3ool

From Proteopedia

(Difference between revisions)

Revision as of 10:51, 18 May 2022

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

Structural highlights

3ool is a 3 chain structure with sequence from Atcc 18824. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	3oor
Gene:	SceI,omega (ATCC 18824)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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'.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Joshi R, Ho KK, Tenney K, Chen JH, Golden BL, Gimble FS. Evolution of I-SceI Homing Endonucleases with Increased DNA Recognition Site Specificity. J Mol Biol. 2010 Oct 26. PMID:21029741 doi:10.1016/j.jmb.2010.10.029

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ool"

@@ Line 1: / Line 1: @@
 ==I-SceI complexed with C/G+4 DNA substrate==
-<StructureSection load='3ool' size='340' side='right' caption='[[3ool]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='3ool' size='340' side='right'caption='[[3ool]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ool]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OOL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ool]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. 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>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3oor|3oor]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3oor|3oor]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SceI,omega ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SceI,omega ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=3ool FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ool OCA], [http://pdbe.org/3ool PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ool RCSB], [http://www.ebi.ac.uk/pdbsum/3ool PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ool ProSAT]</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=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 ==
-[[http://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'.
+[[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 ==
@@ Line 20: / Line 20: @@
 </div>
 <div class="pdbe-citations 3ool" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
 == References ==
 <references/>
@@ Line 25: / Line 28: @@
 </StructureSection>
 [[Category: Atcc 18824]]
+[[Category: Large Structures]]
 [[Category: Chen, J H]]
 [[Category: Gimble, F S]]

3ool

From Proteopedia

Revision as of 10:51, 18 May 2022

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

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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