6ozi
From Proteopedia
(Difference between revisions)
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| - | '''Unreleased structure''' | ||
| - | + | ==Crystal structure of Ciona intestinalis (Ci) Endonuclease V (D234N) in complex with a 23mer DNA containing an inosine followed by a ribo-adenosine== | |
| + | <StructureSection load='6ozi' size='340' side='right'caption='[[6ozi]], [[Resolution|resolution]] 2.30Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[6ozi]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ascidia_intestinalis Ascidia intestinalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OZI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OZI FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr> | ||
| + | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</scene></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LOC100181026 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7719 Ascidia intestinalis])</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=6ozi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ozi OCA], [http://pdbe.org/6ozi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ozi RCSB], [http://www.ebi.ac.uk/pdbsum/6ozi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ozi ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Endonuclease V (EndoV) cleaves the second phosphodiester bond 3' to a deaminated adenosine (inosine). Although highly conserved, EndoV homologs change substrate preference from DNA in bacteria to RNA in eukaryotes. We have characterized EndoV from six different species and determined crystal structures of human EndoV and three EndoV homologs from bacteria to mouse in complex with inosine-containing DNA/RNA hybrid or double-stranded RNA (dsRNA). Inosine recognition is conserved, but changes in several connecting loops in eukaryotic EndoV confer recognition of 3 ribonucleotides upstream and 7 or 8 bp of dsRNA downstream of the cleavage site, and bacterial EndoV binds only 2 or 3 nt flanking the scissile phosphate. In addition to the two canonical metal ions in the active site, a third Mn(2+) that coordinates the nucleophilic water appears necessary for product formation. Comparison of EndoV with its homologs RNase H1 and Argonaute reveals the principles by which these enzymes recognize RNA versus DNA. | ||
| - | + | Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.,Wu J, Samara NL, Kuraoka I, Yang W Mol Cell. 2019 Oct 3;76(1):44-56.e3. doi: 10.1016/j.molcel.2019.06.046. Epub 2019, Aug 20. PMID:31444105<ref>PMID:31444105</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: Samara, N | + | <div class="pdbe-citations 6ozi" style="background-color:#fffaf0;"></div> |
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Ascidia intestinalis]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Samara, N L]] | ||
[[Category: Yang, W]] | [[Category: Yang, W]] | ||
| + | [[Category: Adenosine deamination]] | ||
| + | [[Category: Dna damage]] | ||
| + | [[Category: Hydrolase]] | ||
| + | [[Category: Metal ion dependent catalysis]] | ||
| + | [[Category: Nucleic acid hydrolysis]] | ||
| + | [[Category: Rna recognition]] | ||
Revision as of 07:27, 16 October 2019
Crystal structure of Ciona intestinalis (Ci) Endonuclease V (D234N) in complex with a 23mer DNA containing an inosine followed by a ribo-adenosine
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