DNA topoisomerase 1

Details

Name
DNA topoisomerase 1
Synonyms
  • 5.99.1.2
  • DNA topoisomerase I
  • Omega-protein
  • Relaxing enzyme
  • supX
  • Swivelase
  • Untwisting enzyme
Gene Name
topA
Organism
Escherichia coli (strain K12)
Amino acid sequence
>lcl|BSEQ0016620|DNA topoisomerase 1
MGKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAAKKSADSTSTKTAKKPK
KDERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIA
WHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVS
PLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTH
QNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFG
VKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKEN
SQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDF
RLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEA
SLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNY
DFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQMVLTSIDCP
TCGRKMGIRTASTGVFLGCSGYALPPKERCKTTINLVPENEVLNVLEGEDAETNALRAKR
RCPKCGTAMDSYLIDPKRKLHVCGNNPTCDGYEIEEGEFRIKGYDGPIVECEKCGSEMHL
KMGRFGKYMACTNEECKNTRKILRNGEVAPPKEDPVPLPELPCEKSDAYFVLRDGAAGVF
LAANTFPKSRETRAPLVEELYRFRDRLPEKLRYLADAPQQDPEGNKTMVRFSRKTKQQYV
SSEKDGKATGWSAFYVDGKWVEGKK
Number of residues
865
Molecular Weight
97349.0
Theoretical pI
8.64
GO Classification
Functions
DNA binding / DNA topoisomerase activity / DNA topoisomerase type I activity / DNA topoisomerase type II (ATP-hydrolyzing) activity / magnesium ion binding
Processes
DNA topological change
Components
chromosome / cytosol
General Function
Magnesium ion binding
Specific Function
Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone.
Pfam Domain Function
Transmembrane Regions
Not Available
Cellular Location
Cytoplasmic
Gene sequence
>lcl|BSEQ0016621|DNA topoisomerase 1 (topA)
ATGGGTAAAGCTCTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTAT
CTGGGTAGTGACTACGTGGTGAAATCCAGCGTCGGTCACATCCGCGATTTGCCGACCAGT
GGCTCAGCTGCCAAAAAGAGTGCCGACTCTACCTCCACCAAGACGGCTAAAAAGCCTAAA
AAGGATGAACGTGGCGCTCTCGTCAACCGTATGGGGGTTGACCCGTGGCACAATTGGGAG
GCGCACTATGAAGTGTTGCCTGGTAAAGAGAAGGTCGTCTCTGAACTGAAACAACTGGCT
GAAAAAGCCGACCACATCTATCTCGCAACCGACCTTGACCGCGAAGGGGAAGCCATTGCA
TGGCACCTGCGGGAAGTGATTGGGGGTGATGATGCGCGCTATAGCCGAGTGGTGTTTAAC
GAAATTACTAAAAACGCGATCCGCCAGGCATTTAACAAACCGGGTGAGCTGAATATTGAT
CGTGTTAATGCCCAGCAGGCGCGTCGCTTTATGGACCGCGTGGTGGGGTATATGGTTTCG
CCGCTGCTATGGAAAAAGATCGCTCGTGGCCTGTCTGCCGGTCGTGTGCAGTCGGTGGCG
GTTCGCCTGGTGGTCGAGCGTGAGCGTGAAATTAAAGCGTTCGTGCCGGAAGAGTTCTGG
GAAGTCGATGCCAGCACGACCACGCCATCTGGTGAAGCGTTGGCGTTACAGGTGACTCAT
CAGAACGACAAACCGTTCCGTCCGGTCAACAAAGAACAAACTCAGGCTGCGGTAAGTCTG
