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Abstract
Herein we report the first structure of topoisomerase I determined from the gram-positive
bacterium, S. mutans . Bacterial topoisomerase I is an ATP-independent type 1A topoisomerase
that uses the inherent torsional strain within hyper-negatively supercoiled DNA as
an energy source for its critical function of DNA relaxation. Interest in the enzyme
has gained momentum as it has proven to be essential in various bacterial organisms.
In order to aid in further biochemical characterization, the apo 65-kDa amino-terminal
fragment of DNA topoisomerase I from the gram-positive model organism Streptococcus
mutans was crystalized and a three-dimensional structure was determined to 2.06 Å
resolution via x-ray crystallography. The overall structure illustrates the four classic
major domains that create the traditional topoisomerase I “lock” formation comprised
of a sizable toroidal aperture atop what is considered to be a highly dynamic body.
A catalytic tyrosine residue resides at the interface between two domains and is known
to form a 5’ phosphotyrosine DNA-enzyme intermediate during transient single-stranded
cleavage required for enzymatic relaxation of hyper negative DNA supercoils. Surrounding
the catalytic tyrosine residue is the remainder of the highly conserved active site.
Within 5 Å from the catalytic center, only one dissimilar residue is observed between
topoisomerase I from S. mutans and the gram-negative model organism E. coli . Immediately
adjacent to the conserved active site, however, S. mutans topoisomerase I displays
a somewhat unique nine residue loop extension not present in any bacterial topoisomerase
I structures previously determined other than that of an extremophile.