1xsn: Difference between revisions

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-[[Image:1xsn.gif|left|200px]]<br /><applet load="1xsn" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1xsn, resolution 1.95&Aring;" />
-'''Crystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap and ddTTP'''<br />
-==Overview==
+==Crystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap and ddTTP==
-Pol lambda is a family X member believed to fill short gaps during DNA repair. Here we report crystal structures of Pol lambda representing three steps in filling a single-nucleotide gap. These structures indicate that, unlike other DNA polymerases, Pol lambda does not undergo large subdomain movements during catalysis, and they provide a clear characterization of the geometry and stereochemistry of the in-line nucleotidyl transfer reaction.
+<StructureSection load='1xsn' size='340' side='right'caption='[[1xsn]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1xsn]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XSN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XSN 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]] 1.95&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2DT:3-DEOXYTHYMIDINE-5-MONOPHOSPHATE'>2DT</scene>, <scene name='pdbligand=D3T:2,3-DIDEOXY-THYMIDINE-5-TRIPHOSPHATE'>D3T</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=1xsn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xsn OCA], [https://pdbe.org/1xsn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xsn RCSB], [https://www.ebi.ac.uk/pdbsum/1xsn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xsn ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPOLL_HUMAN DPOLL_HUMAN] Repair polymerase. Involved in base excision repair (BER) responsible for repair of lesions that give rise to abasic (AP) sites in DNA. Has both DNA polymerase and terminal transferase activities. Has a 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity.<ref>PMID:11457865</ref> <ref>PMID:15537631</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/xs/1xsn_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=1xsn ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-XSN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=NA:'>NA</scene>, <scene name='pdbligand=D3T:'>D3T</scene> and <scene name='pdbligand=EDO:'>EDO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XSN OCA].
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
+== References ==
-==Reference==
+<references/>
-A closed conformation for the Pol lambda catalytic cycle., Garcia-Diaz M, Bebenek K, Krahn JM, Kunkel TA, Pedersen LC, Nat Struct Mol Biol. 2005 Jan;12(1):97-8. Epub 2004 Dec 19. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15608652 15608652]
+__TOC__
-[[Category: DNA-directed DNA polymerase]]
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Bebenek, K.]]
+[[Category: Bebenek K]]
-[[Category: Garcia-Diaz, M.]]
+[[Category: Garcia-Diaz M]]
-[[Category: Krahn, J M.]]
+[[Category: Krahn JM]]
-[[Category: Kunkel, T A.]]
+[[Category: Kunkel TA]]
-[[Category: Pedersen, L C.]]
+[[Category: Pedersen LC]]
-[[Category: D3T]]
-[[Category: EDO]]
-[[Category: MG]]
-[[Category: NA]]
-[[Category: dna polymerase lambda]]
-[[Category: helix-hairpin-helix]]
-[[Category: protein-dna complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:58:14 2008''