3c0x: Difference between revisions
Jump to navigation
Jump to search
New page: left|200px <!-- The line below this paragraph, containing "STRUCTURE_3c0x", creates the "Structure Box" on the page. You may change the PDB parameter (which sets the PD... |
No edit summary |
||
| (10 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
==I-SceI in complex with a top nicked DNA substrate== | |||
<StructureSection load='3c0x' size='340' side='right'caption='[[3c0x]], [[Resolution|resolution]] 2.30Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3c0x]] is a 4 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=3C0X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C0X FirstGlance]. <br> | |||
</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=3c0x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c0x OCA], [https://pdbe.org/3c0x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c0x RCSB], [https://www.ebi.ac.uk/pdbsum/3c0x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c0x 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'. | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c0/3c0x_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3c0x ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
I-SceI is a homing endonuclease that specifically cleaves an 18-bp double-stranded DNA. I-SceI exhibits a strong preference for cleaving the bottom strand DNA. The published structure of I-SceI bound to an uncleaved DNA substrate provided a mechanism for bottom strand cleavage but not for top strand cleavage. To more fully elucidate the I-SceI catalytic mechanism, we determined the X-ray structures of I-SceI in complex with DNA substrates that are nicked in either the top or bottom strands. The structures resemble intermediates along the DNA cleavage reaction. In a structure containing a nick in the top strand, the spatial arrangement of metal ions is similar to that observed in the structure that contains uncleaved DNA, suggesting that cleavage of the bottom strand occurs by a common mechanism regardless of whether this strand is cleaved first or second. In the structure containing a nick in the bottom strand, a new metal binding site is present in the active site that cleaves the top strand. This new metal and a candidate nucleophilic water molecule are correctly positioned to cleave the top strand following bottom strand cleavage, providing a plausible mechanism for top strand cleavage. | |||
Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway.,Moure CM, Gimble FS, Quiocho FA Nucleic Acids Res. 2008 Jun;36(10):3287-96. Epub 2008 Apr 19. PMID:18424798<ref>PMID:18424798</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3c0x" style="background-color:#fffaf0;"></div> | |||
== | ==See Also== | ||
*[[Endonuclease 3D structures|Endonuclease 3D structures]] | |||
[[Category: | == References == | ||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Saccharomyces cerevisiae]] | [[Category: Saccharomyces cerevisiae]] | ||
[[Category: Gimble | [[Category: Gimble FS]] | ||
[[Category: Moure | [[Category: Moure CM]] | ||
[[Category: Quiocho | [[Category: Quiocho FA]] | ||
Latest revision as of 15:19, 30 August 2023
I-SceI in complex with a top nicked DNA substrateI-SceI in complex with a top nicked 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'. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedI-SceI is a homing endonuclease that specifically cleaves an 18-bp double-stranded DNA. I-SceI exhibits a strong preference for cleaving the bottom strand DNA. The published structure of I-SceI bound to an uncleaved DNA substrate provided a mechanism for bottom strand cleavage but not for top strand cleavage. To more fully elucidate the I-SceI catalytic mechanism, we determined the X-ray structures of I-SceI in complex with DNA substrates that are nicked in either the top or bottom strands. The structures resemble intermediates along the DNA cleavage reaction. In a structure containing a nick in the top strand, the spatial arrangement of metal ions is similar to that observed in the structure that contains uncleaved DNA, suggesting that cleavage of the bottom strand occurs by a common mechanism regardless of whether this strand is cleaved first or second. In the structure containing a nick in the bottom strand, a new metal binding site is present in the active site that cleaves the top strand. This new metal and a candidate nucleophilic water molecule are correctly positioned to cleave the top strand following bottom strand cleavage, providing a plausible mechanism for top strand cleavage. Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway.,Moure CM, Gimble FS, Quiocho FA Nucleic Acids Res. 2008 Jun;36(10):3287-96. Epub 2008 Apr 19. PMID:18424798[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||