RegulonDB RegulonDB 10.8: Gene Form
   

topB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

topB selD ynjI RcsB-BglJ TSS_2071 TSS_2071 ynjIp1 ynjIp1 ynjIp4 ynjIp4 ynjIp ynjIp ynjIp5 ynjIp5

Gene      
Name: topB    Texpresso search in the literature
Synonym(s): ECK1761, EG11014, b1763, mutR
Genome position(nucleotides): 1844999 <-- 1846960 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
55.15
External database links:  
ASAP:
ABE-0005869
CGSC:
29988
CGSC:
36749
ECHOBASE:
EB1007
OU-MICROARRAY:
b1763
PortEco:
topB
STRING:
511145.b1763
COLOMBOS: topB


Product      
Name: DNA topoisomerase III
Synonym(s): MutR, TopB, Topo III
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 73.217
Isoelectric point: 8.287
Motif(s):
 
Type Positions Sequence
194 -> 199 SVGRVQ
3 -> 135 LFIAEKPSLARAIADVLPKPHRKGDGFIECGNGQVVTWCIGHLLEQAQPDAYDSRYARWNLADLPIVPEKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDREGQLLVDEVLDYLQLAPEKRQQVQRCLIN
1 -> 134 MRLFIAEKPSLARAIADVLPKPHRKGDGFIECGNGQVVTWCIGHLLEQAQPDAYDSRYARWNLADLPIVPEKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDREGQLLVDEVLDYLQLAPEKRQQVQRCLI
158 -> 593 LCVSALARARADWLYGINMTRAYTILGRNAGYQGVLSVGRVQTPVLGLVVRRDEEIENFVAKDFFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPLAEHVVNRISGQPAIVTSYNDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYETHKLITYPRSDCRYLPEEHFAGRHAVMNAISVHAPDLLPQPVVDPDIRNRCWDDKKVDAHHAIIPTARSSAINLTENEAKVYNLIARQYLMQFCPDAVFRKCVIELDIAKGKFVAKARFLAEAGWRTLLGSKERDEENDGTPLPVVAKGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIARFVQDKDLKKILRATDGLGTEATRAGIIELLFKRGFLTKKGRYIHSTDAGKALFHSLPEMATRPDMTAHWESVLTQISEKQCRYQDFMQ

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related --> 2.1.1 - DNA replication
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0043597 - cytoplasmic replication fork
molecular_function GO:0098847 - sequence-specific single stranded DNA binding
GO:0003677 - DNA binding
GO:0003916 - DNA topoisomerase activity
GO:0005515 - protein binding
GO:0016853 - isomerase activity
GO:0046872 - metal ion binding
GO:0003917 - DNA topoisomerase type I (single strand cut, ATP-independent) activity
GO:0000287 - magnesium ion binding
biological_process GO:0006261 - DNA-dependent DNA replication
GO:0006310 - DNA recombination
GO:0006265 - DNA topological change
GO:0051304 - chromosome separation
Note(s): Note(s): ...[more].
Reference(s): [1] Bebenek K., et al., 1983
[2] Bernstein DA., et al., 2003
[3] DiGate RJ. 1999
[4] Gomez-Eichelmann MC., et al., 1995
[5] Hiasa H., et al., 1994
[6] Jarukanont D., et al., 2014
[7] Martel M., et al., 2018
[8] Martel M., et al., 2015
[9] Rydberg B. 1978
[10] Santos ME., et al., 1994
[11] Stockum A., et al., 2012
[12] Uematsu N., et al., 1997
[13] Usongo V., et al., 2016
[14] Usongo V., et al., 2008
[15] Zhang HL., et al., 1995
External database links:  
DIP:
DIP-11012N
ECOCYC:
EG11014-MONOMER
ECOLIWIKI:
b1763
INTERPRO:
IPR023405
INTERPRO:
IPR023406
INTERPRO:
IPR013826
INTERPRO:
IPR013825
INTERPRO:
IPR013824
INTERPRO:
IPR013497
INTERPRO:
IPR006171
INTERPRO:
IPR005738
INTERPRO:
IPR003602
INTERPRO:
IPR003601
INTERPRO:
IPR000380
INTERPRO:
IPR034144
MINT:
MINT-1224249
MODBASE:
P14294
PANTHER:
PTHR11390
PDB:
2O19
PDB:
1I7D
PDB:
1D6M
PDB:
2O54
PDB:
2O59
PDB:
2O5C
PDB:
2O5E
PFAM:
PF01131
PFAM:
PF01751
PRIDE:
P14294
PRINTS:
PR00417
PRODB:
PRO_000024084
PROSITE:
PS00396
PROSITE:
PS50880
REFSEQ:
NP_416277
SMART:
SM00493
SMART:
SM00437
SMART:
SM00436
SMR:
P14294
UNIPROT:
P14294


