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Protein-nucleotide interactions in E. coli DNA topoisomerase I.

Feinberg H, Changela A, Mondragón A
Nat Struct Biol 6 961-8 (1999)
Related entries: 1cy0, 1cy2, 1cy4, 1cy6, 1cy7, 1cy8

Cited: 18 times
EuropePMC logo PMID: 10504732

Abstract

DNA topoisomerases are the enzymes responsible for controlling and maintaining the topological states of DNA. Type IA enzymes work by transiently breaking the phosphodiester backbone of one strand to allow passage of another strand through the break. The protein has to perform complex rearrangements of the DNA, and hence it is likely that different regions of the enzyme bind DNA with different affinities. In order to identify some of the DNA binding sites in the protein, we have solved the structures of several complexes of the 67 kDa N-terminal fragment of Escherichia coli DNA topoisomerase I with mono- and trinucleotides. There are five different binding sites in the complexes, one of which is adjacent to the active site. Two other sites are in the central hole of the protein and may represent general DNA binding regions. The positions of these sites allow us to identify different DNA binding regions and to understand their possible roles in the catalytic cycle.

Articles - 1cy1 mentioned but not cited (3)

  1. New alkaloid antibiotics that target the DNA topoisomerase I of Streptococcus pneumoniae. García MT, Blázquez MA, Ferrándiz MJ, Sanz MJ, Silva-Martín N, Hermoso JA, de la Campa AG. J Biol Chem 286 6402-6413 (2011)
  2. Rapid catalytic template searching as an enzyme function prediction procedure. Nilmeier JP, Kirshner DA, Wong SE, Lightstone FC. PLoS One 8 e62535 (2013)
  3. Letter Identification of proximal sites for unwound DNA substrate in Escherichia coli topoisomerase I with oxidative crosslinking. Cheng B, Zhou Q, Weng L, Leszyk JD, Greenberg MM, Tse-Dinh YC. FEBS Lett 591 28-38 (2017)


Reviews citing this publication (5)

  1. DNA topoisomerases: structure, function, and mechanism. Champoux JJ. Annu Rev Biochem 70 369-413 (2001)
  2. DNA topoisomerases: harnessing and constraining energy to govern chromosome topology. Schoeffler AJ, Berger JM. Q Rev Biophys 41 41-101 (2008)
  3. Electrospray ionization mass spectrometry of oligonucleotide complexes with drugs, metals, and proteins. Beck JL, Colgrave ML, Ralph SF, Sheil MM. Mass Spectrom Rev 20 61-87 (2001)
  4. Covalent trapping of protein-DNA complexes. Verdine GL, Norman DP. Annu Rev Biochem 72 337-366 (2003)
  5. Structure and mechanism of action of type IA DNA topoisomerases. Bugreev DV, Nevinsky GA. Biochemistry (Mosc) 74 1467-1481 (2009)

Articles citing this publication (10)

  1. The structure of Escherichia coli DNA topoisomerase III. Mondragón A, DiGate R. Structure 7 1373-1383 (1999)
  2. Structure of a complex between E. coli DNA topoisomerase I and single-stranded DNA. Perry K, Mondragón A. Structure 11 1349-1358 (2003)
  3. Evolutionary placement of Xanthomonadales based on conserved protein signature sequences. Cutiño-Jiménez AM, Martins-Pinheiro M, Lima WC, Martín-Tornet A, Morales OG, Menck CF. Mol Phylogenet Evol 54 524-534 (2010)
  4. A universal type IA topoisomerase fold. Duguet M, Serre MC, Bouthier de La Tour C. J Mol Biol 359 805-812 (2006)
  5. Experimental and computational investigations of Ser10 and Lys13 in the binding and cleavage of DNA substrates by Escherichia coli DNA topoisomerase I. Strahs D, Zhu CX, Cheng B, Chen J, Tse-Dinh YC. Nucleic Acids Res 34 1785-1797 (2006)
  6. Segmentally variable genes: a new perspective on adaptation. Zheng Y, Roberts RJ, Kasif S. PLoS Biol 2 E81 (2004)
  7. Microheterogeneity of Topoisomerase IA/IB and Their DNA-Bound States. Jeanne Dit Fouque K, Garabedian A, Leng F, Tse-Dinh YC, Fernandez-Lima F. ACS Omega 4 3619-3626 (2019)
  8. Three-dimensional electron microscopy of the reverse gyrase from Sulfolobus tokodaii. Matoba K, Mayanagi K, Nakasu S, Kikuchi A, Morikawa K. Biochem Biophys Res Commun 297 749-755 (2002)
  9. The type IA topoisomerase catalytic cycle: A normal mode analysis and molecular dynamics simulation. Xiong B, Burk DL, Shen J, Luo X, Liu H, Shen J, Berghuis AM. Proteins 71 1984-1994 (2008)
  10. Reverse transcriptase at bacterial telomeres. Lue NF, Jiang S. Proc Natl Acad Sci U S A 101 14307-14308 (2004)


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