5fcl - Revision history

OCA at 12:31, 6 March 2024

OCA — Wed, 06 Mar 2024 12:31:00 GMT

←Older revision		Revision as of 12:31, 6 March 2024
Line 9:		Line 9:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/CAS1_PECAS CAS1_PECAS] 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). Acts as a dsDNA endonuclease. Involved in the integration of spacer DNA into the CRISPR cassette (By similarity).<ref>PMID:23637624</ref>		[https://www.uniprot.org/uniprot/CAS1_PECAS CAS1_PECAS] 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). Acts as a dsDNA endonuclease. Involved in the integration of spacer DNA into the CRISPR cassette (By similarity).<ref>PMID:23637624</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	CRISPR-Cas systems are adaptive immune systems in prokaryotes that provide protection against viruses and other foreign DNA. In the adaptation stage, foreign DNA is integrated into CRISPR (clustered regularly interspaced short palindromic repeat) arrays as new spacers. These spacers are used in the interference stage to guide effector CRISPR associated (Cas) protein(s) to target complementary foreign invading DNA. Cas1 is the integrase enzyme that is central to the catalysis of spacer integration. There are many diverse types of CRISPR-Cas systems, including type I-F systems, which are typified by a unique Cas1-Cas2-3 adaptation complex. In the present study we characterize the Cas1 protein of the potato phytopathogenPectobacterium atrosepticum, an important model organism for understanding spacer acquisition in type I-F CRISPR-Cas systems. We demonstrate by mutagenesis that Cas1 is essential for adaptationin vivoand requires a conserved aspartic acid residue. By X-ray crystallography, we show that althoughP. atrosepticumCas1 adopts a fold conserved among other Cas1 proteins, it possesses remarkable asymmetry as a result of structural plasticity. In particular, we resolve for the first time a flexible, asymmetric loop that may be unique to type I-F Cas1 proteins, and we discuss the implications of these structural features for DNA binding and enzymatic activity.
-
-	Structural plasticity and in vivo activity of Cas1 from the type I-F CRISPR-Cas system.,Wilkinson ME, Nakatani Y, Staals RH, Kieper SN, Opel-Reading HK, McKenzie RE, Fineran PC, Krause KL Biochem J. 2016 Apr 15;473(8):1063-72. doi: 10.1042/BCJ20160078. Epub 2016 Feb, 29. PMID:26929403<ref>PMID:26929403</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5fcl" style="background-color:#fffaf0;"></div>

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

OCA at 06:46, 19 July 2023

OCA — Wed, 19 Jul 2023 06:46:24 GMT

←Older revision		Revision as of 06:46, 19 July 2023
Line 3:		Line 3:
	<StructureSection load='5fcl' size='340' side='right'caption='[[5fcl]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='5fcl' size='340' side='right'caption='[[5fcl]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fcl]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Erwinia_carotovora_subsp._atroseptica Erwinia carotovora subsp. atroseptica~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FCL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FCL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fcl]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pectobacterium_atrosepticum_SCRI1043 Pectobacterium atrosepticum SCRI1043]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FCL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FCL FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~cas1~~, ~~ECA3679 (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=218491 Erwinia carotovora subsp. atroseptica])~~</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]] 2.7Å</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=5fcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fcl OCA], [~~http~~://pdbe.org/5fcl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fcl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fcl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fcl 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=5fcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fcl OCA], [https://pdbe.org/5fcl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fcl RCSB], [https://www.ebi.ac.uk/pdbsum/5fcl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fcl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CAS1_PECAS CAS1_PECAS]] 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). Acts as a dsDNA endonuclease. Involved in the integration of spacer DNA into the CRISPR cassette (By similarity).<ref>PMID:23637624</ref>	+	[https://www.uniprot.org/uniprot/CAS1_PECAS CAS1_PECAS] 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). Acts as a dsDNA endonuclease. Involved in the integration of spacer DNA into the CRISPR cassette (By similarity).<ref>PMID:23637624</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Erwinia carotovora subsp. atroseptica]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fineran~~, P C~~]]	+	[[Category: Pectobacterium atrosepticum SCRI1043]]
-	[[Category: Krause~~, K L~~]]	+	[[Category: Fineran PC]]
-	[[Category: Nakatani, Y]]	+	[[Category: Krause KL]]
-	[[Category: Opel-Reading~~, H K~~]]	+	[[Category: Nakatani Y]]
-	[[Category: Wilkinson~~, M E]]~~	+	[[Category: Opel-Reading HK]]
-	~~[[Category: Adaptation]]~~	+	[[Category: Wilkinson ME]]
-	~~[[Category: Asymmetry]]~~	+
-	~~[[Category: Bacteriophage]]~~	+
-	~~[[Category: Ca]]~~	+
-	~~[[Category: Crispr]]~~	+
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Horizontal gene transfer]]~~	+
-	~~[[Category: Integrase]]~~	+
-	~~[[Category: Plasmid]]~~	+
-	~~[[Category: Structural plasticity~~]]	+

