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==Crystal structure of the post-catalytic nick complex of DNA polymerase lambda with a templating A and incorporated 8-oxo-dGMP==
==Crystal structure of the post-catalytic nick complex of DNA polymerase lambda with a templating A and incorporated 8-oxo-dGMP==
<StructureSection load='4x5v' size='340' side='right' caption='[[4x5v]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
<StructureSection load='4x5v' size='340' side='right'caption='[[4x5v]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4x5v]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X5V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X5V FirstGlance]. <br>
<table><tr><td colspan='2'>[[4x5v]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X5V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X5V FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.15&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4x5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x5v OCA], [http://pdbe.org/4x5v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x5v RCSB], [http://www.ebi.ac.uk/pdbsum/4x5v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x5v ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4x5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x5v OCA], [https://pdbe.org/4x5v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x5v RCSB], [https://www.ebi.ac.uk/pdbsum/4x5v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x5v ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/DPOLL_HUMAN DPOLL_HUMAN]] Repair polymerase. Involved in base excision repair (BER) responsible for repair of lesions that give rise to abasic (AP) sites in DNA. Has both DNA polymerase and terminal transferase activities. Has a 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity.<ref>PMID:11457865</ref> <ref>PMID:15537631</ref>
[https://www.uniprot.org/uniprot/DPOLL_HUMAN DPOLL_HUMAN] Repair polymerase. Involved in base excision repair (BER) responsible for repair of lesions that give rise to abasic (AP) sites in DNA. Has both DNA polymerase and terminal transferase activities. Has a 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity.<ref>PMID:11457865</ref> <ref>PMID:15537631</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
8-Oxo-7,8,-dihydro-2'-deoxyguanosine triphosphate (8-oxo-dGTP) is a major product of oxidative damage in the nucleotide pool. It is capable of mispairing with adenosine (dA), resulting in futile, mutagenic cycles of base excision repair. Therefore, it is critical that DNA polymerases discriminate against 8-oxo-dGTP at the insertion step. Because of its roles in oxidative DNA damage repair and non-homologous end joining, DNA polymerase lambda (Pol lambda) may frequently encounter 8-oxo-dGTP. Here, we have studied the mechanisms of 8-oxo-dGMP incorporation and discrimination by Pol lambda. We have solved high resolution crystal structures showing how Pol lambda accommodates 8-oxo-dGTP in its active site. The structures indicate that when mispaired with dA, the oxidized nucleotide assumes the mutagenic syn-conformation, and is stabilized by multiple interactions. Steady-state kinetics reveal that two residues lining the dNTP binding pocket, Ala(510) and Asn(513), play differential roles in dNTP selectivity. Specifically, Ala(510) and Asn(513) facilitate incorporation of 8-oxo-dGMP opposite dA and dC, respectively. These residues also modulate the balance between purine and pyrimidine incorporation. Our results shed light on the mechanisms controlling 8-oxo-dGMP incorporation in Pol lambda and on the importance of interactions with the incoming dNTP to determine selectivity in family X DNA polymerases.


Nucleotide binding interactions modulate dNTP selectivity and facilitate 8-oxo-dGTP incorporation by DNA polymerase lambda.,Burak MJ, Guja KE, Garcia-Diaz M Nucleic Acids Res. 2015 Sep 18;43(16):8089-99. doi: 10.1093/nar/gkv760. Epub 2015, Jul 28. PMID:26220180<ref>PMID:26220180</ref>
==See Also==
 
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4x5v" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Burak, M J]]
[[Category: Homo sapiens]]
[[Category: Garcia-Diaz, M]]
[[Category: Large Structures]]
[[Category: Guja, K E]]
[[Category: Synthetic construct]]
[[Category: Dna polymerase lambda]]
[[Category: Burak MJ]]
[[Category: Helix-hairpin-helix]]
[[Category: Garcia-Diaz M]]
[[Category: Protein-dna complex]]
[[Category: Guja KE]]
[[Category: Transferase-dna complex]]

Latest revision as of 12:59, 1 March 2024

Crystal structure of the post-catalytic nick complex of DNA polymerase lambda with a templating A and incorporated 8-oxo-dGMP

4x5v, resolution 2.15Å

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