4doz - Revision history

OCA at 08:48, 20 March 2024

OCA — Wed, 20 Mar 2024 08:48:47 GMT

←Older revision		Revision as of 08:48, 20 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4doz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DOZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DOZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4doz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DOZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DOZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3.1Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=4doz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4doz OCA], [https://pdbe.org/4doz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4doz RCSB], [https://www.ebi.ac.uk/pdbsum/4doz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4doz 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=4doz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4doz OCA], [https://pdbe.org/4doz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4doz RCSB], [https://www.ebi.ac.uk/pdbsum/4doz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4doz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CMR2_PYRFU CMR2_PYRFU]] 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), formerly called psiRNA (prokaryotic silencing) in this organism. Part of the Cmr ribonucleoprotein complex which has divalent cation-dependent endoribonuclease activity specific for ssRNA complementary to the crRNA, generating 5' hydroxy- and 3' phosphate or 2'-3' cyclic phosphate termini. It is not known which subunit has endoribonuclease activity. Cmr complex does not cleave ssDNA complementary to the crRNA. Cleavage of invading RNA is guided by the crRNA; substrate cleavage occurs a fixed distance (14 nt) from the 3' end of the crRNA. In vitro reconstitution shows Cmr1-2 and Cmr5 are not necessary for cleavage. Probably not the subunit that cleaves pre-crRNA, as mutation of numerous metal-binding residues have no effect on cleavage by assembled complex.<ref>PMID:19945378</ref>	+	[https://www.uniprot.org/uniprot/CMR2_PYRFU CMR2_PYRFU] 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), formerly called psiRNA (prokaryotic silencing) in this organism. Part of the Cmr ribonucleoprotein complex which has divalent cation-dependent endoribonuclease activity specific for ssRNA complementary to the crRNA, generating 5' hydroxy- and 3' phosphate or 2'-3' cyclic phosphate termini. It is not known which subunit has endoribonuclease activity. Cmr complex does not cleave ssDNA complementary to the crRNA. Cleavage of invading RNA is guided by the crRNA; substrate cleavage occurs a fixed distance (14 nt) from the 3' end of the crRNA. In vitro reconstitution shows Cmr1-2 and Cmr5 are not necessary for cleavage. Probably not the subunit that cleaves pre-crRNA, as mutation of numerous metal-binding residues have no effect on cleavage by assembled complex.<ref>PMID:19945378</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	CRISPR RNAs (crRNAs) mediate sequence-specific silencing of invading viruses and plasmids in prokaryotes. The crRNA-Cmr protein complex cleaves complementary RNA. We report the crystal structure of Pyrococcus furiosus Cmr2 (Cas10), a component of this Cmr complex and the signature protein in type III CRISPR systems. The structure reveals a nucleotide cyclase domain with a set of conserved catalytic residues that associates with an unexpected deviant cyclase domain like dimeric cyclases. Additionally, two helical domains resemble the thumb domain of A-family DNA polymerase and Cmr5, respectively. Our results suggest that Cmr2 possesses novel enzymatic activity that remains to be elucidated.	+
-		+
-	Crystal structure of Cmr2 suggests a nucleotide cyclase-related enzyme in type III CRISPR-Cas systems.,Zhu X, Ye K FEBS Lett. 2012 Mar 23;586(6):939-45. doi: 10.1016/j.febslet.2012.02.036. Epub, 2012 Feb 28. PMID:22449983<ref>PMID:22449983</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 4doz" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==

OCA at 08:32, 21 September 2022

OCA — Wed, 21 Sep 2022 08:32:33 GMT

←Older revision		Revision as of 08:32, 21 September 2022
Line 1:		Line 1:

