3skd: Difference between revisions

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<StructureSection load='3skd' size='340' side='right'caption='[[3skd]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='3skd' size='340' side='right'caption='[[3skd]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3skd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SKD FirstGlance]. <br>
<table><tr><td colspan='2'>[[3skd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SKD FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
</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&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TTHB187 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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=3skd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3skd OCA], [https://pdbe.org/3skd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3skd RCSB], [https://www.ebi.ac.uk/pdbsum/3skd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3skd 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=3skd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3skd OCA], [https://pdbe.org/3skd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3skd RCSB], [https://www.ebi.ac.uk/pdbsum/3skd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3skd ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/CAS3_THET8 CAS3_THET8]] CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Cas3 plus Cascade participate in CRISPR interference, the third stage of CRISPR immunity. The N-terminal domain (residues 6-260) acts as a ssDNA endonuclease, has no activity on dsDNA.<ref>PMID:21775431</ref> 
[https://www.uniprot.org/uniprot/CAS3_THET8 CAS3_THET8] CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Cas3 plus Cascade participate in CRISPR interference, the third stage of CRISPR immunity. The N-terminal domain (residues 6-260) acts as a ssDNA endonuclease, has no activity on dsDNA.<ref>PMID:21775431</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
RNA transcribed from clustered regularly interspaced short palindromic repeats (CRISPRs) protects many prokaryotes from invasion by foreign DNA such as viruses, conjugative plasmids and transposable elements. CRISPR-associated protein 3 (Cas3) is essential for this CRISPR protection and is thought to mediate cleavage of the foreign DNA through its N-terminal histidine-aspartate (HD) domain. We report here the 1.8 A crystal structure of the HD domain of cas3 from Thermus thermophilus HB8. Structural and biochemical studies predict that this enzyme binds two metal ions at its active site. We also demonstrate that the single-stranded DNA endonuclease activity of this T. thermophilus domain is activated not by magnesium, but by transition metal ions such as manganese and nickel. Structure-guided mutagenesis confirms the importance of the metal binding residues for the nuclease activity, and identifies other active site residues. Overall, these results provide a framework for understanding the role of cas3 in the CRISPR system.
 
Structural and biochemical analysis of the nuclease domain of the clustered regularly interspaced short palindromic repeat (CRISPR) associated protein 3(CAS3).,Mulepati S, Bailey S J Biol Chem. 2011 Jul 20. PMID:21775431<ref>PMID:21775431</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3skd" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Thet8]]
[[Category: Thermus thermophilus HB8]]
[[Category: Bailey, S]]
[[Category: Bailey S]]
[[Category: Mulepati, S]]
[[Category: Mulepati S]]
[[Category: Ca]]
[[Category: Crispr]]
[[Category: Hd domain]]
[[Category: Hydrolase]]
[[Category: Nuclease]]

Latest revision as of 09:51, 1 March 2024

Crystal structure of the Thermus thermophilus cas3 HD domain in the presence of Ni2+

3skd, resolution 2.00Å

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