1dmu - Revision history

OCA at 10:36, 14 December 2022

OCA — Wed, 14 Dec 2022 10:36:45 GMT

←Older revision		Revision as of 10:36, 14 December 2022
Line 1:		Line 1:

-	====	+	==Crystal structure of the restriction endonuclease BglI (e.c.3.1.21.4) bound to its dna recognition sequence==
-	<StructureSection load='1dmu' size='340' side='right'caption='[[1dmu]]' scene=''>	+	<StructureSection load='1dmu' size='340' side='right'caption='[[1dmu]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dmu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DMU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DMU FirstGlance]. <br>
-	</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=1dmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dmu OCA], [https://pdbe.org/1dmu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dmu RCSB], [https://www.ebi.ac.uk/pdbsum/1dmu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dmu ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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=1dmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dmu OCA], [https://pdbe.org/1dmu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dmu RCSB], [https://www.ebi.ac.uk/pdbsum/1dmu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dmu ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/T2B1_BACIU T2B1_BACIU] A P subtype restriction enzyme that recognizes the double-stranded sequence 5'-GCCNNNNNGGC-3' and cleaves before N-8.<ref>PMID:9736624</ref> <ref>PMID:12654995</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structure of the type II restriction endonuclease BglI bound to DNA containing its specific recognition sequence has been determined at 2.2 A resolution. This is the first structure of a restriction endonuclease that recognizes and cleaves an interrupted DNA sequence, producing 3' overhanging ends. BglI is a homodimer that binds its specific DNA sequence with the minor groove facing the protein. Parts of the enzyme reach into both the major and minor grooves to contact the edges of the bases within the recognition half-sites. The arrangement of active site residues is strikingly similar to other restriction endonucleases, but the co-ordination of two calcium ions at the active site gives new insight into the catalytic mechanism. Surprisingly, the core of a BglI subunit displays a striking similarity to subunits of EcoRV and PvuII, but the dimer structure is dramatically different. The BglI-DNA complex demonstrates, for the first time, that a conserved subunit fold can dimerize in more than one way, resulting in different DNA cleavage patterns.
		+
		+	Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence.,Newman M, Lunnen K, Wilson G, Greci J, Schildkraut I, Phillips SE EMBO J. 1998 Sep 15;17(18):5466-76. PMID:9736624<ref>PMID:9736624</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1dmu" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus subtilis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Greci J]]
		+	[[Category: Lunnen K]]
		+	[[Category: Newman M]]
		+	[[Category: Phillips SEV]]
		+	[[Category: Schildkraut I]]
		+	[[Category: Wilson G]]

OCA at 18:30, 10 March 2021

OCA — Wed, 10 Mar 2021 18:30:49 GMT

←Older revision		Revision as of 18:30, 10 March 2021
Line 1:		Line 1:

-	==~~Crystal structure of the restriction endonuclease BglI (e.c.3.1.21.4) bound to its dna recognition sequence~~==	+	====
-	<StructureSection load='1dmu' size='340' side='right'caption='[[1dmu]]~~, [[Resolution\|resolution]] 2.20Å~~' scene=''>	+	<StructureSection load='1dmu' size='340' side='right'caption='[[1dmu]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[1dmu]] is a 2 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=~~1DMU~~ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=~~1DMU~~ FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>	+	</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=1dmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dmu OCA], [https://pdbe.org/1dmu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dmu RCSB], [https://www.ebi.ac.uk/pdbsum/1dmu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dmu ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] </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=1dmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dmu OCA], [~~http~~://pdbe.org/1dmu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1dmu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1dmu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1dmu ProSAT]</span></td></tr>	+
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The crystal structure of the type II restriction endonuclease BglI bound to DNA containing its specific recognition sequence has been determined at 2.2 A resolution. This is the first structure of a restriction endonuclease that recognizes and cleaves an interrupted DNA sequence, producing 3' overhanging ends. BglI is a homodimer that binds its specific DNA sequence with the minor groove facing the protein. Parts of the enzyme reach into both the major and minor grooves to contact the edges of the bases within the recognition half-sites. The arrangement of active site residues is strikingly similar to other restriction endonucleases, but the co-ordination of two calcium ions at the active site gives new insight into the catalytic mechanism. Surprisingly, the core of a BglI subunit displays a striking similarity to subunits of EcoRV and PvuII, but the dimer structure is dramatically different. The BglI-DNA complex demonstrates, for the first time, that a conserved subunit fold can dimerize in more than one way, resulting in different DNA cleavage patterns.
-
-	Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence.,Newman M, Lunnen K, Wilson G, Greci J, Schildkraut I, Phillips SE EMBO J. 1998 Sep 15;17(18):5466-76. PMID:9736624<ref>PMID:9736624</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1dmu" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Endonuclease\|Endonuclease]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Type II site~~-~~specific deoxyribonuclease]]~~	+	[[Category: Z-disk]]
-	~~[[Category: Greci, J]]~~	+
-	~~[[Category: Lunnen, K]]~~	+
-	~~[[Category: Newman, M]]~~	+
-	~~[[Category: Phillips, S E.V]]~~	+
-	~~[[Category: Schildkraut, I]]~~	+
-	~~[[Category: Wilson, G]]~~	+
-	~~[[Category: A:a mismatch]]~~	+
-	~~[[Category: Active site calcium ion]]~~	+
-	~~[[Category: Alpha/beta structure]]~~	+
-	~~[[Category: Hydrolase-dna complex]]~~	+
-	~~[[Category: Protein-dna complex~~]]	+

