 |
PDBsum entry 2pfo
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Transferase, lyase/DNA
|
PDB id
|
|
|
|
2pfo
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Role of the catalytic metal during polymerization by DNA polymerase lambda.
|
|
|
Authors
|
|
M.Garcia-Diaz,
K.Bebenek,
J.M.Krahn,
L.C.Pedersen,
T.A.Kunkel.
|
|
|
Ref.
|
|
Dna Repair (amst), 2007,
6,
1333-1340.
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
The incorporation of dNMPs into DNA by polymerases involves a phosphoryl
transfer reaction hypothesized to require two divalent metal ions. Here we
investigate this hypothesis using as a model human DNA polymerase lambda (Pol
lambda), an enzyme suggested to be activated in vivo by manganese. We report the
crystal structures of four complexes of human Pol lambda. In a 1.9 A structure
of Pol lambda containing a 3'-OH and the non-hydrolyzable analog dUpnpp, a
non-catalytic Na+ ion occupies the site for metal A and the ribose of the
primer-terminal nucleotide is found in a conformation that positions the
acceptor 3'-OH out of line with the alpha-phosphate and the bridging oxygen of
the pyrophosphate leaving group. Soaking this crystal in MnCl2 yielded a 2.0 A
structure with Mn2+ occupying the site for metal A. In the presence of Mn2+, the
conformation of the ribose is C3'-endo and the 3'-oxygen is in line with the
leaving oxygen, at a distance from the phosphorus atom of the alpha-phosphate
(3.69 A) consistent with and supporting a catalytic mechanism involving two
divalent metal ions. Finally, soaking with MnCl2 converted a pre-catalytic Pol
lambda/Na+ complex with unreacted dCTP in the active site into a product complex
via catalysis in the crystal. These data provide pre- and post-transition state
information and outline in a single crystal the pathway for the phosphoryl
transfer reaction carried out by DNA polymerases.
|
|
|
|
|
|
|
