PDBsum entry 2b9s

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protein dna_rna ligands Protein-protein interface(s) links
Isomerase/DNA PDB id
Protein chains
426 a.a. *
52 a.a. *
Waters ×130
* Residue conservation analysis
PDB id:
Name: Isomerase/DNA
Title: Crystal structure of heterodimeric l. Donovani topoisomerase i-vanadate-DNA complex
Structure: 5'-d( Ap Ap Ap Ap Ap Gp Ap Cp Tp T)-3'. Chain: c. Engineered: yes. 5'-d( Ap Gp Ap Ap Ap Ap Ap Tp Tp Tp Tp T)-3'. Chain: d. Engineered: yes. 5'- d( Ap Ap Ap Ap Ap Tp Tp Tp Tp Tp Cp Tp Ap Ap Gp Tp Cp Tp Tp Tp Tp T)-3'.
Source: Synthetic: yes. Leishmania donovani. Organism_taxid: 5661. Gene: topoisomerase i, large subunit (ldtop1l). Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: topoisomerase i, small subunit (ldtop1s).
Biol. unit: Pentamer (from PQS)
2.27Å     R-factor:   0.233     R-free:   0.275
Authors: D.R.Davies,W.G.J.Hol
Key ref:
D.R.Davies et al. (2006). The structure of the transition state of the heterodimeric topoisomerase I of Leishmania donovani as a vanadate complex with nicked DNA. J Mol Biol, 357, 1202-1210. PubMed id: 16487540 DOI: 10.1016/j.jmb.2006.01.022
12-Oct-05     Release date:   17-Jan-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9GPZ9  (Q9GPZ9_LEIIN) -  DNA topoisomerase I
635 a.a.
426 a.a.
Protein chain
Pfam   ArchSchema ?
Q8WQM6  (Q8WQM6_LEIDO) -  DNA topoisomerase I-like protein
262 a.a.
52 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain A: E.C.  - Dna topoisomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     chromosome   1 term 
  Biological process     DNA topological change   1 term 
  Biochemical function     DNA binding     3 terms  


DOI no: 10.1016/j.jmb.2006.01.022 J Mol Biol 357:1202-1210 (2006)
PubMed id: 16487540  
The structure of the transition state of the heterodimeric topoisomerase I of Leishmania donovani as a vanadate complex with nicked DNA.
D.R.Davies, A.Mushtaq, H.Interthal, J.J.Champoux, W.G.Hol.
Type IB topoisomerases are essential enzymes that are responsible for relaxing superhelical tension in DNA by forming a transient covalent nick in one strand of the DNA duplex. Topoisomerase I is a target for anti-cancer drugs such as camptothecin, and these drugs also target the topoisomerases I in pathogenic trypanosomes including Leishmania species and Trypanosoma brucei. Most eukaryotic enzymes, including human topoisomerase I, are monomeric. However, for Leishmania donovani, the DNA-binding activity and the majority of residues involved in catalysis are located in a large subunit, designated TOP1L, whereas the catalytic tyrosine residue responsible for covalent attachment to DNA is located in a smaller subunit, called TOP1S. Here, we present the 2.27A crystal structure of an active truncated L.donovani TOP1L/TOP1S heterodimer bound to nicked double-stranded DNA captured as a vanadate complex. The vanadate forms covalent linkages between the catalytic tyrosine residue of the small subunit and the nicked ends of the scissile DNA strand, mimicking the previously unseen transition state of the topoisomerase I catalytic cycle. This structure fills a critical gap in the existing ensemble of topoisomerase I structures and provides crucial insights into the catalytic mechanism.
  Selected figure(s)  
Figure 1.
Figure 1. The overall structure of the LdTOP1LS–vanadate–DNA complex and general comparison with human topoisomerase IB. (a) Schematic alignment of human and L. donovani topoisomerase I subunits. Upper, human topoisomerase I; middle, LdTOP1L; bottom, LdTOP1S. Color-coding of domains matches that used for ribbon diagrams where the core subdomains of hTopo I are purple, the hTopoI C-terminal domain is red, the LdTOP1L core subdomains are blue and the LdTOP1S C-terminal domain is yellow. Vertical positioning represents approximate sequence alignment and catalytic residues are labeled. (b) Ribbon representations of the LdTOP1LS–vanadate–DNA complex. The LdTOP1L subunit is blue, the LdTOP1S subunit is yellow-orange, and the DNA backbone is green. The left-hand view is parallel with the DNA duplex axis; and the middle view is perpendicular to the DNA duplex axis. The right-hand view is a superposition of the LdTOP1LS complex with the human “reconstituted Topo I” (PDB 1A31), with the core subdomains purple, the C-terminal domain red and the DNA yellow. All Figures were created using Ribbons.^36
Figure 3.
Figure 3. Stereoview of structures along the pathway of DNA cleavage for topoisomerase I. (a) The non-covalent hTopo I–DNA complex (PDB ID 1A35). The limited hydrogen bonding pattern with a single non-bridging phosphate oxygen atom represents a “ground state” for the cleavage reaction. (b) A non-covalent hTopo I complex with DNA containing a cytosine at the −1 position (PDB ID 1EJ9). Due to the more extensive hydrogen bonding pattern, this structure is considered to be more advanced along the DNA cleavage reaction pathway. (c) The LdTOP1LS–vanadate–DNA complex described in this work. The vanadate structure is a mimic of the transition state for the catalytic reaction. (d) The end-point of DNA cleavage, the covalent complex structure captured by a suicide substrate (PDB ID 1A31). The coloration of the ribbon and the ball-and-stick structures is the same as in Figure 1 and Figure 2. (Although structures in (a) and (b) were solved with Y723F mutants, a semi-transparent phenolic oxygen atom is shown for reference.)
