1cyq: Difference between revisions

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-[[Image:1cyq.gif|left|200px]]
- {{Structure
+==INTRON ENCODED HOMING ENDONUCLEASE I-PPOI (H98A)/DNA HOMING SITE COMPLEX==
-|PDB= 1cyq |SIZE=350|CAPTION= <scene name='initialview01'>1cyq</scene>, resolution 1.93&Aring;
+<StructureSection load='1cyq' size='340' side='right'caption='[[1cyq]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
+<table><tr><td colspan='2'>[[1cyq]] is a 4 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=1CYQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CYQ FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.93&#8491;</td></tr>
-|GENE=
+<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>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1cyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cyq OCA], [https://pdbe.org/1cyq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cyq RCSB], [https://www.ebi.ac.uk/pdbsum/1cyq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cyq ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1a73|1A73]], [[1a74|1A74]], [[1ipp|1IPP]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1cyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cyq OCA], [http://www.ebi.ac.uk/pdbsum/1cyq PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1cyq RCSB]</span>
+== Function ==
-}}
+[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.
-'''INTRON ENCODED HOMING ENDONUCLEASE I-PPOI (H98A)/DNA HOMING SITE COMPLEX'''
+==See Also==
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-A novel mechanism of DNA endonucleolytic cleavage has been visualized for the homing endonuclease I-PpoI by trapping the uncleaved enzyme-substrate complex and comparing it to the previously visualized product complex. This enzyme employs a unique single metal mechanism. A magnesium ion is coordinated by an asparagine residue and two DNA oxygen atoms and stabilizes the phosphoanion transition state and the 3'oxygen leaving group. A hydrolytic water molecule is activated by a histidine residue for an in-line attack on the scissile phosphate. A strained enzyme-substrate-metal complex is formed before cleavage, then relaxed during the reaction.
+[[Category: Large Structures]]
-==About this Structure==
-CYQ is a [[Single protein]] structure of 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=1CYQ OCA].
-==Reference==
-A novel endonuclease mechanism directly visualized for I-PpoI., Galburt EA, Chevalier B, Tang W, Jurica MS, Flick KE, Monnat RJ Jr, Stoddard BL, Nat Struct Biol. 1999 Dec;6(12):1096-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10581547 10581547]
 [[Category: Physarum polycephalum]]
-[[Category: Single protein]]
+[[Category: Chevalier B]]
-[[Category: Chevalier, B.]]
+[[Category: Flick KE]]
-[[Category: Flick, K E.]]
+[[Category: Galburt EA]]
-[[Category: Galburt, E A.]]
+[[Category: Jurica MS]]
-[[Category: Jurica, M S.]]
+[[Category: Stoddard BL]]
-[[Category: Stoddard, B L.]]
-[[Category: beta sheet dna binding]]
-[[Category: distorted dna]]
-[[Category: his-cys box zinc binding site]]
-[[Category: protein-dna complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:31:02 2008''