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2pfq

From Proteopedia

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[[Image:2pfq.gif|left|200px]]<br /><applet load="2pfq" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:2pfq.gif|left|200px]]
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caption="2pfq, resolution 2.100&Aring;" />
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'''Manganese promotes catalysis in a DNA polymerase lambda-DNA crystal'''<br />
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{{Structure
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|PDB= 2pfq |SIZE=350|CAPTION= <scene name='initialview01'>2pfq</scene>, resolution 2.100&Aring;
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|SITE=
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|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=DCP:2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE'>DCP</scene> and <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene>
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|ACTIVITY=
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|GENE= POLL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
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}}
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'''Manganese promotes catalysis in a DNA polymerase lambda-DNA crystal'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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2PFQ 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>, <scene name='pdbligand=MN:'>MN</scene>, <scene name='pdbligand=DCP:'>DCP</scene> and <scene name='pdbligand=PPV:'>PPV</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PFQ OCA].
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2PFQ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PFQ OCA].
==Reference==
==Reference==
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17475573 17475573]
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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:[http://www.ncbi.nlm.nih.gov/pubmed/17475573 17475573]
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Single protein]]
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[[Category: phosphoryl transfer reaction]]
[[Category: phosphoryl transfer reaction]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:28:59 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:12:25 2008''

Revision as of 16:12, 20 March 2008

Image:2pfq.gif


PDB ID 2pfq

Drag the structure with the mouse to rotate
, resolution 2.100Å
Ligands: , , , and
Gene: POLL (Homo sapiens)
Coordinates: save as pdb, mmCIF, xml



Manganese promotes catalysis in a DNA polymerase lambda-DNA crystal


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 1.9 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 Structure

2PFQ is a Single protein structure of sequence from Homo sapiens. 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 Sep 1;6(9):1333-40. Epub 2007 May 1. PMID:17475573

Page seeded by OCA on Thu Mar 20 18:12:25 2008

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