2v4q: Difference between revisions

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-{{Seed}}
-[[Image:2v4q.png|left|200px]]
-<!--
+==Post-insertion complex of the Y-family DNA polymerase Dpo4 with M1dG containing template DNA==
-The line below this paragraph, containing "STRUCTURE_2v4q", creates the "Structure Box" on the page.
+<StructureSection load='2v4q' size='340' side='right'caption='[[2v4q]], [[Resolution|resolution]] 2.60&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'>[[2v4q]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V4Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V4Q 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]] 2.6&#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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=M1G:3-(2-DEOXY-BETA-D-RIBOFURANOSYL)-PYRIDO[5,6-A]-PURINE-10-ONE-5-MONOPHOSPHATE'>M1G</scene></td></tr>
-{{STRUCTURE_2v4q|  PDB=2v4q  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2v4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v4q OCA], [https://pdbe.org/2v4q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v4q RCSB], [https://www.ebi.ac.uk/pdbsum/2v4q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v4q ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPO4_SACS2 DPO4_SACS2] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. It is involved in translesional synthesis.
+== 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/v4/2v4q_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=2v4q ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Oxidative stress can induce the formation of reactive electrophiles, such as DNA peroxidation products, e.g. base propenals, and lipid peroxidation products, e.g. malondialdehyde. Base propenals and malondialdehyde react with DNA to form adducts, including 3-(2'-deoxy-ss-D-erythro-pentofuranosyl)-pyrimido[1,2-alpha]purin-10(3H)-o ne (M1dG). When paired opposite cytosine in duplex DNA at physiological pH, M1dG undergoes ring opening to form N2-(3-oxo-1-propenyl)-dG (N2-OPdG). Previous work has shown that M1dG is mutagenic in bacteria and mammalian cells and that its mutagenicity in Escherichia coli is dependent on induction of the SOS response, indicating a role for translesion DNA polymerases in the bypass of M1dG. To probe the mechanism by which translesion polymerases bypass M1dG, kinetic and structural studies were conducted with a model Y-family DNA polymerase, Dpo4 from Sulfolobus solfataricus. Steady-state incorporation of dNTPs opposite M1dG was reduced 260- to 2,900-fold and exhibited a preference for dATP incorporation. LC-MS/MS analysis of the full-length extension products revealed a spectrum of products arising principally by incorporation of dC or dA opposite M1dG followed by partial or full-length extension. A greater proportion of -1 deletions were observed when dT was positioned 5' of M1dG. Two crystal structures were solved, including a "Type II" frameshift deletion complex and another complex with Dpo4 bound to a dC:M1dG pair located in the post-insertion context. Importantly, M1dG was in the ring-closed state in both structures and in the structure with dC opposite M1dG, the dC residue moved out of the Dpo4 active site, into the minor groove. The results are consistent with the reported mutagenicity of M1dG and illustrate how the lesion may affect replication events.
-===POST-INSERTION COMPLEX OF THE Y-FAMILY DNA POLYMERASE DPO4 WITH M1DG CONTAINING TEMPLATE DNA===
+Structural and Functional Analysis of Sulfolobus solfataricus Y-family DNA polymerase Dpo4-catalyzed Bypass of the Malondialdehyde-deoxyguanosine Adduct.,Eoff RL, Stafford JB, Szekely J, Rizzo CJ, Egli M, Guengerich FP, Marnett LJ Biochemistry. 2009 Jun 4. PMID:19492857<ref>PMID:19492857</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2v4q" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19492857}}, adds the Publication Abstract to the page
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19492857 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19492857}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-V4Q is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V4Q OCA].
+[[Category: Saccharolobus solfataricus P2]]
+[[Category: Egli M]]
-==Reference==
+[[Category: Eoff RL]]
-<ref group="xtra">PMID:19492857</ref><references group="xtra"/>
+[[Category: Guengerich FP]]
-[[Category: DNA-directed DNA polymerase]]
+[[Category: Marnett LJ]]
-[[Category: Sulfolobus solfataricus]]
+[[Category: Rizzo CJ]]
-[[Category: Egli, M.]]
+[[Category: Stafford JB]]
-[[Category: Eoff, R L.]]
+[[Category: Szekely J]]
-[[Category: Guengerich, F P.]]
-[[Category: Marnett, L J.]]
-[[Category: Rizzo, C J.]]
-[[Category: Stafford, J B.]]
-[[Category: Szekely, J.]]
-[[Category: Cytoplasm]]
-[[Category: Dna adduct]]
-[[Category: Dna damage]]
-[[Category: Dna repair]]
-[[Category: Dna replication]]
-[[Category: Dna-binding]]
-[[Category: Dna-directed dna polymerase]]
-[[Category: Dpo4]]
-[[Category: M1dg]]
-[[Category: Magnesium]]
-[[Category: Metal-binding]]
-[[Category: Mutator protein]]
-[[Category: Nucleotidyltransferase]]
-[[Category: Polymerase]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jun 25 08:27:16 2009''