4GFJ

Crystal structure of Topo-78, an N-terminal 78kDa fragment of topoisomerase V


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification of one of the apurinic/apyrimidinic lyase active sites of topoisomerase V by structural and functional studies.

Rajan, R.Prasad, R.Taneja, B.Wilson, S.H.Mondragon, A.

(2013) Nucleic Acids Res 41: 657-666

  • DOI: 10.1093/nar/gks1017
  • Primary Citation of Related Structures:  
    4GFJ

  • PubMed Abstract: 
  • Topoisomerase V (Topo-V) is the only member of a novel topoisomerase subtype. Topo-V is unique because it is a bifunctional enzyme carrying both topoisomerase and DNA repair lyase activities within the same protein. Previous studies had shown that the topoisomerase domain spans the N-terminus of the protein and is followed by 12 tandem helix-hairpin-helix [(HhH)(2)] domains ...

    Topoisomerase V (Topo-V) is the only member of a novel topoisomerase subtype. Topo-V is unique because it is a bifunctional enzyme carrying both topoisomerase and DNA repair lyase activities within the same protein. Previous studies had shown that the topoisomerase domain spans the N-terminus of the protein and is followed by 12 tandem helix-hairpin-helix [(HhH)(2)] domains. There are at least two DNA repair lyase active sites for apurinic/apyrimidinic (AP) site processing, one within the N-terminal region and the second within the C-terminal domain of Topo-V, but their exact locations and characteristics are unknown. In the present study, the N-terminal 78-kDa fragment of Topo-V (Topo-78), containing the topoisomerase domain and one of the lyase DNA repair domains, was characterized by structural and biochemical studies. The results show that an N-terminal 69-kDa fragment is the minimal fragment with both topoisomerase and AP lyase activities. The lyase active site of Topo-78 is at the junction of the fifth and sixth (HhH)(2) domains. From the biochemical and structural data, it appears that Lys571 is the most probable nucleophile responsible for the lyase activity. Our experiments also suggest that Topo-V most likely acts as a Class I AP endonuclease in vivo.


    Organizational Affiliation

    Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Topoisomerase VA685Methanopyrus kandleri AV19Mutation(s): 0 
Gene Names: MK1436Topoisomerase V
Find proteins for F1SVL0 (Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938))
Explore F1SVL0 
Go to UniProtKB:  F1SVL0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.634α = 90
b = 161.634β = 90
c = 58.227γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-05
    Type: Initial release
  • Version 1.1: 2013-01-09
    Changes: Database references