1ik9: Difference between revisions

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-[[Image:1ik9.jpg|left|200px]]<br /><applet load="1ik9" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1ik9, resolution 2.30&Aring;" />
-'''CRYSTAL STRUCTURE OF A XRCC4-DNA LIGASE IV COMPLEX'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF A XRCC4-DNA LIGASE IV COMPLEX==
-A complex of two proteins, Xrcc4 and DNA ligase IV, plays a fundamental role in DNA non-homologous end joining (NHEJ), a cellular function required for double-strand break repair and V(D)J recombination. Here we report the crystal structure of human Xrcc4 bound to a polypeptide that corresponds to the DNA ligase IV sequence linking its two BRCA1 C-terminal (BRCT) domains. In the complex, a single ligase chain binds asymmetrically to an Xrcc4 dimer. The helical tails of Xrcc4 undergo a substantial conformational change relative to the uncomplexed protein, forming a coiled coil that unwinds upon ligase binding, leading to a flat interaction surface. A buried network of charged hydrogen bonds surrounded by extensive hydrophobic contacts explains the observed tightness of the interaction. The strong conservation of residues at the interface between the two proteins provides evidence that the observed mode of interaction has been maintained in NHEJ throughout evolution.
+<StructureSection load='1ik9' size='340' side='right'caption='[[1ik9]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1ik9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. The July 2004 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''DNA Ligase''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2004_7 10.2210/rcsb_pdb/mom_2004_7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IK9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IK9 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=1ik9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ik9 OCA], [https://pdbe.org/1ik9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ik9 RCSB], [https://www.ebi.ac.uk/pdbsum/1ik9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ik9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/XRCC4_HUMAN XRCC4_HUMAN] Involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. Binds to DNA and to DNA ligase IV (LIG4). The LIG4-XRCC4 complex is responsible for the NHEJ ligation step, and XRCC4 enhances the joining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends.<ref>PMID:8548796</ref> <ref>PMID:10854421</ref> <ref>PMID:10757784</ref> <ref>PMID:16412978</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/ik/1ik9_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=1ik9 ConSurf].
+<div style="clear:both"></div>
-==Disease==
+==See Also==
-Known diseases associated with this structure: LIG4 syndrome OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=601837 601837]], Multiple myeloma, resistance to OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=601837 601837]]
+*[[DNA ligase 3D structures|DNA ligase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-IK9 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. The following page contains interesting information on the relation of 1IK9 with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb55_1.html DNA Ligase]]. Active as [http://en.wikipedia.org/wiki/DNA_ligase_(ATP) DNA ligase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.1 6.5.1.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IK9 OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Crystal structure of an Xrcc4-DNA ligase IV complex., Sibanda BL, Critchlow SE, Begun J, Pei XY, Jackson SP, Blundell TL, Pellegrini L, Nat Struct Biol. 2001 Dec;8(12):1015-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11702069 11702069]
 [[Category: DNA Ligase]]
-[[Category: DNA ligase (ATP)]]
 [[Category: Homo sapiens]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Begun, J.]]
+[[Category: RCSB PDB Molecule of the Month]]
-[[Category: Blundell, T L.]]
+[[Category: Begun J]]
-[[Category: Critchlow, S E.]]
+[[Category: Blundell TL]]
-[[Category: Jackson, S P.]]
+[[Category: Critchlow SE]]
-[[Category: Pei, X Y.]]
+[[Category: Jackson SP]]
-[[Category: Pellegrini, L.]]
+[[Category: Pei XY]]
-[[Category: Sibanda, B L.]]
+[[Category: Pellegrini L]]
-[[Category: coiled coil]]
+[[Category: Sibanda BL]]
-[[Category: dna end joining]]
-[[Category: double-strand break repair]]
-[[Category: protein-protein complex]]
-[[Category: v(d)j recombination]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:12:44 2008''