	==Crystal structure of Pyrococcus furiosus Cmr2 (Cas10)==		==Crystal structure of Pyrococcus furiosus Cmr2 (Cas10)==
-	<StructureSection load='4doz' size='340' side='right' caption='[[4doz]], [[Resolution\|resolution]] 3.10Å' scene=''>	+	<StructureSection load='4doz' size='340' side='right'caption='[[4doz]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4doz]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pyrfu Pyrfu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DOZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4DOZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4doz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DOZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DOZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])~~</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=4doz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4doz OCA], [https://pdbe.org/4doz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4doz RCSB], [https://www.ebi.ac.uk/pdbsum/4doz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4doz ProSAT]</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=4doz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4doz OCA], [~~http~~://pdbe.org/4doz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4doz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4doz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4doz ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CMR2_PYRFU CMR2_PYRFU]] 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), formerly called psiRNA (prokaryotic silencing) in this organism. Part of the Cmr ribonucleoprotein complex which has divalent cation-dependent endoribonuclease activity specific for ssRNA complementary to the crRNA, generating 5' hydroxy- and 3' phosphate or 2'-3' cyclic phosphate termini. It is not known which subunit has endoribonuclease activity. Cmr complex does not cleave ssDNA complementary to the crRNA. Cleavage of invading RNA is guided by the crRNA; substrate cleavage occurs a fixed distance (14 nt) from the 3' end of the crRNA. In vitro reconstitution shows Cmr1-2 and Cmr5 are not necessary for cleavage. Probably not the subunit that cleaves pre-crRNA, as mutation of numerous metal-binding residues have no effect on cleavage by assembled complex.<ref>PMID:19945378</ref>	+	[[https://www.uniprot.org/uniprot/CMR2_PYRFU CMR2_PYRFU]] 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), formerly called psiRNA (prokaryotic silencing) in this organism. Part of the Cmr ribonucleoprotein complex which has divalent cation-dependent endoribonuclease activity specific for ssRNA complementary to the crRNA, generating 5' hydroxy- and 3' phosphate or 2'-3' cyclic phosphate termini. It is not known which subunit has endoribonuclease activity. Cmr complex does not cleave ssDNA complementary to the crRNA. Cleavage of invading RNA is guided by the crRNA; substrate cleavage occurs a fixed distance (14 nt) from the 3' end of the crRNA. In vitro reconstitution shows Cmr1-2 and Cmr5 are not necessary for cleavage. Probably not the subunit that cleaves pre-crRNA, as mutation of numerous metal-binding residues have no effect on cleavage by assembled complex.<ref>PMID:19945378</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 20:

	==See Also==		==See Also==
-	*[[Endonuclease\|Endonuclease]]	+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pyrfu~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Ye, K~~]]	+	[[Category: Pyrococcus furiosus DSM 3638]]
-	[[Category: ~~Zhu, X~~]]	+	[[Category: Ye K]]
-	[[Category: ~~Antiviral protein]]~~	+	[[Category: Zhu X]]
-	~~[[Category: Crispr]]~~	+
-	~~[[Category: Cyclase]]~~	+
-	~~[[Category: Zn~~]]	+

OCA at 15:55, 4 August 2016

OCA — Thu, 04 Aug 2016 15:55:15 GMT

←Older revision		Revision as of 15:55, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Pyrococcus furiosus Cmr2 (Cas10)==		==Crystal structure of Pyrococcus furiosus Cmr2 (Cas10)==
	<StructureSection load='4doz' size='340' side='right' caption='[[4doz]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='4doz' size='340' side='right' caption='[[4doz]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4doz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrococcus_furiosus_dsm_3638 Pyrococcus furiosus dsm 3638~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DOZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DOZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4doz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DOZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DOZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 ~~Pyrococcus furiosus DSM 3638~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=4doz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4doz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4doz RCSB], [http://www.ebi.ac.uk/pdbsum/4doz 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=4doz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4doz OCA], [http://pdbe.org/4doz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4doz RCSB], [http://www.ebi.ac.uk/pdbsum/4doz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4doz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		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 4doz" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 24:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pyrococcus furiosus dsm 3638~~]]	+	[[Category: Pyrfu]]
	[[Category: Ye, K]]		[[Category: Ye, K]]
	[[Category: Zhu, X]]		[[Category: Zhu, X]]

OCA at 16:43, 24 December 2014

OCA — Wed, 24 Dec 2014 16:43:48 GMT

←Older revision		Revision as of 16:43, 24 December 2014
Line 7:		Line 7:
	<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=4doz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4doz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4doz RCSB], [http://www.ebi.ac.uk/pdbsum/4doz 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=4doz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4doz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4doz RCSB], [http://www.ebi.ac.uk/pdbsum/4doz PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CMR2_PYRFU CMR2_PYRFU]] 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), formerly called psiRNA (prokaryotic silencing) in this organism. Part of the Cmr ribonucleoprotein complex which has divalent cation-dependent endoribonuclease activity specific for ssRNA complementary to the crRNA, generating 5' hydroxy- and 3' phosphate or 2'-3' cyclic phosphate termini. It is not known which subunit has endoribonuclease activity. Cmr complex does not cleave ssDNA complementary to the crRNA. Cleavage of invading RNA is guided by the crRNA; substrate cleavage occurs a fixed distance (14 nt) from the 3' end of the crRNA. In vitro reconstitution shows Cmr1-2 and Cmr5 are not necessary for cleavage. Probably not the subunit that cleaves pre-crRNA, as mutation of numerous metal-binding residues have no effect on cleavage by assembled complex.<ref>PMID:19945378</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 17:
	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>
		+
		+	==See Also==
		+	*[[Endonuclease\|Endonuclease]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:10, 21 December 2014

