4fo6

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Crystal structure of the pre-catalytic ternary complex of polymerase lambda with a dATP analog opposite a templating T and an rCMP at the primer terminus.

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 ==Crystal structure of the pre-catalytic ternary complex of polymerase lambda with a dATP analog opposite a templating T and an rCMP at the primer terminus.==
-<StructureSection load='4fo6' size='340' side='right' caption='[[4fo6]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
+<StructureSection load='4fo6' size='340' side='right'caption='[[4fo6]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4fo6]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3uq1 3uq1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FO6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FO6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4fo6]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3uq1 3uq1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FO6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FO6 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F2A:2-DEOXY-5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]ADENOSINE'>F2A</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></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]] 2.007&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3upq|3upq]], [[3uq0|3uq0]], [[3uq2|3uq2]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F2A:2-DEOXY-5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]ADENOSINE'>F2A</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></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">POLL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4fo6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fo6 OCA], [https://pdbe.org/4fo6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fo6 RCSB], [https://www.ebi.ac.uk/pdbsum/4fo6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fo6 ProSAT]</span></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=4fo6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fo6 OCA], [http://pdbe.org/4fo6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fo6 RCSB], [http://www.ebi.ac.uk/pdbsum/4fo6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fo6 ProSAT]</span></td></tr>
 </table>
 == 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 ==
-Although most DNA polymerases discriminate against ribonucleotide triphosphaets (rNTPs) during DNA synthesis, recent studies have shown that large numbers of ribonucleotides are incorporated into the eukaryotic nuclear genome. Here, we investigate how a DNA polymerase can stably incorporate an rNTP. The X-ray crystal structure of a variant of human DNA polymerase lambda reveals that the rNTP occupies the nucleotide binding pocket without distortion of the active site, despite an unfavorable interaction between the 2'-O and Tyr505 backbone carbonyl. This indicates an energetically unstable binding state for the rNTP, stabilized by additional protein-nucleotide interactions. Supporting this idea is the 200-fold lower catalytic efficiency for rNTP relative to deoxyribonucleotide triphosphate (dNTP) incorporation, reflecting a higher apparent Km value for the rNTP. Furthermore, distortion observed in the structure of the post-catalytic product complex suggests that once the bond between the alpha- and beta-phosphates of the rNTP is broken, the unfavorable binding state of the ribonucleotide cannot be maintained. Finally, structural and biochemical evaluation of dNTP insertion onto an ribonucleotide monophosphate (rNMP)-terminated primer indicates that a primer-terminal rNMP does not impede extension. The results are relevant to how ribonucleotides are incorporated into DNA in vivo, during replication and during repair, perhaps especially in non-proliferating cells when rNTP:dNTP ratios are high.
-The catalytic cycle for ribonucleotide incorporation by human DNA Pol lambda,Gosavi RA, Moon AF, Kunkel TA, Pedersen LC, Bebenek K Nucleic Acids Res. 2012 May 14. PMID:22584622<ref>PMID:22584622</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4fo6" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[DNA polymerase|DNA polymerase]]
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Bebenek, K]]
+[[Category: Large Structures]]
-[[Category: Gosavi, R A]]
+[[Category: Bebenek K]]
-[[Category: Kunkel, T A]]
+[[Category: Gosavi RA]]
-[[Category: Moon, A F]]
+[[Category: Kunkel TA]]
-[[Category: Pedersen, L C]]
+[[Category: Moon AF]]
-[[Category: Dna polymerase]]
+[[Category: Pedersen LC]]
-[[Category: Lyase-dna complex]]
-[[Category: Transferase]]

4fo6

From Proteopedia

Current revision

Crystal structure of the pre-catalytic ternary complex of polymerase lambda with a dATP analog opposite a templating T and an rCMP at the primer terminus.

Structural highlights

Function

See Also

References

Contents

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