CTGGAAAAAGCGCGCTACAGCGTGCTGGAACGTGAAGACAAACCGACAACCAGTAAACCT
GGCGCTCCTTTTATTACCTCTACGCTGCAACAAGCTGCCAGCACCCGTCTTGGATTTGGC
GTGAAAAAAACCATGATGATGGCGCAGCGTTTGTATGAAGCAGGCTATATCACTTACATG
CGTACCGACTCCACTAACCTGAGTCAGGACGCGGTAAATATGGTTCGCGGTTATATCAGC
GATAATTTTGGTAAGAAATATCTGCCGGAAAGTCCGAATCAGTACGCCAGCAAAGAAAAC
TCACAGGAAGCGCACGAAGCGATTCGTCCTTCTGACGTCAATGTGATGGCGGAATCGCTG
AAGGATATGGAAGCAGATGCGCAGAAACTGTACCAGTTAATCTGGCGTCAGTTCGTTGCC
TGCCAGATGACCCCAGCGAAATATGACTCCACGACGCTGACCGTTGGTGCGGGCGATTTC
CGCCTGAAAGCACGCGGTCGTATTTTGCGTTTTGATGGCTGGACAAAAGTGATGCCTGCG
TTGCGTAAAGGCGATGAAGATCGCATCTTACCAGCAGTTAATAAAGGCGATGCTCTGACG
CTCGTTGAACTTACACCAGCCCAGCACTTTACCAAGCCGCCAGCCCGTTTCAGTGAAGCA
TCGCTGGTTAAAGAGCTGGAAAAACGCGGTATCGGTCGTCCGTCTACCTATGCGTCGATC
ATTTCGACCATTCAGGATCGTGGCTACGTGCGAGTAGAAAATCGTCGTTTCTATGCGGAA
AAAATGGGCGAAATCGTCACCGATCGCCTTGAAGAAAATTTCCGCGAGTTAATGAACTAC
GACTTTACCGCGCAGATGGAAAACAGCCTCGACCAGGTGGCAAATCACGAAGCAGAGTGG
AAAGCTGTACTGGATCACTTCTTCTCGGATTTCACCCAGCAGTTAGATAAAGCTGAAAAA
GATCCGGAAGAGGGTGGTATGCGCCCGAACCAGATGGTTCTGACCAGCATTGACTGCCCG
ACTTGTGGTCGCAAAATGGGGATTCGCACAGCGAGCACCGGGGTATTCCTTGGCTGTTCT
GGCTATGCGCTGCCGCCGAAAGAGCGTTGCAAAACCACCATTAACCTGGTGCCGGAAAAC
GAAGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGT
CGTTGCCCGAAATGCGGCACGGCGATGGACAGCTATCTCATCGATCCGAAACGTAAGTTG
CATGTCTGTGGTAATAACCCAACCTGCGACGGTTACGAGATCGAAGAGGGCGAATTCCGC
ATTAAAGGTTATGACGGCCCGATCGTTGAGTGTGAAAAATGTGGCTCTGAAATGCACCTG
AAAATGGGGCGTTTCGGTAAATACATGGCCTGCACCAACGAAGAGTGTAAAAACACACGT
AAGATTTTACGTAACGGCGAAGTGGCACCACCGAAAGAAGATCCGGTGCCATTACCTGAG
CTGCCGTGCGAAAAATCAGATGCTTATTTCGTGCTGCGTGACGGTGCTGCCGGTGTGTTC
CTGGCTGCCAACACTTTCCCGAAATCGCGTGAAACGCGTGCGCCACTGGTGGAAGAGCTT
TATCGCTTCCGCGACCGTCTGCCGGAAAAACTGCGTTATCTGGCCGATGCGCCACAGCAG
GATCCGGAAGGTAATAAGACCATGGTTCGCTTTAGCCGTAAAACCAAACAGCAATATGTC
TCTTCGGAAAAAGACGGAAAGGCGACTGGCTGGTCAGCATTTTATGTTGATGGCAAATGG
GTTGAAGGAAAAAAATAA
Chromosome Location
Not Available
Locus
Not Available
External Identifiers
ResourceLink
UniProtKB IDP06612
UniProtKB Entry NameTOP1_ECOLI
GenBank Protein ID415338
GenBank Gene IDX04475
General References
  1. Tse-Dinh YC, Wang JC: Complete nucleotide sequence of the topA gene encoding Escherichia coli DNA topoisomerase I. J Mol Biol. 1986 Oct 5;191(3):321-31. [Article]
  2. Aiba H, Baba T, Hayashi K, Inada T, Isono K, Itoh T, Kasai H, Kashimoto K, Kimura S, Kitakawa M, Kitagawa M, Makino K, Miki T, Mizobuchi K, Mori H, Mori T, Motomura K, Nakade S, Nakamura Y, Nashimoto H, Nishio Y, Oshima T, Saito N, Sampei G, Horiuchi T, et al.: A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map. DNA Res. 1996 Dec 31;3(6):363-77. [Article]
