3skd - Revision history

OCA at 09:51, 1 March 2024

OCA — Fri, 01 Mar 2024 09:51:18 GMT

←Older revision		Revision as of 09:51, 1 March 2024
Line 3:		Line 3:
	<StructureSection load='3skd' size='340' side='right'caption='[[3skd]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3skd' size='340' side='right'caption='[[3skd]], [[Resolution\|resolution]] 2.00Å' 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]] 2Å</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®/PubMed®, 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/>
Line 24:		Line 15:
	</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~~]]	+

OCA at 07:59, 29 June 2022

OCA — Wed, 29 Jun 2022 07:59:45 GMT

←Older revision		Revision as of 07:59, 29 June 2022
Line 1:		Line 1:

	==Crystal structure of the Thermus thermophilus cas3 HD domain in the presence of Ni2+==		==Crystal structure of the Thermus thermophilus cas3 HD domain in the presence of Ni2+==
-	<StructureSection load='3skd' size='340' side='right' caption='[[3skd]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='3skd' size='340' side='right'caption='[[3skd]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3skd]] is a 1 chain structure with sequence from [~~http~~://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 [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/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/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>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>	+	</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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TTHB187 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</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='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=3skd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3skd OCA], [~~http~~://pdbe.org/3skd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3skd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3skd PDBsum], [~~http~~://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 ==
-	[[~~http~~://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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Thet8]]		[[Category: Thet8]]
	[[Category: Bailey, S]]		[[Category: Bailey, S]]

OCA at 09:38, 11 August 2016

OCA — Thu, 11 Aug 2016 09:38:29 GMT

←Older revision		Revision as of 09:38, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the Thermus thermophilus cas3 HD domain in the presence of Ni2+==		==Crystal structure of the Thermus thermophilus cas3 HD domain in the presence of Ni2+==
	<StructureSection load='3skd' size='340' side='right' caption='[[3skd]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3skd' size='340' side='right' caption='[[3skd]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3skd]] is a 1 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SKD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3skd]] is a 1 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SKD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TTHB187 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 ~~Thermus thermophilus HB8~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TTHB187 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</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=3skd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3skd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3skd RCSB], [http://www.ebi.ac.uk/pdbsum/3skd PDBsum]</span></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=3skd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3skd OCA], [http://pdbe.org/3skd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3skd RCSB], [http://www.ebi.ac.uk/pdbsum/3skd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3skd ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 18:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3skd" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Thermus thermophilus hb8~~]]	+	[[Category: Thet8]]
	[[Category: Bailey, S]]		[[Category: Bailey, S]]
	[[Category: Mulepati, S]]		[[Category: Mulepati, S]]

OCA at 09:59, 4 January 2015

OCA — Sun, 04 Jan 2015 09:59:43 GMT

←Older revision		Revision as of 09:59, 4 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3skd]] is a 1 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SKD FirstGlance]. <br>		<table><tr><td colspan='2'>[[3skd]] is a 1 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SKD FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TTHB187 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 Thermus thermophilus HB8])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TTHB187 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 Thermus thermophilus HB8])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3skd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3skd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3skd RCSB], [http://www.ebi.ac.uk/pdbsum/3skd PDBsum]</span></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=3skd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3skd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3skd RCSB], [http://www.ebi.ac.uk/pdbsum/3skd PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 13:		Line 13:
	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>		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 ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	== References ==		== References ==
Line 20:		Line 20:
	</StructureSection>		</StructureSection>
	[[Category: Thermus thermophilus hb8]]		[[Category: Thermus thermophilus hb8]]
-	[[Category: Bailey, S.]]	+	[[Category: Bailey, S]]
-	[[Category: Mulepati, S.]]	+	[[Category: Mulepati, S]]
	[[Category: Ca]]		[[Category: Ca]]
	[[Category: Crispr]]		[[Category: Crispr]]

