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| ==L116A MUTANT OF THE HOMING ENDONUCLEASE I-PPOI COMPLEXED TO HOMING SITE DNA.== | | ==L116A MUTANT OF THE HOMING ENDONUCLEASE I-PPOI COMPLEXED TO HOMING SITE DNA.== |
| <StructureSection load='1evw' size='340' side='right' caption='[[1evw]], [[Resolution|resolution]] 3.10Å' scene=''> | | <StructureSection load='1evw' size='340' side='right'caption='[[1evw]], [[Resolution|resolution]] 3.10Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[1evw]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Physarum_polycephalum Physarum polycephalum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EVW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EVW FirstGlance]. <br> | | <table><tr><td colspan='2'>[[1evw]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Physarum_polycephalum Physarum polycephalum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EVW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EVW FirstGlance]. <br> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3.1Å</td></tr> |
| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1a73|1a73]], [[1evx|1evx]], [[1cz0|1cz0]], [[1cyq|1cyq]]</td></tr> | | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1evw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1evw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1evw RCSB], [http://www.ebi.ac.uk/pdbsum/1evw PDBsum]</span></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=1evw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1evw OCA], [https://pdbe.org/1evw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1evw RCSB], [https://www.ebi.ac.uk/pdbsum/1evw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1evw ProSAT]</span></td></tr> |
| </table> | | </table> |
| == Function == | | == Function == |
| [[http://www.uniprot.org/uniprot/PPO1_PHYPO PPO1_PHYPO]] Mediates the homing of a group I intron in the ribosomal DNA. Makes a four-base staggered cut in its ribosomal DNA target sequence. | | [https://www.uniprot.org/uniprot/PPO1_PHYPO PPO1_PHYPO] Mediates the homing of a group I intron in the ribosomal DNA. Makes a four-base staggered cut in its ribosomal DNA target sequence. |
| <div style="background-color:#fffaf0;">
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| == Publication Abstract from PubMed ==
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| The homing endonuclease I-PpoI severely bends its DNA target, resulting in significant deformations of the minor and major groove near the scissile phosphate groups. To study the role of conformational changes within the protein catalyst and the DNA substrate, we have determined the structure of the enzyme in the absence of bound DNA, performed gel retardation analyses of DNA binding and bending, and have mutagenized a leucine residue that contacts an adenine nucleotide at the site of cleavage. The structure of the L116A/DNA complex has been determined and the effects of the mutation on affinity and catalysis have been measured. The wild-type protein displays a rigid-body rotation of its individual subunits upon DNA binding. Homing site DNA is not detectably bent in the absence of protein, but is sharply bent in both the wild-type and L116A complexes. These results indicate that binding involves a large distortion of the DNA and a smaller change in protein conformation. Leucine 116 is critical for binding and catalysis: it appears to be important for forming a well-ordered protein-DNA complex at the cleavage site, for maximal deformation of the DNA, and for desolvation of the nucleotide bases that are partially unstacked in the enzyme complex.
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| Conformational changes and cleavage by the homing endonuclease I-PpoI: a critical role for a leucine residue in the active site.,Galburt EA, Chadsey MS, Jurica MS, Chevalier BS, Erho D, Tang W, Monnat RJ Jr, Stoddard BL J Mol Biol. 2000 Jul 21;300(4):877-87. PMID:10891275<ref>PMID:10891275</ref>
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| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| ==See Also== | | ==See Also== |
| *[[Endonuclease|Endonuclease]] | | *[[Endonuclease 3D structures|Endonuclease 3D structures]] |
| == References ==
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| <references/>
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] |
| [[Category: Physarum polycephalum]] | | [[Category: Physarum polycephalum]] |
| [[Category: Chevalier, B S]] | | [[Category: Chevalier BS]] |
| [[Category: Erho, D]] | | [[Category: Erho D]] |
| [[Category: Galburt, E A]] | | [[Category: Galburt EA]] |
| [[Category: Jurica, M S]] | | [[Category: Jurica MS]] |
| [[Category: Stoddard, B L]] | | [[Category: Stoddard BL]] |
| [[Category: Bent dna]]
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| [[Category: C-terminal exchanged dimer interface]]
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| [[Category: Dna binding b-sheet]]
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| [[Category: Hydrolase-dna complex]]
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