3l8b: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3l8b.png|left|200px]]
-<!--
+==Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin==
-The line below this paragraph, containing "STRUCTURE_3l8b", creates the "Structure Box" on the page.
+<StructureSection load='3l8b' size='340' side='right'caption='[[3l8b]], [[Resolution|resolution]] 2.15&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'>[[3l8b]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_RB69 Escherichia phage RB69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L8B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3L8B 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]] 2.15&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G35:(5R)-5-CARBAMIMIDAMIDO-1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)IMIDAZOLIDINE-2,4-DIONE'>G35</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3l8b|  PDB=3l8b  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3l8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l8b OCA], [https://pdbe.org/3l8b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3l8b RCSB], [https://www.ebi.ac.uk/pdbsum/3l8b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3l8b ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPOL_BPR69 DPOL_BPR69] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.
+== 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/l8/3l8b_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=3l8b ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The oxidation of guanine generates one of the most common DNA lesions, 8-oxo-7,8-dihydroguanine (8-oxoG). The further oxidation of 8-oxoG can produce either guanidinohydantoin (Gh) in duplex DNA or spiroiminodihydantoin (Sp) in nucleosides and ssDNA. Although Gh can be a strong block for replicative DNA polymerases such as RB69 DNA polymerase, this lesion is also mutagenic: DNA polymerases bypass Gh by preferentially incorporating a purine with a slight preference for adenine, which results in G.C --&gt; T.A or G.C --&gt; C.G transversions. The 2.15 A crystal structure of the replicative RB69 DNA polymerase in complex with DNA containing Gh reveals that Gh is extrahelical and rotated toward the major groove. In this conformation Gh is no longer in position to serve as a templating base for the incorporation of an incoming nucleotide. This work also constitutes the first crystallographic structure of Gh, which is stabilized in the R configuration in the two polymerase/DNA complexes present in the crystal asymmetric unit. In contrast to 8-oxoG, Gh is found in a high syn conformation in the DNA duplex and therefore presents the same hydrogen bond donor and acceptor pattern as thymine, which explains the propensity of DNA polymerases to incorporate a purine opposite Gh when bypass occurs.
-===Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin===
+Crystal Structure of a Replicative DNA Polymerase Bound to the Oxidized Guanine Lesion Guanidinohydantoin (,).,Aller P, Ye Y, Wallace SS, J Burrows C, Doublie S Biochemistry. 2010 Feb 25. PMID:20166752<ref>PMID:20166752</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3l8b" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20166752}}, 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 20166752 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20166752}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia phage RB69]]
-L8B is a 6 chains structure with sequences from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L8B OCA].
+[[Category: Large Structures]]
+[[Category: Aller P]]
-==Reference==
+[[Category: Burrows CJ]]
-<ref group="xtra">PMID:20166752</ref><references group="xtra"/>
+[[Category: Doublie S]]
-[[Category: DNA-directed DNA polymerase]]
+[[Category: Wallace SS]]
-[[Category: Enterobacteria phage rb69]]
+[[Category: Ye Y]]
-[[Category: Aller, P.]]
-[[Category: Burrows, C J.]]
-[[Category: Doublie, S.]]
-[[Category: Wallace, S S.]]
-[[Category: Ye, Y.]]
-[[Category: Dna polymerase rb69 gp43]]
-[[Category: Dna replication]]
-[[Category: Dna-binding]]
-[[Category: Dna-directed dna polymerase]]
-[[Category: Exonuclease]]
-[[Category: Guanidinohydantoin]]
-[[Category: Hydrolase]]
-[[Category: Nuclease]]
-[[Category: Nucleotidyltransferase]]
-[[Category: Oxidative dna lesion]]
-[[Category: Protein-dna complex]]
-[[Category: Transferase]]
-[[Category: Transferase-dna complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr  7 10:12:21 2010''