Poxviruses encode their own type IB topoisomerases (TopIBs), which release
superhelical tension generated by replication and transcription of their
genomes. To investigate the reaction catalyzed by viral TopIBs, we have
determined the structure of a variola virus topoisomerase-DNA complex trapped as
a vanadate transition state mimic. The structure reveals how the viral TopIB
enzymes are likely to position the DNA duplex for ligation following relaxation
of supercoils and identifies the sources of friction observed in single-molecule
experiments that argue against free rotation. The structure also identifies a
conformational change in the leaving group sugar that must occur prior to
cleavage and reveals a mechanism for promoting ligation following relaxation of
supercoils that involves an Asp-minor groove interaction. Overall, the new
structural data support a common catalytic mechanism for the TopIB superfamily
but indicate distinct methods for controlling duplex rotation in the small
versus large enzyme subfamilies.