OCA — Sun, 21 Dec 2014 09:10:55 GMT

←Older revision		Revision as of 09:10, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4doz\| PDB~~=4doz \| ~~SCENE~~= }}	+	==Crystal structure of Pyrococcus furiosus Cmr2 (Cas10)==
-	===~~Crystal~~ structure of Pyrococcus furiosus ~~Cmr2~~ (~~Cas10~~)===	+	<StructureSection load='4doz' size='340' side='right' caption='[[4doz]], [[Resolution\|resolution]] 3.10Å' scene=''>
-	~~{{ABSTRACT_PUBMED_22449983}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4doz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus_dsm_3638 Pyrococcus furiosus dsm 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DOZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DOZ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 Pyrococcus furiosus DSM 3638])</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=4doz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4doz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4doz RCSB], [http://www.ebi.ac.uk/pdbsum/4doz PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	CRISPR RNAs (crRNAs) mediate sequence-specific silencing of invading viruses and plasmids in prokaryotes. The crRNA-Cmr protein complex cleaves complementary RNA. We report the crystal structure of Pyrococcus furiosus Cmr2 (Cas10), a component of this Cmr complex and the signature protein in type III CRISPR systems. The structure reveals a nucleotide cyclase domain with a set of conserved catalytic residues that associates with an unexpected deviant cyclase domain like dimeric cyclases. Additionally, two helical domains resemble the thumb domain of A-family DNA polymerase and Cmr5, respectively. Our results suggest that Cmr2 possesses novel enzymatic activity that remains to be elucidated.

-	~~==Function==~~	+	Crystal structure of Cmr2 suggests a nucleotide cyclase-related enzyme in type III CRISPR-Cas systems.,Zhu X, Ye K FEBS Lett. 2012 Mar 23;586(6):939-45. doi: 10.1016/j.febslet.2012.02.036. Epub, 2012 Feb 28. PMID:22449983<ref>PMID:22449983</ref>
-	~~[[http://www~~.~~uniprot.org/uniprot/CMR2_PYRFU CMR2_PYRFU]] 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~~)~~, formerly called psiRNA (prokaryotic silencing) in this organism. Part of the Cmr ribonucleoprotein complex which has divalent cation~~-~~dependent endoribonuclease activity specific for ssRNA complementary to the crRNA, generating 5' hydroxy- and 3' phosphate or 2'-3' cyclic phosphate termini~~. ~~It is not known which subunit has endoribonuclease activity~~. ~~Cmr complex does not cleave ssDNA complementary to the crRNA~~. ~~Cleavage of invading RNA is guided by the crRNA; substrate cleavage occurs a fixed distance (14 nt) from the 3' end of the crRNA~~. ~~In vitro reconstitution shows Cmr1-2 and Cmr5 are not necessary for cleavage~~. ~~Probably not the subunit that cleaves pre-crRNA~~, ~~as mutation of numerous metal-binding residues have no effect on cleavage by assembled complex~~.<ref>PMID:~~19945378~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4doz]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pyrococcus_furiosus_dsm_3638 Pyrococcus furiosus dsm 3638]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4DOZ OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:022449983</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Pyrococcus furiosus dsm 3638]]		[[Category: Pyrococcus furiosus dsm 3638]]
-	[[Category: Ye, K.]]	+	[[Category: Ye, K]]
-	[[Category: Zhu, X.]]	+	[[Category: Zhu, X]]
	[[Category: Antiviral protein]]		[[Category: Antiviral protein]]
	[[Category: Crispr]]		[[Category: Crispr]]
	[[Category: Cyclase]]		[[Category: Cyclase]]
	[[Category: Zn]]		[[Category: Zn]]

