2pfq
From Proteopedia
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|PDB= 2pfq |SIZE=350|CAPTION= <scene name='initialview01'>2pfq</scene>, resolution 2.100Å | |PDB= 2pfq |SIZE=350|CAPTION= <scene name='initialview01'>2pfq</scene>, resolution 2.100Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DCP:2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= POLL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]) | |GENE= POLL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2pfn|2PFN]], [[2pfo|2PFO]], [[2pfp|2PFP]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pfq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pfq OCA], [http://www.ebi.ac.uk/pdbsum/2pfq PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2pfq RCSB]</span> | ||
}} | }} | ||
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[[Category: Kunkel, T A.]] | [[Category: Kunkel, T A.]] | ||
[[Category: Pedersen, L C.]] | [[Category: Pedersen, L C.]] | ||
| - | [[Category: DCP]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: MN]] | ||
| - | [[Category: NA]] | ||
| - | [[Category: PPV]] | ||
[[Category: dna polymerase]] | [[Category: dna polymerase]] | ||
[[Category: dna repair]] | [[Category: dna repair]] | ||
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[[Category: phosphoryl transfer reaction]] | [[Category: phosphoryl transfer reaction]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:35:15 2008'' |
Revision as of 01:35, 31 March 2008
| |||||||
| , resolution 2.100Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , , , | ||||||
| Gene: | POLL (Homo sapiens) | ||||||
| Related: | 2PFN, 2PFO, 2PFP
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| 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
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