3ool

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{{Seed}}
 
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[[Image:3ool.jpg|left|200px]]
 
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==I-SceI complexed with C/G+4 DNA substrate==
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The line below this paragraph, containing "STRUCTURE_3ool", creates the "Structure Box" on the page.
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<StructureSection load='3ool' size='340' side='right'caption='[[3ool]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3ool]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OOL FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#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=CA:CALCIUM+ION'>CA</scene></td></tr>
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{{STRUCTURE_3ool| PDB=3ool | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ool FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ool OCA], [https://pdbe.org/3ool PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ool RCSB], [https://www.ebi.ac.uk/pdbsum/3ool PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ool ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SCE1_YEAST SCE1_YEAST] Mitochondrial DNA endonuclease involved in intron homing. It introduces a specific double-strand break in the DNA of the 21S rRNA gene and thus mediates the insertion of an intron, containing its own coding sequence (group I intron), into an intronless gene. Specifically recognizes and cleaves the sequence 5'-TAGGGATAACAGGGTAAT-3'.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Elucidating how homing endonucleases undergo changes in recognition site specificity will facilitate efforts to engineer proteins for gene therapy applications. I-SceI is a monomeric homing endonuclease that recognizes and cleaves within an 18-bp target. It tolerates limited degeneracy in its target sequence, including substitution of a C:G(+4) base pair for the wild-type A:T(+4) base pair. Libraries encoding randomized amino acids at I-SceI residue positions that contact or are proximal to A:T(+4) were used in conjunction with a bacterial one-hybrid system to select I-SceI derivatives that bind to recognition sites containing either the A:T(+4) or the C:G(+4) base pairs. As expected, isolates encoding wild-type residues at the randomized positions were selected using either target sequence. All I-SceI proteins isolated using the C:G(+4) recognition site included small side-chain substitutions at G100 and either contained (K86R/G100T, K86R/G100S and K86R/G100C) or lacked (G100A, G100T) a K86R substitution. Interestingly, the binding affinities of the selected variants for the wild-type A:T(+4) target are 4- to 11-fold lower than that of wild-type I-SceI, whereas those for the C:G(+4) target are similar. The increased specificity of the mutant proteins is also evident in binding experiments in vivo. These differences in binding affinities account for the observed approximately 36-fold difference in target preference between the K86R/G100T and wild-type proteins in DNA cleavage assays. An X-ray crystal structure of the K86R/G100T mutant protein bound to a DNA duplex containing the C:G(+4) substitution suggests how sequence specificity of a homing enzyme can increase. This biochemical and structural analysis defines one pathway by which site specificity is augmented for a homing endonuclease.
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===I-SceI complexed with C/G+4 DNA substrate===
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Evolution of I-SceI Homing Endonucleases with Increased DNA Recognition Site Specificity.,Joshi R, Ho KK, Tenney K, Chen JH, Golden BL, Gimble FS J Mol Biol. 2010 Oct 26. PMID:21029741<ref>PMID:21029741</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3ool" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_21029741}}, adds the Publication Abstract to the page
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 21029741 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_21029741}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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3OOL is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OOL OCA].
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==Reference==
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<ref group="xtra">PMID:21029741</ref><references group="xtra"/>
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[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
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[[Category: Chen, J-H.]]
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[[Category: Chen J-H]]
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[[Category: Gimble, F S.]]
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[[Category: Gimble FS]]
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[[Category: Golden, B L.]]
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[[Category: Golden BL]]
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[[Category: Joshi, R.]]
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[[Category: Joshi R]]
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[[Category: Homing endonuclease]]
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[[Category: Hydrolase-dna complex]]
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[[Category: Intron homing]]
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[[Category: Laglidadg]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Nov 18 00:53:36 2010''
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Current revision

I-SceI complexed with C/G+4 DNA substrate

PDB ID 3ool

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