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 357, 1202-1210) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21186185 S.Sengupta, A.Ganguly, A.Roy, S.Bosedasgupta, I.D'Annessa, A.Desideri, and H.K.Majumder (2011).
ATP independent type IB topoisomerase of Leishmania donovani is stimulated by ATP: an insight into the functional mechanism.
  Nucleic Acids Res, 39, 3295-3309.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
20541510 A.Patel, L.Yakovleva, S.Shuman, and A.Mondragón (2010).
Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site.
  Structure, 18, 725-733.
PDB code: 3m4a
20462863 B.Gibb, K.Gupta, K.Ghosh, R.Sharp, J.Chen, and G.D.Van Duyne (2010).
Requirements for catalysis in the Cre recombinase active site.
  Nucleic Acids Res, 38, 5817-5832.
PDB code: 3mgv
19883377 C.Tesauro, P.Fiorani, I.D'Annessa, G.Chillemi, G.Turchi, and A.Desideri (2010).
Erybraedin C, a natural compound from the plant Bituminaria bituminosa, inhibits both the cleavage and religation activities of human topoisomerase I.
  Biochem J, 425, 531-539.  
20723754 D.A.Koster, A.Crut, S.Shuman, M.A.Bjornsti, and N.H.Dekker (2010).
Cellular strategies for regulating DNA supercoiling: a single-molecule perspective.
  Cell, 142, 519-530.  
20152159 K.Perry, Y.Hwang, F.D.Bushman, and G.D.Van Duyne (2010).
Insights from the structure of a smallpox virus topoisomerase-DNA transition state mimic.
  Structure, 18, 127-137.
PDB code: 3igc
19332675 A.Roy, S.BoseDasgupta, A.Ganguly, P.Jaisankar, and H.K.Majumder (2009).
Topoisomerase I gene mutations at F270 in the large subunit and N184 in the small subunit contribute to the resistance mechanism of the unicellular parasite Leishmania donovani towards 3,3'-diindolylmethane.
  Antimicrob Agents Chemother, 53, 2589-2598.  
18755053 A.J.Schoeffler, and J.M.Berger (2008).
DNA topoisomerases: harnessing and constraining energy to govern chromosome topology.
  Q Rev Biophys, 41, 41.  
18367446 L.Yakovleva, S.Chen, S.M.Hecht, and S.Shuman (2008).
Chemical and traditional mutagenesis of vaccinia DNA topoisomerase provides insights to cleavage site recognition and transesterification chemistry.
  J Biol Chem, 283, 16093-16103.  
17222179 B.B.Das, S.Bose Dasgupta, A.Ganguly, S.Mazumder, A.Roy, and H.K.Majumder (2007).
Leishmania donovani bisubunit topoisomerase I gene fusion leads to an active enzyme with conserved type IB enzyme function.
  FEBS J, 274, 150-163.  
17367810 C.H.Ma, A.Kwiatek, S.Bolusani, Y.Voziyanov, and M.Jayaram (2007).
Unveiling hidden catalytic contributions of the conserved His/Trp-III in tyrosine recombinases: assembly of a novel active site in Flp recombinase harboring alanine at this position.
  J Mol Biol, 368, 183-196.  
17317566 K.L.Whiteson, Y.Chen, N.Chopra, A.C.Raymond, and P.A.Rice (2007).
Identification of a potential general acid/base in the reversible phosphoryl transfer reactions catalyzed by tyrosine recombinases: Flp H305.
  Chem Biol, 14, 121-129.  
18000548 R.Díaz González, Y.Pérez Pertejo, D.Ordóñez, R.Balaña-Fouce, and R.M.Reguera (2007).
Deletion Study of DNA Topoisomerase IB from Leishmania donovani: Searching for a Minimal Functional Heterodimer.
  PLoS ONE, 2, e1177.  
17042788 B.B.Das, T.Sengupta, A.Ganguly, and H.K.Majumder (2006).
Topoisomerases of kinetoplastid parasites: why so fascinating?
  Mol Microbiol, 62, 917-927.  
16885024 K.Perry, Y.Hwang, F.D.Bushman, and G.D.Van Duyne (2006).
Structural basis for specificity in the poxvirus topoisomerase.
  Mol Cell, 23, 343-354.
PDB codes: 2h7f 2h7g
16846801 R.Balaña-Fouce, C.M.Redondo, Y.Pérez-Pertejo, R.Díaz-González, and R.M.Reguera (2006).
Targeting atypical trypanosomatid DNA topoisomerase I.
  Drug Discov Today, 11, 733-740.  
17032643 Y.Hwang, N.Minkah, K.Perry, G.D.Van Duyne, and F.D.Bushman (2006).
Regulation of catalysis by the smallpox virus topoisomerase.
  J Biol Chem, 281, 38052-38060.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.