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Escherichia coli K-12 substr. MG1655 Enzyme: DNA topoisomerase III

Gene: topB Accession Numbers: EG11014 (EcoCyc), b1763, ECK1761

Synonyms: mutR, Topo III

Regulation Summary Diagram: ?

Regulation summary diagram for topB

DNA topoisomerase III (Topo III) is a type I topoisomerase which can decatenate DNA; at high temperatures in vitro, the enzyme can also relax negative supercoils in DNA [DiGate88]. RecQ helicase can stimulate Topo III to fully catenate dsDNA [Harmon99].

Cells lacking topoisomerase III show an increased frequency of spontaneous deletions [Schofield92, Uematsu97]. topB can act as a multicopy supressor of a null mutation in topA [Broccoli00] as well as a temperature-sensitive allele of parC [Nurse03].

The crystal structure of an inactive mutant DNA topoisomerase III in complex with an 8-base ssDNA oligonucleotide has been solved at 2.05 A resolution [Changela01]. A series of crystal structures of roughly the same resolution have been made using active topoisomerase III at three different pHs to examine different conformational states of the enzyme [Changela07].

Gene Citations: [Sawers91]

Locations: cytosol

Map Position: [1,843,023 <- 1,844,984] (39.72 centisomes, 143°)
Length: 1962 bp / 653 aa

Molecular Weight of Polypeptide: 73.217 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0005869 , CGSC:29988 , CGSC:36749 , DIP:DIP-11012N , EchoBASE:EB1007 , EcoGene:EG11014 , EcoliWiki:b1763 , Mint:MINT-1224249 , ModBase:P14294 , OU-Microarray:b1763 , PortEco:topB , PR:PRO_000024084 , Pride:P14294 , Protein Model Portal:P14294 , RefSeq:NP_416277 , RegulonDB:EG11014 , SMR:P14294 , String:511145.b1763 , UniProt:P14294

Relationship Links: InterPro:IN-FAMILY:IPR000380 , InterPro:IN-FAMILY:IPR003601 , InterPro:IN-FAMILY:IPR003602 , InterPro:IN-FAMILY:IPR005738 , InterPro:IN-FAMILY:IPR006171 , InterPro:IN-FAMILY:IPR013497 , InterPro:IN-FAMILY:IPR013824 , InterPro:IN-FAMILY:IPR013825 , InterPro:IN-FAMILY:IPR023405 , InterPro:IN-FAMILY:IPR023406 , Panther:IN-FAMILY:PTHR11390 , PDB:Structure:1D6M , PDB:Structure:1I7D , PDB:Structure:2O5C , PDB:Structure:2O5E , PDB:Structure:2O19 , PDB:Structure:2O54 , PDB:Structure:2O59 , Pfam:IN-FAMILY:PF01131 , Pfam:IN-FAMILY:PF01751 , Prints:IN-FAMILY:PR00417 , Prosite:IN-FAMILY:PS00396 , Prosite:IN-FAMILY:PS50880 , Smart:IN-FAMILY:SM00436 , Smart:IN-FAMILY:SM00437 , Smart:IN-FAMILY:SM00493

In Paralogous Gene Group: 271 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006310 - DNA recombination Inferred from experiment [Lopez05a]
GO:0051304 - chromosome separation Inferred from experiment [Nurse03]
GO:0006261 - DNA-dependent DNA replication
GO:0006265 - DNA topological change Inferred by computational analysis [GOA06, GOA01]
GO:0006351 - transcription, DNA-templated
Molecular Function: GO:0003917 - DNA topoisomerase type I activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, GOA01, Srivenugopal84]
GO:0000287 - magnesium ion binding Inferred by computational analysis [GOA06]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0003916 - DNA topoisomerase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer DNA related DNA replication
information transfer RNA related Transcription related

Essentiality data for topB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Enzymatic reaction of: topoisomerase

EC Number:

a negatively supercoiled DNA <=> a relaxed DNA

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

Reversibility of this reaction is unspecified.

pH(opt): 8 [BRENDA14, Perry02]

