1cyq: Difference between revisions

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[[Image:1cyq.gif|left|200px]]


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==INTRON ENCODED HOMING ENDONUCLEASE I-PPOI (H98A)/DNA HOMING SITE COMPLEX==
The line below this paragraph, containing "STRUCTURE_1cyq", creates the "Structure Box" on the page.
<StructureSection load='1cyq' size='340' side='right'caption='[[1cyq]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
or leave the SCENE parameter empty for the default display.
</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>
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<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>
{{STRUCTURE_1cyq|  PDB=1cyq  |  SCENE= }}
<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>
== 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==
1CYQ 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: 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 Fri May  2 13:15:03 2008''

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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