1A41 | pdb_00001a41

TYPE 1-TOPOISOMERASE CATALYTIC FRAGMENT FROM VACCINIA VIRUS

• PDB DOI: https://doi.org/10.2210/pdb1A41/pdb

• Classification: ISOMERASE
• Organism(s): Orthopoxvirus vaccinia
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 1998-02-10 Released: 1999-06-01 
• Deposition Author(s): Cheng, C., Kussie, P., Pavletich, N., Shuman, S.

---

Experimental Data Snapshot

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

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

• PubMed: 9529259 
• DOI: https://doi.org/10.1016/s0092-8674(00)81411-7
• Primary Citation 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. 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.37 kDa 
• Atom Count: 1,868 
• Modeled Residue Count: 221 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TOPOISOMERASE I	A	234	Orthopoxvirus vaccinia	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

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

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.7	α = 90
b = 81.7	β = 90
c = 84.5	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-06-01 
Deposition Author(s): Cheng, C., Kussie, P., Pavletich, N., Shuman, S.

Revision History  

• 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
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other