1A41

TYPE 1-TOPOISOMERASE CATALYTIC FRAGMENT FROM VACCINIA VIRUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Conservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases.

Cheng, C.Kussie, P.Pavletich, N.Shuman, S.

(1998) Cell 92: 841-850

  • DOI: 10.1016/s0092-8674(00)81411-7
  • Primary Citation of Related Structures:  
    1A41

  • PubMed Abstract: 
  • Vaccinia DNA topoisomerase breaks and rejoins DNA strands through a DNA-(3'-phosphotyrosyl)-enzyme intermediate. A C-terminal catalytic domain, Topo(81-314), suffices for transesterification chemistry. The domain contains a constellation of five amino acids, conserved in all eukaryotic type IB topoisomerases, that catalyzes attack of the tyrosine nucleophile on the scissile phosphate ...

    Vaccinia DNA topoisomerase breaks and rejoins DNA strands through a DNA-(3'-phosphotyrosyl)-enzyme intermediate. A C-terminal catalytic domain, Topo(81-314), suffices for transesterification chemistry. The domain contains a constellation of five amino acids, conserved in all eukaryotic type IB topoisomerases, that catalyzes attack of the tyrosine nucleophile on the scissile phosphate. The structure of the catalytic domain, consisting of ten alpha helices and a three-strand beta sheet, resembles the catalytic domains of site-specific recombinases that act via a topoisomerase IB-like mechanism. The topoisomerase catalytic pentad is conserved in the tertiary structures of the recombinases despite scant sequence similarity overall. This implies that the catalytic domains of type IB topoisomerases and recombinases derive from a common ancestral strand transferase.


    Organizational Affiliation

    Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10021, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TOPOISOMERASE IA234Vaccinia virusMutation(s): 0 
EC: 5.99.1.2 (PDB Primary Data), 5.6.2.1 (UniProt)
UniProt
Find proteins for P68698 (Vaccinia virus (strain Western Reserve))
Explore P68698 
Go to UniProtKB:  P68698
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.7α = 90
b = 81.7β = 90
c = 84.5γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-06-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance