2B9S

Crystal Structure of heterodimeric L. donovani topoisomerase I-vanadate-DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 

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This is version 1.3 of the entry. See complete history


Literature

The Structure of the Transition State of the Heterodimeric Topoisomerase I of Leishmania donovani as a Vanadate Complex with Nicked DNA.

Davies, D.R.Mushtaq, A.Interthal, H.Champoux, J.J.Hol, W.G.

(2006) J Mol Biol 357: 1202-1210

  • DOI: 10.1016/j.jmb.2006.01.022
  • Primary Citation of Related Structures:  
    2B9S

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    Department of Biochemistry, Box 357742, University of Washington, Seattle, WA 98195-7742, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
topoisomerase I-like proteinD [auth A]432Leishmania donovaniMutation(s): 0 
Gene Names: topoisomerase Ilarge subunit (LdTOP1L)
EC: 5.99.1.2 (PDB Primary Data), 5.6.2.1 (UniProt)
UniProt
Find proteins for Q9GPZ9 (Leishmania infantum)
Explore Q9GPZ9 
Go to UniProtKB:  Q9GPZ9
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UniProt GroupQ9GPZ9
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase I-like proteinE [auth B]62Leishmania donovaniMutation(s): 0 
Gene Names: topoisomerase Ismall subunit (LdTOP1S)
EC: 5.99.1.2
UniProt
Find proteins for Q8WQM6 (Leishmania donovani)
Explore Q8WQM6 
Go to UniProtKB:  Q8WQM6
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UniProt GroupQ8WQM6
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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3'A [auth C]10N/A
Protein Feature View
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*AP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'B [auth D]12N/A
Protein Feature View
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Entity ID: 3
MoleculeChainsLengthOrganismImage
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'C [auth E]22N/A
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VO4
Query on VO4

Download Ideal Coordinates CCD File 
F [auth B]VANADATE ION
O4 V
LSGOVYNHVSXFFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.433α = 90
b = 106.102β = 90
c = 126.691γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description