3mfi: Difference between revisions

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-{{Seed}}
-[[Image:3mfi.jpg|left|200px]]
-<!--
+==DNA Polymerase Eta in Complex With a cis-syn Thymidine Dimer==
-The line below this paragraph, containing "STRUCTURE_3mfi", creates the "Structure Box" on the page.
+<StructureSection load='3mfi' size='340' side='right'caption='[[3mfi]], [[Resolution|resolution]] 1.76&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3mfi]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MFI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MFI FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.76&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TTD:CIS-SYN+CYCLOBUTANE+THYMINE+DIMER'>TTD</scene></td></tr>
-{{STRUCTURE_3mfi|  PDB=3mfi  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3mfi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mfi OCA], [https://pdbe.org/3mfi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3mfi RCSB], [https://www.ebi.ac.uk/pdbsum/3mfi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3mfi ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/POLH_YEAST POLH_YEAST] 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. Efficiently incorporates nucleotides opposite to other UV or oxidative DNA damages like O(6)-methylguanine, 7,8-dihydro-8-oxoguanine, 2,6-diamino-4-hydroxy-5-formamidopyrimidine of 2'-deoxyguanosine (FaPydG), or p-benzoquinone DNA adducts.<ref>PMID:9409821</ref> <ref>PMID:10347143</ref> <ref>PMID:10601233</ref> <ref>PMID:9974380</ref> <ref>PMID:10924462</ref> <ref>PMID:10713149</ref> <ref>PMID:11027270</ref> <ref>PMID:10932195</ref> <ref>PMID:10725365</ref> <ref>PMID:11062246</ref> <ref>PMID:11545742</ref> <ref>PMID:11113193</ref> <ref>PMID:11238937</ref> <ref>PMID:11054429</ref> <ref>PMID:12110599</ref> <ref>PMID:11861920</ref> <ref>PMID:12899630</ref> <ref>PMID:12665597</ref> <ref>PMID:12888515</ref> <ref>PMID:12692307</ref> <ref>PMID:14527996</ref> <ref>PMID:15157108</ref> <ref>PMID:15544332</ref> <ref>PMID:15284331</ref> <ref>PMID:15333698</ref> <ref>PMID:15024063</ref> <ref>PMID:15779911</ref> <ref>PMID:16181813</ref> <ref>PMID:15520252</ref> <ref>PMID:16366567</ref> <ref>PMID:15743815</ref> <ref>PMID:16866379</ref> <ref>PMID:16387871</ref> <ref>PMID:16415180</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mf/3mfi_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3mfi ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+DNA polymerase eta (Poleta) is unique among eukaryotic polymerases in its proficient ability for error-free replication through ultraviolet-induced cyclobutane pyrimidine dimers, and inactivation of Poleta (also known as POLH) in humans causes the variant form of xeroderma pigmentosum (XPV). We present the crystal structures of Saccharomyces cerevisiae Poleta (also known as RAD30) in ternary complex with a cis-syn thymine-thymine (T-T) dimer and with undamaged DNA. The structures reveal that the ability of Poleta to replicate efficiently through the ultraviolet-induced lesion derives from a simple and yet elegant mechanism, wherein the two Ts of the T-T dimer are accommodated in an active site cleft that is much more open than in other polymerases. We also show by structural, biochemical and genetic analysis that the two Ts are maintained in a stable configuration in the active site via interactions with Gln 55, Arg 73 and Met 74. Together, these features define the basis for Poleta's action on ultraviolet-damaged DNA that is crucial in suppressing the mutagenic and carcinogenic consequences of sun exposure, thereby reducing the incidence of skin cancers in humans.
-===DNA Polymerase Eta in Complex With a cis-syn Thymidine Dimer===
+Structural basis for the suppression of skin cancers by DNA polymerase eta.,Silverstein TD, Johnson RE, Jain R, Prakash L, Prakash S, Aggarwal AK Nature. 2010 Jun 24;465(7301):1039-43. PMID:20577207<ref>PMID:20577207</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3mfi" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-MFI is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MFI OCA].
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-[[Category: DNA-directed DNA polymerase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Aggarwal, A K.]]
+[[Category: Aggarwal AK]]
-[[Category: Jain, R.]]
+[[Category: Jain R]]
-[[Category: Johnson, R E.]]
+[[Category: Johnson RE]]
-[[Category: Prakash, L.]]
+[[Category: Prakash L]]
-[[Category: Prakash, S.]]
+[[Category: Prakash S]]
-[[Category: Silverstein, T D.]]
+[[Category: Silverstein TD]]
-[[Category: Cpd]]
-[[Category: Dna damage]]
-[[Category: Dna polymerase eta]]
-[[Category: Dna repair]]
-[[Category: Dna replication]]
-[[Category: Dna synthesis]]
-[[Category: Dna-binding]]
-[[Category: Dna-directed dna polymerase]]
-[[Category: Magnesium]]
-[[Category: Metal-binding]]
-[[Category: Mutator protein]]
-[[Category: Nucleotidyltransferase]]
-[[Category: Nucleus]]
-[[Category: Protein-dna complex]]
-[[Category: Thymidine dimer]]
-[[Category: Transferase-dna complex]]
-[[Category: Uv-damage]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 23 08:50:59 2010''