3ool: Difference between revisions
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< | ==I-SceI complexed with C/G+4 DNA substrate== | ||
<StructureSection load='3ool' size='340' side='right'caption='[[3ool]], [[Resolution|resolution]] 2.30Å' scene=''> | |||
== Structural highlights == | |||
or the | <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> | ||
or | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> | ||
-- | <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> | ||
<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> | |||
</table> | |||
== Function == | |||
[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'. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3ool" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Endonuclease 3D structures|Endonuclease 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
[[ | |||
== | |||
< | |||
[[Category: Saccharomyces cerevisiae]] | [[Category: Saccharomyces cerevisiae]] | ||
[[Category: Chen | [[Category: Chen J-H]] | ||
[[Category: Gimble | [[Category: Gimble FS]] | ||
[[Category: Golden | [[Category: Golden BL]] | ||
[[Category: Joshi | [[Category: Joshi R]] | ||
Latest revision as of 12:42, 6 September 2023
I-SceI complexed with C/G+4 DNA substrateI-SceI complexed with C/G+4 DNA substrate
Structural highlights
FunctionSCE1_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'. Publication Abstract from PubMedElucidating 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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