OCA at 05:25, 5 June 2014

OCA — Thu, 05 Jun 2014 05:25:01 GMT

←Older revision		Revision as of 05:25, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3skd.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of the Thermus thermophilus cas3 HD domain in the presence of Ni2+==
		+	<StructureSection load='3skd' size='340' side='right' caption='[[3skd]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3skd]] is a 1 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SKD FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TTHB187 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 Thermus thermophilus HB8])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3skd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3skd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3skd RCSB], [http://www.ebi.ac.uk/pdbsum/3skd PDBsum]</span></td></tr>
		+	<table>
		+	<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>
-	~~The line below this paragraph, containing "STRUCTURE_3skd", creates~~ the ~~"Structure Box" on~~ the ~~page.~~	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter~~ (~~which sets the initial scene displayed when the page is loaded~~),	+
-	~~or leave the SCENE parameter empty for the default display~~.	+
-	-->	+
-	~~{{STRUCTURE_3skd\| PDB=3skd \| SCENE= }}~~	+

-	~~===Crystal structure~~ of the ~~Thermus thermophilus cas3 HD domain in the presence of Ni2+===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21775431}}, adds the Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 21775431 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_21775431}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3skd]] is a 1 chain structure with sequence from [http:~~/~~/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].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:021775431<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Thermus thermophilus hb8]]		[[Category: Thermus thermophilus hb8]]
	[[Category: Bailey, S.]]		[[Category: Bailey, S.]]

OCA at 05:02, 10 August 2011

OCA — Wed, 10 Aug 2011 05:02:41 GMT

←Older revision		Revision as of 05:02, 10 August 2011
Line 11:		Line 11:
	===Crystal structure of the Thermus thermophilus cas3 HD domain in the presence of Ni2+===		===Crystal structure of the Thermus thermophilus cas3 HD domain in the presence of Ni2+===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21775431}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21775431 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21775431}}

	==About this Structure==		==About this Structure==
	[[3skd]] is a 1 chain structure with sequence from [http://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].		[[3skd]] is a 1 chain structure with sequence from [http://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].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021775431</ref><references group="xtra"/>
	[[Category: Thermus thermophilus hb8]]		[[Category: Thermus thermophilus hb8]]
	[[Category: Bailey, S.]]		[[Category: Bailey, S.]]

OCA at 05:05, 27 July 2011

OCA — Wed, 27 Jul 2011 05:05:17 GMT

←Older revision		Revision as of 05:05, 27 July 2011
Line 1:		Line 1:
-	[[Image:3skd.~~jpg~~\|left\|200px]]	+	[[Image:3skd.png\|left\|200px]]

	<!--		<!--

OCA at 06:58, 20 July 2011

OCA — Wed, 20 Jul 2011 06:58:47 GMT

←Older revision		Revision as of 06:58, 20 July 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3skd.jpg\|left\|200px]]

-	The ~~entry 3skd~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3skd", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3skd\| PDB=3skd \| SCENE= }}

-	~~Authors: Bailey, S., Mulepati, S.~~	+	===Crystal structure of the Thermus thermophilus cas3 HD domain in the presence of Ni2+===

-	~~Description: Crystal~~ structure ~~of the~~ Thermus thermophilus ~~cas3 HD~~ domain ~~in the presence of Ni2+~~	+
		+	==About this Structure==
		+	[[3skd]] is a 1 chain structure with sequence from [http://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].
		+	[[Category: Thermus thermophilus hb8]]
		+	[[Category: Bailey, S.]]
		+	[[Category: Mulepati, S.]]
		+	[[Category: Ca]]
		+	[[Category: Crispr]]
		+	[[Category: Hd domain]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nuclease]]

OCA at 06:51, 13 July 2011

OCA — Wed, 13 Jul 2011 06:51:57 GMT

←Older revision		Revision as of 06:51, 13 July 2011
Line 3:		Line 3:
	The entry 3skd is ON HOLD		The entry 3skd is ON HOLD

-	Authors: Bailey, S, Mulepati, S	+	Authors: Bailey, S., Mulepati, S.

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

OCA: Protected "3skd" [edit=sysop:move=sysop]

OCA — Wed, 29 Jun 2011 05:48:00 GMT

Protected "3skd" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:48, 29 June 2011