Sequence Features

Protein sequence of DNA topoisomerase III with features indicated

Feature Class Location Citations Comment
Conserved-Region 1 -> 134
UniProt: Toprim.
Metal-Binding-Site 7
UniProt: Magnesium 1; catalytic; Non-Experimental Qualifier: by similarity.
Amino-Acid-Site 61
UniProt: Interaction with DNA; Sequence Annotation Type: site.
Metal-Binding-Site 103
UniProt: Magnesium 1; catalytic; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 105
UniProt: Magnesium 2; Non-Experimental Qualifier: by similarity.
Amino-Acid-Site 170
UniProt: Interaction with DNA; Sequence Annotation Type: site.
Amino-Acid-Site 178
UniProt: Interaction with DNA; Sequence Annotation Type: site.
Amino-Acid-Site 185
UniProt: Interaction with DNA; Sequence Annotation Type: site.
Protein-Segment 194 -> 199
UniProt: Interaction with DNA; Sequence Annotation Type: region of interest.
Active-Site 328
[Mondragon99, UniProt13]
UniProt: O-(5'-phospho-DNA)-tyrosine intermediate.
Amino-Acid-Site 330
UniProt: Interaction with DNA; Sequence Annotation Type: site.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b1763 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11014; confirmed by SwissProt match.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

Broccoli00: Broccoli S, Phoenix P, Drolet M (2000). "Isolation of the topB gene encoding DNA topoisomerase III as a multicopy suppressor of topA null mutations in Escherichia coli." Mol Microbiol 35(1);58-68. PMID: 10632877

Changela01: Changela A, DiGate RJ, Mondragon A (2001). "Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule." Nature 411(6841);1077-81. PMID: 11429611

Changela07: Changela A, Digate RJ, Mondragon A (2007). "Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate." J Mol Biol 368(1);105-18. PMID: 17331537

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

DiGate88: DiGate RJ, Marians KJ (1988). "Identification of a potent decatenating enzyme from Escherichia coli." J Biol Chem 263(26);13366-73. PMID: 2843517

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Harmon99: Harmon FG, DiGate RJ, Kowalczykowski SC (1999). "RecQ helicase and topoisomerase III comprise a novel DNA strand passage function: a conserved mechanism for control of DNA recombination." Mol Cell 3(5);611-20. PMID: 10360177

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Lopez05a: Lopez CR, Yang S, Deibler RW, Ray SA, Pennington JM, Digate RJ, Hastings PJ, Rosenberg SM, Zechiedrich EL (2005). "A role for topoisomerase III in a recombination pathway alternative to RuvABC." Mol Microbiol 58(1);80-101. PMID: 16164551

Mondragon99: Mondragon A, DiGate R (1999). "The structure of Escherichia coli DNA topoisomerase III." Structure 7(11);1373-83. PMID: 10574789

Nurse03: Nurse P, Levine C, Hassing H, Marians KJ (2003). "Topoisomerase III can serve as the cellular decatenase in Escherichia coli." J Biol Chem 278(10);8653-60. PMID: 12509418

Perry02: Perry K, Mondragon A (2002). "Biochemical characterization of an invariant histidine involved in Escherichia coli DNA topoisomerase I catalysis." J Biol Chem 277(15);13237-45. PMID: 11809772

Sawers91: Sawers G, Heider J, Zehelein E, Bock A (1991). "Expression and operon structure of the sel genes of Escherichia coli and identification of a third selenium-containing formate dehydrogenase isoenzyme." J Bacteriol 1991;173(16);4983-93. PMID: 1650339

Schofield92: Schofield MA, Agbunag R, Michaels ML, Miller JH (1992). "Cloning and sequencing of Escherichia coli mutR shows its identity to topB, encoding topoisomerase III." J Bacteriol 174(15);5168-70. PMID: 1321123

Srivenugopal84: Srivenugopal KS, Lockshon D, Morris DR (1984). "Escherichia coli DNA topoisomerase III: purification and characterization of a new type I enzyme." Biochemistry 23(9);1899-906. PMID: 6326814

Uematsu97: 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. PMID: 9164483

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Other References Related to Gene Regulation

DiGate89: DiGate RJ, Marians KJ (1989). "Molecular cloning and DNA sequence analysis of Escherichia coli topB, the gene encoding topoisomerase III." J Biol Chem 264(30);17924-30. PMID: 2553698

Zaslaver06: Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U (2006). "A comprehensive library of fluorescent transcriptional reporters for Escherichia coli." Nat Methods 3(8);623-8. PMID: 16862137

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Fri Aug 28, 2015, BIOCYC14B.