5dlg

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'''Unreleased structure'''
 
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The entry 5dlg is ON HOLD
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==Crystal Structure of Human DNA Polymerase Eta Inserting dGMPNPP Opposite O4-Methylhymidine==
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<StructureSection load='5dlg' size='340' side='right'caption='[[5dlg]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[5dlg]] is a 3 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=5DLG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DLG FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.351&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5DB:1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-4-METHOXY-5-METHYLPYRIMIDIN-2(1H)-ONE'>5DB</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=XG4:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE'>XG4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5dlg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dlg OCA], [https://pdbe.org/5dlg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dlg RCSB], [https://www.ebi.ac.uk/pdbsum/5dlg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dlg ProSAT]</span></td></tr>
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</table>
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== Disease ==
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[https://www.uniprot.org/uniprot/POLH_HUMAN POLH_HUMAN] Defects in POLH are the cause of xeroderma pigmentosum variant type (XPV) [MIM:[https://omim.org/entry/278750 278750]; also designated as XP-V. Xeroderma pigmentosum (XP) is an autosomal recessive disease due to deficient nucleotide excision repair. It is characterized by hypersensitivity of the skin to sunlight, followed by high incidence of skin cancer and frequent neurologic abnormalities. XPV shows normal nucleotide excision repair, but an exaggerated delay in recovery of replicative DNA synthesis. Most XPV patients do not develop clinical symptoms and skin neoplasias until a later age. Clinical manifestations are limited to photo-induced deterioration of the skin and eyes.<ref>PMID:10385124</ref> <ref>PMID:10398605</ref> <ref>PMID:11032022</ref> <ref>PMID:11121129</ref> <ref>PMID:11773631</ref>
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== Function ==
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[https://www.uniprot.org/uniprot/POLH_HUMAN POLH_HUMAN] DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Plays an important role in the repair of UV-induced pyrimidine dimers. Depending on the context, it inserts the correct base, but causes frequent base transitions and transversions. May play a role in hypermutation at immunoglobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but does not have lyase activity. Targets POLI to replication foci.<ref>PMID:10385124</ref> <ref>PMID:11743006</ref> <ref>PMID:11376341</ref> <ref>PMID:14630940</ref> <ref>PMID:14734526</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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DNA lesions that elude repair may undergo translesion synthesis catalyzed by Y-family DNA polymerases. O(4)-Alkylthymidines, persistent adducts that can result from carcinogenic agents, may be encountered by DNA polymerases. The influence of lesion orientation around the C4-O(4) bond on processing by human DNA polymerase eta (hPol eta) was studied for oligonucleotides containing O(4)-methylthymidine, O(4)-ethylthymidine, and analogs restricting the O(4)-methylene group in an anti-orientation. Primer extension assays revealed that the O(4)-alkyl orientation influences hPol eta bypass. Crystal structures of hPol eta*DNA*dNTP ternary complexes with O(4)-methyl- or O(4)-ethylthymidine in the template strand showed the nucleobase of the former lodged near the ceiling of the active site, with the syn-O(4)-methyl group engaged in extensive hydrophobic interactions. This unique arrangement for O(4)-methylthymidine with hPol eta, inaccessible for the other analogs due to steric/conformational restriction, is consistent with differences observed for nucleotide incorporation and supports the concept that lesion conformation influences extension across DNA damage. Together, these results provide mechanistic insights on the mutagenicity of O(4)MedT and O(4)EtdT when acted upon by hPol eta.
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Authors: Patra, A., OFlaherty, D.K., Egli, M.
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Lesion Orientation of O(4)-Alkylthymidine Influences Replication by Human DNA Polymerase eta.,O'Flaherty DK, Patra A, Su Y, Guengerich FP, Egli M, Wilds CJ Chem Sci. 2016 Aug 1;7(8):4896-4904. doi: 10.1039/C6SC00666C. Epub 2016 Apr 26. PMID:27574558<ref>PMID:27574558</ref>
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Description: Crystal Structure of Human DNA Polymerase Eta Inserting dGMPNPP Opposite O4-Methylhymidine
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[Category: Unreleased Structures]]
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</div>
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[[Category: Oflaherty, D.K]]
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<div class="pdbe-citations 5dlg" style="background-color:#fffaf0;"></div>
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[[Category: Egli, M]]
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[[Category: Patra, A]]
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==See Also==
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Homo sapiens]]
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[[Category: Large Structures]]
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[[Category: Synthetic construct]]
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[[Category: Egli M]]
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[[Category: OFlaherty DK]]
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[[Category: Patra A]]

Current revision

Crystal Structure of Human DNA Polymerase Eta Inserting dGMPNPP Opposite O4-Methylhymidine

PDB ID 5dlg

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