Operon      
Name: ydjA-selD-topB         
Operon arrangement:
Transcription unit        Promoter
selD-topB
selD-topB
ydjA-selD-topB


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 ynjIp5 1844886 reverse Similarity to the consensus
Read more >
[ICWHO] [16]
  promoter ynjIp4 1844902 reverse Similarity to the consensus
Read more >
[ICWHO] [16]
  promoter ynjIp1 1845011 reverse Similarity to the consensus
Read more >
[ICWHO] [16]
  promoter TSS_2071 1847772 reverse nd [RS-EPT-CBR] [17]


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] Bebenek K., Janion C., 1983, Involvement of the mismatch repair system in base analogue-induced mutagenesis., Mol Gen Genet 191(2):276-81

 [2] Bernstein DA., Zittel MC., Keck JL., 2003, High-resolution structure of the E.coli RecQ helicase catalytic core., EMBO J 22(19):4910-21

 [3] DiGate RJ., 1999, Overexpression and purification of Escherichia coli DNA topoisomerase III., Methods Mol Biol 94:153-62

 [4] Gomez-Eichelmann MC., Camacho-Carranza R., 1995, [DNA supercoiling and topoisomerases in Escherichia coli]., Rev Latinoam Microbiol 37(3):291-304

 [5] Hiasa H., Marians KJ., 1994, Topoisomerase III, but not topoisomerase I, can support nascent chain elongation during theta-type DNA replication., J Biol Chem 269(51):32655-9

 [6] Jarukanont D., Coimbra JT., Bauerhenne B., Fernandes PA., Patel S., Ramos MJ., Garcia ME., 2014, Biomolecular structure manipulation using tailored electromagnetic radiation: a proof of concept on a simplified model of the active site of bacterial DNA topoisomerase., Phys Chem Chem Phys 16(39):21768-77

 [7] Martel M., Balleydier A., Brochu J., Drolet M., 2018, Detection of oriC-Independent Replication in Escherichia coli Cells., Methods Mol Biol 1703:131-138

 [8] Martel M., Balleydier A., Sauriol A., Drolet M., 2015, Constitutive stable DNA replication in Escherichia coli cells lacking type 1A topoisomerase activity., DNA Repair (Amst) 35:37-47

 [9] Rydberg B., 1978, Bromouracil mutagenesis and mismatch repair in mutator strains of Escherichia coli., Mutat Res 52(1):11-24

 [10] Santos ME., Drake JW., 1994, Rates of spontaneous mutation in bacteriophage T4 are independent of host fidelity determinants., Genetics 138(3):553-64

 [11] Stockum A., Lloyd RG., Rudolph CJ., 2012, On the viability of Escherichia coli cells lacking DNA topoisomerase I., BMC Microbiol 12:26

 [12] Uematsu N., Eda S., Yamamoto K., 1997, An Escherichia coli topB mutant increases deletion and frameshift mutations in the supF target gene., Mutat Res 383(3):223-30

 [13] Usongo V., Martel M., Balleydier A., Drolet M., 2016, Mutations reducing replication from R-loops suppress the defects of growth, chromosome segregation and DNA supercoiling in cells lacking topoisomerase I and RNase HI activity., DNA Repair (Amst) 40:1-17

 [14] Usongo V., Nolent F., Sanscartier P., Tanguay C., Broccoli S., Baaklini I., Drlica K., Drolet M., 2008, Depletion of RNase HI activity in Escherichia coli lacking DNA topoisomerase I leads to defects in DNA supercoiling and segregation., Mol Microbiol 69(4):968-81

 [15] Zhang HL., DiGate RJ., 1995, The carboxyl-terminal residues of Escherichia coli DNA topoisomerase III are involved in substrate binding., J Biol Chem 270(35):20870

 [16] 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

 [17] 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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