4yqw: Difference between revisions

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-'''Unreleased structure'''
-The entry 4yqw is ON HOLD
+==Mutant Human DNA Polymerase Eta Q38A/R61A Inserting dCTP Opposite Template G==
+<StructureSection load='4yqw' size='340' side='right'caption='[[4yqw]], [[Resolution|resolution]] 2.06&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4yqw]] 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=4YQW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YQW FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.064&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=4yqw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yqw OCA], [https://pdbe.org/4yqw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yqw RCSB], [https://www.ebi.ac.uk/pdbsum/4yqw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yqw ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[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>
+== Function ==
+[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>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Like the other Y-Family DNA polymerases, human DNA polymerase eta (hpol eta) has relatively low fidelity and is able to tolerate damage during DNA synthesis, including 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxoG), one of the most abundant DNA lesions in the genome. Crystal structures show that Arg-61 and Gln-38 are located near the active site and may play important roles in the fidelity and efficiency of hpol eta. Site-directed mutagenesis was used to replace these side chains either alone or together, and the wild type or mutant proteins were purified and tested by replicating DNA past deoxyguanosine (G) or 8-oxoG. The catalytic activity of hpol eta was dramatically disrupted by the R61M and Q38A/R61A mutations, as opposed to the R61A and Q38A single mutants. Crystal structures of hpol eta mutant ternary complexes reveal that polarized water molecules can mimic and partially compensate for the missing side chains of Arg-61 and Gln-38 in the Q38A/R61A mutant. The combined data indicate that the positioning and positive charge of Arg-61 synergistically contribute to the nucleotidyl transfer reaction, with additional influence exerted by Gln-38. In addition, gel filtration chromatography separated multimeric and monomeric forms of wild type and mutant hpol eta, indicating the possibility that hpol eta forms multimers in vivo.
-Authors: Su, Y., Patra, A., Harp, J.M., Egli, M., Guengerich, F.P.
+Roles of Residues Arg-61 and Gln-38 of Human DNA Polymerase Eta in Bypass of Deoxyguanosine and 7,8-Dihydro-8-oxo-2'-deoxyguanosine.,Su Y, Patra A, Harp JM, Egli M, Guengerich FP J Biol Chem. 2015 May 6. pii: jbc.M115.653691. PMID:25947374<ref>PMID:25947374</ref>
-Description: Mutant Human DNA Polymerase Eta Q38A/R61A Inserting dCTP Opposite Template G
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Guengerich, F.P]]
+<div class="pdbe-citations 4yqw" style="background-color:#fffaf0;"></div>
-[[Category: Harp, J.M]]
-[[Category: Su, Y]]
+==See Also==
-[[Category: Egli, M]]
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-[[Category: Patra, A]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Synthetic construct]]
+[[Category: Egli M]]
+[[Category: Guengerich FP]]
+[[Category: Harp JM]]
+[[Category: Patra A]]
+[[Category: Su Y]]