OCA at 08:57, 1 January 2020

OCA — Wed, 01 Jan 2020 08:57:46 GMT

←Older revision		Revision as of 08:57, 1 January 2020
Line 1:		Line 1:

	==Crystal structure of Cas1 from Pectobacterium atrosepticum==		==Crystal structure of Cas1 from Pectobacterium atrosepticum==
-	<StructureSection load='5fcl' size='340' side='right' caption='[[5fcl]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='5fcl' size='340' side='right'caption='[[5fcl]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5fcl]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Erwinia_carotovora_subsp._atroseptica Erwinia carotovora subsp. atroseptica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FCL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FCL FirstGlance]. <br>		<table><tr><td colspan='2'>[[5fcl]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Erwinia_carotovora_subsp._atroseptica Erwinia carotovora subsp. atroseptica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FCL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FCL FirstGlance]. <br>
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5fcl" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5fcl" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 23:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Erwinia carotovora subsp. atroseptica]]		[[Category: Erwinia carotovora subsp. atroseptica]]
		+	[[Category: Large Structures]]
	[[Category: Fineran, P C]]		[[Category: Fineran, P C]]
	[[Category: Krause, K L]]		[[Category: Krause, K L]]

OCA at 13:18, 16 November 2017

OCA — Thu, 16 Nov 2017 13:18:41 GMT

←Older revision		Revision as of 13:18, 16 November 2017
Line 3:		Line 3:
	<StructureSection load='5fcl' size='340' side='right' caption='[[5fcl]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='5fcl' size='340' side='right' caption='[[5fcl]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fcl]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FCL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FCL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fcl]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Erwinia_carotovora_subsp._atroseptica Erwinia carotovora subsp. atroseptica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FCL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FCL FirstGlance]. <br>
-	</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=5fcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fcl OCA], [http://pdbe.org/5fcl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fcl RCSB], [http://www.ebi.ac.uk/pdbsum/5fcl PDBsum]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cas1, ECA3679 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=218491 Erwinia carotovora subsp. atroseptica])</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=5fcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fcl OCA], [http://pdbe.org/5fcl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fcl RCSB], [http://www.ebi.ac.uk/pdbsum/5fcl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fcl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Erwinia carotovora subsp. atroseptica]]
	[[Category: Fineran, P C]]		[[Category: Fineran, P C]]
	[[Category: Krause, K L]]		[[Category: Krause, K L]]

OCA at 15:49, 10 May 2016

OCA — Tue, 10 May 2016 15:49:43 GMT

←Older revision		Revision as of 15:49, 10 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5fcl is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of Cas1 from Pectobacterium atrosepticum==
		+	<StructureSection load='5fcl' size='340' side='right' caption='[[5fcl]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5fcl]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FCL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FCL FirstGlance]. <br>
		+	</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=5fcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fcl OCA], [http://pdbe.org/5fcl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fcl RCSB], [http://www.ebi.ac.uk/pdbsum/5fcl PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CAS1_PECAS CAS1_PECAS]] 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). Acts as a dsDNA endonuclease. Involved in the integration of spacer DNA into the CRISPR cassette (By similarity).<ref>PMID:23637624</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	CRISPR-Cas systems are adaptive immune systems in prokaryotes that provide protection against viruses and other foreign DNA. In the adaptation stage, foreign DNA is integrated into CRISPR (clustered regularly interspaced short palindromic repeat) arrays as new spacers. These spacers are used in the interference stage to guide effector CRISPR associated (Cas) protein(s) to target complementary foreign invading DNA. Cas1 is the integrase enzyme that is central to the catalysis of spacer integration. There are many diverse types of CRISPR-Cas systems, including type I-F systems, which are typified by a unique Cas1-Cas2-3 adaptation complex. In the present study we characterize the Cas1 protein of the potato phytopathogenPectobacterium atrosepticum, an important model organism for understanding spacer acquisition in type I-F CRISPR-Cas systems. We demonstrate by mutagenesis that Cas1 is essential for adaptationin vivoand requires a conserved aspartic acid residue. By X-ray crystallography, we show that althoughP. atrosepticumCas1 adopts a fold conserved among other Cas1 proteins, it possesses remarkable asymmetry as a result of structural plasticity. In particular, we resolve for the first time a flexible, asymmetric loop that may be unique to type I-F Cas1 proteins, and we discuss the implications of these structural features for DNA binding and enzymatic activity.

