1cyq: Difference between revisions

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==INTRON ENCODED HOMING ENDONUCLEASE I-PPOI (H98A)/DNA HOMING SITE COMPLEX==
==INTRON ENCODED HOMING ENDONUCLEASE I-PPOI (H98A)/DNA HOMING SITE COMPLEX==
<StructureSection load='1cyq' size='340' side='right' caption='[[1cyq]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
<StructureSection load='1cyq' size='340' side='right'caption='[[1cyq]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1cyq]] is a 4 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=1CYQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CYQ FirstGlance]. <br>
<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>
</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]] 1.93&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1a73|1a73]], [[1a74|1a74]], [[1ipp|1ipp]]</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=1cyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cyq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1cyq RCSB], [http://www.ebi.ac.uk/pdbsum/1cyq 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=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>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[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.
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.
 
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:10581547<ref>PMID:10581547</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[Endonuclease|Endonuclease]]
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Physarum polycephalum]]
[[Category: Physarum polycephalum]]
[[Category: Chevalier, B]]
[[Category: Chevalier B]]
[[Category: Flick, K E]]
[[Category: Flick KE]]
[[Category: Galburt, E A]]
[[Category: Galburt EA]]
[[Category: Jurica, M S]]
[[Category: Jurica MS]]
[[Category: Stoddard, B L]]
[[Category: Stoddard BL]]
[[Category: Beta sheet dna binding]]
[[Category: Distorted dna]]
[[Category: His-cys box zinc binding site]]
[[Category: Hydrolase-dna complex]]
[[Category: Protein-dna complex]]

Latest revision as of 09:46, 7 February 2024

INTRON ENCODED HOMING ENDONUCLEASE I-PPOI (H98A)/DNA HOMING SITE COMPLEXINTRON ENCODED HOMING ENDONUCLEASE I-PPOI (H98A)/DNA HOMING SITE COMPLEX

Structural highlights

1cyq is a 4 chain structure with sequence from Physarum polycephalum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.93Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.

See Also

1cyq, resolution 1.93Å

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