2pfq: Difference between revisions
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'''Manganese promotes catalysis in a DNA polymerase lambda-DNA crystal''' | '''Manganese promotes catalysis in a DNA polymerase lambda-DNA crystal''' | ||
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[[Category: Kunkel, T A.]] | [[Category: Kunkel, T A.]] | ||
[[Category: Pedersen, L C.]] | [[Category: Pedersen, L C.]] | ||
[[Category: | [[Category: Dna polymerase]] | ||
[[Category: | [[Category: Dna repair]] | ||
[[Category: | [[Category: Manganese]] | ||
[[Category: | [[Category: Phosphoryl transfer reaction]] | ||
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Revision as of 13:01, 4 May 2008
Manganese promotes catalysis in a DNA polymerase lambda-DNA crystal
OverviewOverview
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.
About this StructureAbout this Structure
2PFQ is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.
ReferenceReference
Role of the catalytic metal during polymerization by DNA polymerase lambda., Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA, DNA Repair (Amst). 2007 Sep 1;6(9):1333-40. Epub 2007 May 1. PMID:17475573 Page seeded by OCA on Sun May 4 13:01:23 2008