1rpl: Difference between revisions

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-[[Image:1rpl.jpg|left|200px]]<br /><applet load="1rpl" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1rpl, resolution 2.3&Aring;" />
-'''2.3 ANGSTROMS CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF DNA POLYMERASE BETA'''<br />
-==Overview==
+==2.3 ANGSTROMS CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF DNA POLYMERASE BETA==
-The crystal structure of the catalytic domain of rat DNA polymerase beta, (pol beta) has been determined at 2.3 A resolution and refined to an R, factor of 0.22. The mixed alpha/beta protein has three subdomains arranged, in an overall U shape reminiscent of other polymerase structures. The, folding topology of pol beta, however, is unique. Two divalent metals bind, near three aspartic acid residues implicated in the catalytic activity. In, the presence of Mn2+ and dTTP, interpretable electron density is seen for, two metals and the triphosphate, but not the deoxythymidine moiety. The, principal interaction of the triphosphate moiety is with the bound, divalent metals.
+<StructureSection load='1rpl' size='340' side='right'caption='[[1rpl]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1rpl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RPL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RPL 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]] 2.3&#8491;</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=1rpl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rpl OCA], [https://pdbe.org/1rpl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rpl RCSB], [https://www.ebi.ac.uk/pdbsum/1rpl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rpl ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPOLB_RAT DPOLB_RAT] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.
+== 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/rp/1rpl_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=1rpl ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-RPL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RPL OCA].
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-.3 A crystal structure of the catalytic domain of DNA polymerase beta., Davies JF 2nd, Almassy RJ, Hostomska Z, Ferre RA, Hostomsky Z, Cell. 1994 Mar 25;76(6):1123-33. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8137427 8137427]
+[[Category: Large Structures]]
 [[Category: Rattus norvegicus]]
-[[Category: Single protein]]
+[[Category: Almassy RJ]]
-[[Category: Almassy, R.J.]]
+[[Category: Davies II JF]]
-[[Category: II, J.F.Davies.]]
-[[Category: nucleotidyltransferase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 01:46:34 2007''