3qe9: Difference between revisions

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 ==Crystal structure of human exonuclease 1 Exo1 (D173A) in complex with DNA (complex I)==
-<StructureSection load='3qe9' size='340' side='right' caption='[[3qe9]], [[Resolution|resolution]] 2.51&Aring;' scene=''>
+<StructureSection load='3qe9' size='340' side='right'caption='[[3qe9]], [[Resolution|resolution]] 2.51&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3qe9]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QE9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QE9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3qe9]] is a 6 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=3QE9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QE9 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.51&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3qea|3qea]], [[3qeb|3qeb]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">EXO1, EXOI, HEX1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3qe9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qe9 OCA], [https://pdbe.org/3qe9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qe9 RCSB], [https://www.ebi.ac.uk/pdbsum/3qe9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qe9 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3qe9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qe9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qe9 RCSB], [http://www.ebi.ac.uk/pdbsum/3qe9 PDBsum]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/EXO1_HUMAN EXO1_HUMAN] 5'->3' double-stranded DNA exonuclease which may also possess a cryptic 3'->5' double-stranded DNA exonuclease activity. Functions in DNA mismatch repair (MMR) to excise mismatch-containing DNA tracts directed by strand breaks located either 5' or 3' to the mismatch. Also exhibits endonuclease activity against 5'-overhanging flap structures similar to those generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Required for somatic hypermutation (SHM) and class switch recombination (CSR) of immunoglobulin genes. Essential for male and female meiosis.<ref>PMID:10364235</ref> <ref>PMID:10608837</ref> <ref>PMID:11809771</ref> <ref>PMID:11842105</ref> <ref>PMID:12414623</ref> <ref>PMID:12704184</ref> <ref>PMID:14636568</ref> <ref>PMID:14676842</ref> <ref>PMID:15225546</ref> <ref>PMID:15886194</ref> <ref>PMID:16143102</ref> <ref>PMID:9685493</ref>
-Human exonuclease 1 (hExo1) plays important roles in DNA repair and recombination processes that maintain genomic integrity. It is a member of the 5' structure-specific nuclease family of exonucleases and endonucleases that includes FEN-1, XPG, and GEN1. We present structures of hExo1 in complex with a DNA substrate, followed by mutagenesis studies, and propose a common mechanism by which this nuclease family recognizes and processes diverse DNA structures. hExo1 induces a sharp bend in the DNA at nicks or gaps. Frayed 5' ends of nicked duplexes resemble flap junctions, unifying the mechanisms of endo- and exonucleolytic processing. Conformational control of a mobile region in the catalytic site suggests a mechanism for allosteric regulation by binding to protein partners. The relative arrangement of substrate binding sites in these enzymes provides an elegant solution to a complex geometrical puzzle of substrate recognition and processing.
-Structures of human exonuclease 1 DNA complexes suggest a unified mechanism for nuclease family.,Orans J, McSweeney EA, Iyer RR, Hast MA, Hellinga HW, Modrich P, Beese LS Cell. 2011 Apr 15;145(2):212-23. PMID:21496642<ref>PMID:21496642</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Exonuclease|Exonuclease]]
+*[[Exonuclease 3D structures|Exonuclease 3D structures]]
 == References ==
 <references/>
@@ Line 24: / Line 18: @@
 </StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Beese, L S]]
+[[Category: Large Structures]]
-[[Category: Hast, M A]]
+[[Category: Beese LS]]
-[[Category: Hellinga, H W]]
+[[Category: Hast MA]]
-[[Category: Iyer, R R]]
+[[Category: Hellinga HW]]
-[[Category: McSweeney, E A]]
+[[Category: Iyer RR]]
-[[Category: Modrich, P]]
+[[Category: McSweeney EA]]
-[[Category: Orans, J]]
+[[Category: Modrich P]]
-[[Category: Exonuclease]]
+[[Category: Orans J]]
-[[Category: Hydrolase-dna complex]]