1rys: Difference between revisions

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-{{Seed}}
-[[Image:1rys.png|left|200px]]
-<!--
+==REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION==
-The line below this paragraph, containing "STRUCTURE_1rys", creates the "Structure Box" on the page.
+<StructureSection load='1rys' size='340' side='right'caption='[[1rys]], [[Resolution|resolution]] 2.03&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'>[[1rys]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1pm8 1pm8]. The July 2007 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Thymine Dimers''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2007_7 10.2210/rcsb_pdb/mom_2007_7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RYS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RYS 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]] 2.03&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-{{STRUCTURE_1rys|  PDB=1rys  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rys OCA], [https://pdbe.org/1rys PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rys RCSB], [https://www.ebi.ac.uk/pdbsum/1rys PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rys 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/ry/1rys_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=1rys ConSurf].
+<div style="clear:both"></div>
-===REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION===
+==See Also==
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
+__TOC__
-<!--
+</StructureSection>
-The line below this paragraph, {{ABSTRACT_PUBMED_12904819}}, adds the Publication Abstract to the page
+[[Category: Large Structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12904819 is the PubMed ID number.
+[[Category: RCSB PDB Molecule of the Month]]
--->
+[[Category: Saccharolobus solfataricus]]
-{{ABSTRACT_PUBMED_12904819}}
-==About this Structure==
-RYS is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1pm8 1pm8]. Additional information on 1RYS is available in a page on [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb91_1.html Thymine Dimers] at the RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RYS OCA].
-==Reference==
-Replication of a cis-syn thymine dimer at atomic resolution., Ling H, Boudsocq F, Plosky BS, Woodgate R, Yang W, Nature. 2003 Aug 28;424(6952):1083-7. Epub 2003 Aug 6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12904819 12904819]
-[[Category: DNA-directed DNA polymerase]]
-[[Category: Single protein]]
-[[Category: Sulfolobus solfataricus]]
 [[Category: Thymine Dimers]]
-[[Category: Boudsocq, F.]]
+[[Category: Boudsocq F]]
-[[Category: Ling, H.]]
+[[Category: Ling H]]
-[[Category: Plosky, B.]]
+[[Category: Plosky B]]
-[[Category: Woodgate, R.]]
+[[Category: Woodgate R]]
-[[Category: Yang, W.]]
+[[Category: Yang W]]
-[[Category: Cpd dimer]]
-[[Category: Lesion bypass]]
-[[Category: Polymerase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 23 10:48:02 2008''