DNA Polymerase Beta MOVIES
The enzyme DNA polymerase beta (pol B) fills single nucleotide (nt)
gaps in DNA produced by the base excision repair pathway of mammalian
cells. Four movies depicting conformational changes of pol B during one
turnover of substrate have been constructed using three isomorphous
crystallographic structures. To re-run the movie, click on the Reload
button on your Netscape window.
MOVIE 1 depicts conformational changes of the THUMB
during the catalytic cycle.
MOVIE 2 depicts how thumb conformation affects CATALYTIC
MOVIE 3 depicts how thumb conformation affects dNTP
MOVIE 4 depicts how thumb conformation affects TEMPLATE
Polymerase Beta CRYSTAL STRUCTURES
The movies are based on three crystal structures of human DNA
polymerase beta, each in a different ligation state:
(1) double stranded DNA substrate
containing a single nucleotide gap (gap).
(2) gap and ddCTP
(3) double stranded DNA product containing
a nick in the phosphodiester backbone.
These crystal structures are depicted in the first, middle, and last
frames (respectively) of the movies. All the intervening frames were
interpolated by incremental rigid rotations and translations of domains
and side chains (using X-plor). No energy terms were used to simulate
dynamics of protein motion. There is a more detailed description of
the significance of these conformational changes in the following
Sawaya, M.R., Prasad, R., Wilson, S.H., Kraut, J., & Pelletier, H.
"Crystal Structures of Human DNA Polymerase Beta Complexed with Gapped
and Nicked DNA: Evidence for an Induced Fit Mechanism," (1997) Biochemistry,
volume 36, pages 11205-11215.
CONSTRUCTION OF Polymerase Beta MOVIEs
containing 40 frames each, were assembled using GIFMerge . Images
were constructed with the graphics program SETOR written by Stephen Evans
(firstname.lastname@example.org) If you dont have Netscape Version 2.0 or
better and the image below is static you may download an upgraded
version of Netscape
An ENLARGED version of MOVIE 1 may be viewed with SGI's movieplayer
software. To view the movie, click on
MOVIE 1. A special thanks goes
to Sunny Kim for her help in assembling the movie.
If you have any comments about my movie, please click on my email
Michael R. Sawaya (email@example.com).
A screen should pop up (its self explanatory) and there will be buttons
for send and cancel. You may also wish to visit my homepage.
Some Useful Links to Look At
Michael R. Sawaya
Post Graduate Research Chemist 1995-1997