-	~~Authors: Wilkinson, M.E~~., ~~Nakatani~~, Y., Opel-Reading, ~~H.K.~~, Fineran, P.C.~~, Krause, K~~.L.	+	Structural plasticity and in vivo activity of Cas1 from the type I-F CRISPR-Cas system.,Wilkinson ME, Nakatani Y, Staals RH, Kieper SN, Opel-Reading HK, McKenzie RE, Fineran PC, Krause KL Biochem J. 2016 Apr 15;473(8):1063-72. doi: 10.1042/BCJ20160078. Epub 2016 Feb, 29. PMID:26929403<ref>PMID:26929403</ref>

-	~~Description: Crystal structure~~ of ~~Cas1 from Pectobacterium atrosepticum~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Wilkinson~~, ~~M.E~~]]	+	<div class="pdbe-citations 5fcl" style="background-color:#fffaf0;"></div>
-	[[Category: Krause, K.L]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Fineran, P C]]
		+	[[Category: Krause, K L]]
	[[Category: Nakatani, Y]]		[[Category: Nakatani, Y]]
-	[[Category: Opel-Reading, H.K]]	+	[[Category: Opel-Reading, H K]]
-	[[Category: ~~Fineran~~, ~~P.C~~]]	+	[[Category: Wilkinson, M E]]
		+	[[Category: Adaptation]]
		+	[[Category: Asymmetry]]
		+	[[Category: Bacteriophage]]
		+	[[Category: Ca]]
		+	[[Category: Crispr]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Horizontal gene transfer]]
		+	[[Category: Integrase]]
		+	[[Category: Plasmid]]
		+	[[Category: Structural plasticity]]

OCA at 23:54, 20 February 2016

OCA — Sat, 20 Feb 2016 23:54:12 GMT

←Older revision		Revision as of 23:54, 20 February 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5fcl is ON HOLD	+	The entry 5fcl is ON HOLD until Paper Publication

	Authors: Wilkinson, M.E., Nakatani, Y., Opel-Reading, H.K., Fineran, P.C., Krause, K.L.		Authors: Wilkinson, M.E., Nakatani, Y., Opel-Reading, H.K., Fineran, P.C., Krause, K.L.

OCA at 14:23, 10 February 2016

OCA — Wed, 10 Feb 2016 14:23:48 GMT

←Older revision		Revision as of 14:23, 10 February 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5fcl is ON HOLD ~~until Paper Publication~~	+	The entry 5fcl is ON HOLD

	Authors: Wilkinson, M.E., Nakatani, Y., Opel-Reading, H.K., Fineran, P.C., Krause, K.L.		Authors: Wilkinson, M.E., Nakatani, Y., Opel-Reading, H.K., Fineran, P.C., Krause, K.L.

OCA at 12:54, 3 February 2016

OCA — Wed, 03 Feb 2016 12:54:53 GMT

←Older revision		Revision as of 12:54, 3 February 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5fcl is ON HOLD	+	The entry 5fcl is ON HOLD until Paper Publication

	Authors: Wilkinson, M.E., Nakatani, Y., Opel-Reading, H.K., Fineran, P.C., Krause, K.L.		Authors: Wilkinson, M.E., Nakatani, Y., Opel-Reading, H.K., Fineran, P.C., Krause, K.L.

OCA: Protected "5fcl" [edit=sysop:move=sysop]

OCA — Wed, 23 Dec 2015 11:27:28 GMT

Protected "5fcl" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:27, 23 December 2015

OCA: New page: '''Unreleased structure''' The entry 5fcl is ON HOLD Authors: Wilkinson, M.E., Nakatani, Y., Opel-Reading, H.K., Fineran, P.C., Krause, K.L. Description: Crystal structure of Cas1 from...

OCA — Wed, 23 Dec 2015 11:27:27 GMT

New page: '''Unreleased structure''' The entry 5fcl is ON HOLD Authors: Wilkinson, M.E., Nakatani, Y., Opel-Reading, H.K., Fineran, P.C., Krause, K.L. Description: Crystal structure of Cas1 from...

New page

'''Unreleased structure'''

The entry 5fcl is ON HOLD

Authors: Wilkinson, M.E., Nakatani, Y., Opel-Reading, H.K., Fineran, P.C., Krause, K.L.

Description: Crystal structure of Cas1 from Pectobacterium atrosepticum
[[Category: Unreleased Structures]]
[[Category: Wilkinson, M.E]]
[[Category: Krause, K.L]]
[[Category: Nakatani, Y]]
[[Category: Opel-Reading, H.K]]
[[Category: Fineran, P.C]]