OCA at 23:25, 5 June 2019

OCA — Wed, 05 Jun 2019 23:25:38 GMT

←Older revision		Revision as of 23:25, 5 June 2019
Line 1:		Line 1:

	==Crystal structure of the restriction endonuclease BglI (e.c.3.1.21.4) bound to its dna recognition sequence==		==Crystal structure of the restriction endonuclease BglI (e.c.3.1.21.4) bound to its dna recognition sequence==
-	<StructureSection load='1dmu' size='340' side='right' caption='[[1dmu]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='1dmu' size='340' side='right'caption='[[1dmu]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1dmu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DMU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DMU FirstGlance]. <br>		<table><tr><td colspan='2'>[[1dmu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DMU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DMU FirstGlance]. <br>
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Type II site-specific deoxyribonuclease]]		[[Category: Type II site-specific deoxyribonuclease]]
	[[Category: Greci, J]]		[[Category: Greci, J]]

OCA at 04:02, 30 August 2017

OCA — Wed, 30 Aug 2017 04:02:44 GMT

←Older revision		Revision as of 04:02, 30 August 2017
Line 1:		Line 1:
		+
	==Crystal structure of the restriction endonuclease BglI (e.c.3.1.21.4) bound to its dna recognition sequence==		==Crystal structure of the restriction endonuclease BglI (e.c.3.1.21.4) bound to its dna recognition sequence==
	<StructureSection load='1dmu' size='340' side='right' caption='[[1dmu]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1dmu' size='340' side='right' caption='[[1dmu]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dmu]] is a 2 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DMU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DMU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dmu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DMU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DMU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] </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=1dmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dmu OCA], [http://pdbe.org/1dmu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dmu RCSB], [http://www.ebi.ac.uk/pdbsum/1dmu 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=1dmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dmu OCA], [http://pdbe.org/1dmu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dmu RCSB], [http://www.ebi.ac.uk/pdbsum/1dmu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dmu ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus globigii migula 1900]]
	[[Category: Type II site-specific deoxyribonuclease]]		[[Category: Type II site-specific deoxyribonuclease]]
	[[Category: Greci, J]]		[[Category: Greci, J]]

OCA at 23:55, 10 September 2015

OCA — Thu, 10 Sep 2015 23:55:33 GMT

←Older revision		Revision as of 23:55, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1dmu' size='340' side='right' caption='[[1dmu]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1dmu' size='340' side='right' caption='[[1dmu]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dmu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_subtilis Bacillus subtilis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DMU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DMU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dmu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DMU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DMU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] </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=1dmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dmu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dmu RCSB], [http://www.ebi.ac.uk/pdbsum/1dmu 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=1dmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dmu OCA], [http://pdbe.org/1dmu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dmu RCSB], [http://www.ebi.ac.uk/pdbsum/1dmu PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 15:
	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 1dmu" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus ~~subtilis~~]]	+	[[Category: Bacillus globigii migula 1900]]
	[[Category: Type II site-specific deoxyribonuclease]]		[[Category: Type II site-specific deoxyribonuclease]]
	[[Category: Greci, J]]		[[Category: Greci, J]]

OCA at 20:04, 22 December 2014

OCA — Mon, 22 Dec 2014 20:04:27 GMT

←Older revision		Revision as of 20:04, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1dmu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DMU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DMU FirstGlance]. <br>		<table><tr><td colspan='2'>[[1dmu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DMU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DMU FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] </span></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=1dmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dmu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dmu RCSB], [http://www.ebi.ac.uk/pdbsum/1dmu 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=1dmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dmu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dmu RCSB], [http://www.ebi.ac.uk/pdbsum/1dmu 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 24:		Line 24:
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Type II site-specific deoxyribonuclease]]		[[Category: Type II site-specific deoxyribonuclease]]
-	[[Category: Greci, J.]]	+	[[Category: Greci, J]]
-	[[Category: Lunnen, K.]]	+	[[Category: Lunnen, K]]
-	[[Category: Newman, M.]]	+	[[Category: Newman, M]]
-	[[Category: Phillips, S E.V.]]	+	[[Category: Phillips, S E.V]]
-	[[Category: Schildkraut, I.]]	+	[[Category: Schildkraut, I]]
-	[[Category: Wilson, G.]]	+	[[Category: Wilson, G]]
	[[Category: A:a mismatch]]		[[Category: A:a mismatch]]
	[[Category: Active site calcium ion]]		[[Category: Active site calcium ion]]

