2pfp
From Proteopedia
(New page: 200px<br /> <applet load="2pfp" size="450" color="white" frame="true" align="right" spinBox="true" caption="2pfp, resolution 2.100Å" /> '''DNA Polymerase lam...) |
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| - | [[Image:2pfp.gif|left|200px]]<br /> | + | [[Image:2pfp.gif|left|200px]]<br /><applet load="2pfp" size="350" color="white" frame="true" align="right" spinBox="true" |
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caption="2pfp, resolution 2.100Å" /> | caption="2pfp, resolution 2.100Å" /> | ||
'''DNA Polymerase lambda in complex with DNA and dCTP'''<br /> | '''DNA Polymerase lambda in complex with DNA and dCTP'''<br /> | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2PFP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with MG, NA and DCP as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 2PFP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=NA:'>NA</scene> and <scene name='pdbligand=DCP:'>DCP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PFP OCA]. |
==Reference== | ==Reference== | ||
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[[Category: phosphoryl transfer reaction]] | [[Category: phosphoryl transfer reaction]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 13:43:15 2008'' |
Revision as of 11:43, 23 January 2008
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DNA Polymerase lambda in complex with DNA and dCTP
Overview
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, 1.9A 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 MnCl(2) yielded a 2.0A structure with Mn(2+) occupying the site, for metal A. In the presence of Mn(2+), 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 (3.69A), consistent with and supporting a catalytic mechanism involving two, divalent metal ions. Finally, soaking with MnCl(2) 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 Structure
2PFP is a Single protein structure of sequence from Homo sapiens with , and as ligands. Full crystallographic information is available from OCA.
Reference
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 Apr 30;. PMID:17475573
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