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Di-ubiquitinated
PCNA. The crystal structure did not give resolution on the third
ubiquitin molecule. There is little to no structural difference
between the ubiquitinated and non-ub forms of PCNA. The
ubiquitin (green) extends radially away from the ring at Lysine
164 (colored by structure as on previous page), making it
flexible and easier to interact with. The cyan shows the PIP box
binding site (residues 119-134) which is on an Interdomain
Connector Loop, connecting the N-terminal and C-terminal domains
of each monomer. Many polymerases and other PCNA interactors
have one or more PIP box domains allowing them to bind to PCNA
at these locations.
Another
view with the same coloring showing ribbon structure for all
except the PIP box binding domain. Notice that these binding
domains are on the opposite face of PCNA from the ubiquitin.
Therefore, it is unlikely that the ubiquitin has any effect on
proteins binding to the PIP boxes. When oriented on DNA, the PIP
box binding sites would bind the Pol, while the ub would extend
from the back of PCNA.
This
last view shows the variability in position for each atom, with
blue being low variability and red being high variability.
Notice that the rigid structure of PCNA has very little
variability with the exception of some of the loops, but that
the ubiquitin has area of high variability, conducive to
interactions with other proteins.
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