1. Catalytic Mechanism of DNA Topoisomerase IB
Berit O Krogh, Stewart Shuman 
Molecular Cell 
Volume 5, Issue 6, Pages (June 2000)
DOI: /S (00)

2. Figure 1 Mechanism of Transesterification by Vaccinia Topoisomerase
The reaction is postulated to proceed through a pentacoordinate phosphorane transition state in which the entering and leaving groups are positioned apically. The attack of the active site tyrosine on the scissile phosphodiester Tp↓A might be promoted by abstraction of a proton by a general base catalyst (−B:) on the enzyme. Expulsion of the leaving strand might be catalyzed by donation of a proton from a general acid (−AH).
Molecular Cell 2000 5, DOI: ( /S (00) )

3. Figure 2
5′-Bridging Phosphorothiolate Effects on Single-Turnover DNA Cleavage by Wild-Type Vaccinia Topoisomerase and Mutants K167A and H265A
The 18-mer/30-mer suicide substrate is shown with the cleavage site indicated by the arrow. The 5′ 32P-labeled scissile strand contained either a standard Tp↓A scissile phosphodiester or a 5′-bridging phosphorothiolate Tp↓(s)A. Covalent adduct formation by wild-type topoisomerase (left panel), K167A (middle panel), and H265A (right panel) is plotted as a function of time.
Molecular Cell 2000 5, DOI: ( /S (00) )

4. Figure 3
5′-Bridging Phosphorothiolate Effects on Equilibrium DNA Cleavage by Wild-Type Vaccinia Topoisomerase and Mutants K167A and R223A
The 34-mer/60-mer equilibrium substrate is shown with the cleavage site indicated by the arrow. The 5′ 32P-labeled scissile strand contained either a standard Tp↓A scissile phosphodiester or a 5′-bridging phosphorothiolate Tp↓(s)A. Covalent adduct formation by wild-type topoisomerase (left panel), K167A (middle panel), and R233A (right panel) is plotted as a function of time.
Molecular Cell 2000 5, DOI: ( /S (00) )

5. Figure 4
Conserved Lysine in the β2–β3 Loop Is Accessible to the 5′-O Leaving Group
Stereo view of the “reactive” protomer of Cre in the CreY324F-loxS cocrystal (PDB ID code 5CRX). The lysine side chain of the β2-β3 hairpin loop projects into the minor groove where it interacts with guanine N3 and thymine O2. Rotation about chi2 positions the lysine Nζ near the 5′-O of the scissile phosphodiester, such that the lysine can serve as the general acid for expulsion of the 5′-OH leaving strand.
Molecular Cell 2000 5, DOI: ( /S (00) )