OCA at 06:30, 4 September 2014

OCA — Thu, 04 Sep 2014 06:30:48 GMT

←Older revision		Revision as of 06:30, 4 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1dmu.~~png~~\|~~left\|200px~~]]	+	==Crystal structure of the restriction endonuclease BglI (e.c.3.1.21.4) bound to its dna recognition sequence==
		+	<StructureSection load='1dmu' size='340' side='right' caption='[[1dmu]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1dmu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DMU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DMU FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] </span></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=1dmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dmu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dmu RCSB], [http://www.ebi.ac.uk/pdbsum/1dmu PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structure of the type II restriction endonuclease BglI bound to DNA containing its specific recognition sequence has been determined at 2.2 A resolution. This is the first structure of a restriction endonuclease that recognizes and cleaves an interrupted DNA sequence, producing 3' overhanging ends. BglI is a homodimer that binds its specific DNA sequence with the minor groove facing the protein. Parts of the enzyme reach into both the major and minor grooves to contact the edges of the bases within the recognition half-sites. The arrangement of active site residues is strikingly similar to other restriction endonucleases, but the co-ordination of two calcium ions at the active site gives new insight into the catalytic mechanism. Surprisingly, the core of a BglI subunit displays a striking similarity to subunits of EcoRV and PvuII, but the dimer structure is dramatically different. The BglI-DNA complex demonstrates, for the first time, that a conserved subunit fold can dimerize in more than one way, resulting in different DNA cleavage patterns.

-	~~{{STRUCTURE_1dmu\| PDB=1dmu \| SCENE= }}~~	+	Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence.,Newman M, Lunnen K, Wilson G, Greci J, Schildkraut I, Phillips SE EMBO J. 1998 Sep 15;17(18):5466-76. PMID:9736624<ref>PMID:9736624</ref>

-	~~===Crystal structure~~ of the ~~restriction endonuclease BglI (e~~.c.3.~~1.21.4) bound to its dna recognition sequence===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_9736624}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1dmu]] is a 2 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DMU OCA].~~	+

	==See Also==		==See Also==
	*[[Endonuclease\|Endonuclease]]		*[[Endonuclease\|Endonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:009736624<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Type II site-specific deoxyribonuclease]]		[[Category: Type II site-specific deoxyribonuclease]]

OCA at 14:25, 20 October 2012

OCA — Sat, 20 Oct 2012 14:25:01 GMT

←Older revision		Revision as of 14:25, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1dmu]] is a 2 chain structure ~~of [[Endonuclease]]~~ with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DMU OCA].	+	[[1dmu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DMU OCA].

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

OCA: Protected "1dmu" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 15:04:02 GMT

Protected "1dmu" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:04, 26 July 2012

OCA at 15:04, 26 July 2012

OCA — Thu, 26 Jul 2012 15:04:00 GMT

←Older revision		Revision as of 15:04, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1dmu.png\|left\|200px]]		[[Image:1dmu.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1dmu", 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_1dmu\| PDB=1dmu \| SCENE= }}		{{STRUCTURE_1dmu\| PDB=1dmu \| SCENE= }}

	===Crystal structure of the restriction endonuclease BglI (e.c.3.1.21.4) bound to its dna recognition sequence===		===Crystal structure of the restriction endonuclease BglI (e.c.3.1.21.4) bound to its dna recognition sequence===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_9736624}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 9736624 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_9736624}}		{{ABSTRACT_PUBMED_9736624}}

	==About this Structure==		==About this Structure==
-	~~1DMU~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DMU OCA].	+	[[1dmu]] is a 2 chain structure of [[Endonuclease]] with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DMU OCA].
		+
		+	==See Also==
		+	*[[Endonuclease\|Endonuclease]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~9736624~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:009736624</ref><references group="xtra"/>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Type II site-specific deoxyribonuclease]]		[[Category: Type II site-specific deoxyribonuclease]]
Line 37:		Line 28:
	[[Category: Hydrolase-dna complex]]		[[Category: Hydrolase-dna complex]]
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 6 05:35:30 2010''