  3. Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y: The complete genome sequence of Escherichia coli K-12. Science. 1997 Sep 5;277(5331):1453-62. [Article]
  4. Hayashi K, Morooka N, Yamamoto Y, Fujita K, Isono K, Choi S, Ohtsubo E, Baba T, Wanner BL, Mori H, Horiuchi T: Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol Syst Biol. 2006;2:2006.0007. Epub 2006 Feb 21. [Article]
  5. Ostrowski J, Jagura-Burdzy G, Kredich NM: DNA sequences of the cysB regions of Salmonella typhimurium and Escherichia coli. J Biol Chem. 1987 May 5;262(13):5999-6005. [Article]
  6. VanBogelen RA, Abshire KZ, Moldover B, Olson ER, Neidhardt FC: Escherichia coli proteome analysis using the gene-protein database. Electrophoresis. 1997 Aug;18(8):1243-51. [Article]
  7. Chen SJ, Wang JC: Identification of active site residues in Escherichia coli DNA topoisomerase I. J Biol Chem. 1998 Mar 13;273(11):6050-6. [Article]
  8. Zhu CX, Tse-Dinh YC: The acidic triad conserved in type IA DNA topoisomerases is required for binding of Mg(II) and subsequent conformational change. J Biol Chem. 2000 Feb 25;275(8):5318-22. [Article]
  9. Lima CD, Wang JC, Mondragon A: Three-dimensional structure of the 67K N-terminal fragment of E. coli DNA topoisomerase I. Nature. 1994 Jan 13;367(6459):138-46. [Article]
  10. Yu L, Zhu CX, Tse-Dinh YC, Fesik SW: Solution structure of the C-terminal single-stranded DNA-binding domain of Escherichia coli topoisomerase I. Biochemistry. 1995 Jun 13;34(23):7622-8. [Article]
  11. Feinberg H, Lima CD, Mondragon A: Conformational changes in E. coli DNA topoisomerase I. Nat Struct Biol. 1999 Oct;6(10):918-22. [Article]
  12. Feinberg H, Changela A, Mondragon A: Protein-nucleotide interactions in E. coli DNA topoisomerase I. Nat Struct Biol. 1999 Oct;6(10):961-8. [Article]
  13. Perry K, Mondragon A: Structure of a complex between E. coli DNA topoisomerase I and single-stranded DNA. Structure. 2003 Nov;11(11):1349-58. [Article]
  14. Zhang Z, Cheng B, Tse-Dinh YC: Crystal structure of a covalent intermediate in DNA cleavage and rejoining by Escherichia coli DNA topoisomerase I. Proc Natl Acad Sci U S A. 2011 Apr 26;108(17):6939-44. doi: 10.1073/pnas.1100300108. Epub 2011 Apr 11. [Article]

Drug Relations

Drug Relations
DrugBank IDNameDrug groupPharmacological action?ActionsDetails
DB01643Thymidine monophosphateexperimentalunknownDetails
DB01812Adenosine 3',5'-diphosphateexperimentalunknownDetails
DB04205Thymidine-3',5'-DiphosphateexperimentalunknownDetails