OCA at 07:41, 30 June 2013

OCA — Sun, 30 Jun 2013 07:41:55 GMT

←Older revision		Revision as of 07:41, 30 June 2013
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-	[[Image:4doz.jpg\|left\|200px]]
-
-	<!--
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-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_4doz\| PDB=4doz \| SCENE= }}		{{STRUCTURE_4doz\| PDB=4doz \| SCENE= }}
-
	===Crystal structure of Pyrococcus furiosus Cmr2 (Cas10)===		===Crystal structure of Pyrococcus furiosus Cmr2 (Cas10)===
		+	{{ABSTRACT_PUBMED_22449983}}

		+	==Function==
		+	[[http://www.uniprot.org/uniprot/CMR2_PYRFU CMR2_PYRFU]] 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), formerly called psiRNA (prokaryotic silencing) in this organism. Part of the Cmr ribonucleoprotein complex which has divalent cation-dependent endoribonuclease activity specific for ssRNA complementary to the crRNA, generating 5' hydroxy- and 3' phosphate or 2'-3' cyclic phosphate termini. It is not known which subunit has endoribonuclease activity. Cmr complex does not cleave ssDNA complementary to the crRNA. Cleavage of invading RNA is guided by the crRNA; substrate cleavage occurs a fixed distance (14 nt) from the 3' end of the crRNA. In vitro reconstitution shows Cmr1-2 and Cmr5 are not necessary for cleavage. Probably not the subunit that cleaves pre-crRNA, as mutation of numerous metal-binding residues have no effect on cleavage by assembled complex.<ref>PMID:19945378</ref>

	==About this Structure==		==About this Structure==
-	[[4doz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrococcus_furiosus~~ Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DOZ OCA].	+	[[4doz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus_dsm_3638 Pyrococcus furiosus dsm 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DOZ OCA].
-	[[Category: Pyrococcus furiosus]]	+
		+	==Reference==
		+	<ref group="xtra">PMID:022449983</ref><references group="xtra"/><references/>
		+	[[Category: Pyrococcus furiosus dsm 3638]]
	[[Category: Ye, K.]]		[[Category: Ye, K.]]
	[[Category: Zhu, X.]]		[[Category: Zhu, X.]]

OCA at 07:53, 21 March 2012

OCA — Wed, 21 Mar 2012 07:53:54 GMT

←Older revision		Revision as of 07:53, 21 March 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4doz.jpg\|left\|200px]]

-	The ~~entry 4doz~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_4doz", 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_4doz\| PDB=4doz \| SCENE= }}

-	~~Authors: Zhu, X., Ye, K.~~	+	===Crystal structure of Pyrococcus furiosus Cmr2 (Cas10)===

-	~~Description: Crystal~~ structure of Pyrococcus furiosus ~~Cmr2 (Cas10)~~	+
		+	==About this Structure==
		+	[[4doz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DOZ OCA].
		+	[[Category: Pyrococcus furiosus]]
		+	[[Category: Ye, K.]]
		+	[[Category: Zhu, X.]]
		+	[[Category: Antiviral protein]]
		+	[[Category: Crispr]]
		+	[[Category: Cyclase]]
		+	[[Category: Zn]]

OCA at 08:23, 29 February 2012

OCA — Wed, 29 Feb 2012 08:23:35 GMT

←Older revision		Revision as of 08:23, 29 February 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4doz is ON HOLD	+	The entry 4doz is ON HOLD until Paper Publication

	Authors: Zhu, X., Ye, K.		Authors: Zhu, X., Ye, K.

	Description: Crystal structure of Pyrococcus furiosus Cmr2 (Cas10)		Description: Crystal structure of Pyrococcus furiosus Cmr2 (Cas10)

OCA: Protected "4doz" [edit=sysop:move=sysop]

OCA — Wed, 22 Feb 2012 07:31:32 GMT

Protected "4doz" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:31, 22 February 2012

OCA: New page: '''Unreleased structure''' The entry 4doz is ON HOLD Authors: Zhu, X., Ye, K. Description: Crystal structure of Pyrococcus furiosus Cmr2 (Cas10)

OCA — Wed, 22 Feb 2012 07:31:30 GMT

New page: '''Unreleased structure''' The entry 4doz is ON HOLD Authors: Zhu, X., Ye, K. Description: Crystal structure of Pyrococcus furiosus Cmr2 (Cas10)

New page

'''Unreleased structure'''

The entry 4doz is ON HOLD

Authors: Zhu, X., Ye, K.

Description: Crystal structure of Pyrococcus furiosus Cmr2 (Cas10)