IPR006171
INTERPRO:
 IPR011557
INTERPRO:
 IPR041423
INTERPRO:
 IPR013759
INTERPRO:
 IPR013760
INTERPRO:
 IPR014721
INTERPRO:
 IPR018522
INTERPRO:
 IPR020568
INTERPRO:
 IPR034160
INTERPRO:
 IPR036890
INTERPRO:
 IPR003594
INTERPRO:
 IPR002288
INTERPRO:
 IPR001241
INTERPRO:
 IPR013506
PDB:
 4DUH
PDB:
 6RKW
PDB:
 6RKV
PDB:
 6RKU
PDB:
 6RKS
PDB:
 6F94
PDB:
 6F8J
PDB:
 6F86
PDB:
 6ENG
PDB:
 5Z9Q
PDB:
 1AJ6
PDB:
 1EI1
PDB:
 1KZN
PDB:
 3G7E
PDB:
 3NUH
PDB:
 4HYP
PDB:
 4KFG
PDB:
 4PRV
PDB:
 4PRX
PDB:
 4PU9
PDB:
 4WUB
PDB:
 4WUC
PDB:
 4WUD
PDB:
 4XTJ
PDB:
 4ZVI
PDB:
 5L3J
PDB:
 5MMN
PDB:
 5MMO
PDB:
 5MMP
PDB:
 5Z4H
PDB:
 5Z4O
PDB:
 5Z9B
PDB:
 5Z9E
PDB:
 5Z9F
PDB:
 5Z9L
PDB:
 5Z9M
PDB:
 5Z9N
PFAM:
 PF00986
PFAM:
 PF01751
PFAM:
 PF02518
PFAM:
 PF00204
PFAM:
 PF18053
PRIDE:
 P0AES6
PRODB:
 PRO_000022856
PROSITE:
 PS50880
PROSITE:
 PS00177
REFSEQ:
 YP_026241
SMART:
 SM00387
SMART:
 SM00433
SMR:
 P0AES6
SWISSMODEL:
 P0AES6
UNIPROT:
 P0AES6


Operon      
Name: gyrB         
Operon arrangement:
Transcription unit        Promoter
gyrB
gyrB


Transcriptional Regulation      
Display Regulation             
Repressed by: 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 yidBp3 3877615 reverse nd [ICWHO] [1]
  promoter TSS_4259 3878251 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_4260 (cluster) 3878769 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_4261 3878772 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_4262 3879127 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_4263 3879564 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_4264 3880140 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_4265 (cluster) 3880152 reverse nd [RS-EPT-CBR] [2]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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


Reference(s)    

 [1] 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

 [2] 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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