1dc1 - Revision history

OCA at 06:51, 7 February 2024

OCA — Wed, 07 Feb 2024 06:51:52 GMT

←Older revision		Revision as of 06:51, 7 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1dc1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DC1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1dc1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DC1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</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]] 1.7Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</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=1dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dc1 OCA], [https://pdbe.org/1dc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dc1 RCSB], [https://www.ebi.ac.uk/pdbsum/1dc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dc1 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=1dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dc1 OCA], [https://pdbe.org/1dc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dc1 RCSB], [https://www.ebi.ac.uk/pdbsum/1dc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dc1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/T2B1_GEOSE T2B1_GEOSE] Recognizes the double-stranded sequence CYCGRG and cleaves after C-1.		[https://www.uniprot.org/uniprot/T2B1_GEOSE T2B1_GEOSE] Recognizes the double-stranded sequence CYCGRG and cleaves after C-1.
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	BACKGROUND: Restriction endonucleases form a diverse family of proteins with substantial variation in sequence, structure, and interaction with recognition site DNA. BsoBI is a thermophilic restriction endonuclease that exhibits both base-specific and degenerate recognition within the sequence CPyCGPuG. RESULTS: The structure of BsoBI complexed to cognate DNA has been determined to 1.7 A resolution, revealing several unprecedented features. Each BsoBI monomer is formed by inserting a helical domain into an expanded EcoRI-type catalytic domain. DNA is completely encircled by a BsoBI dimer. Recognition sequence DNA lies within a 20 A long tunnel of protein that excludes bulk solvent. Interactions with the specific bases are made in both grooves through direct and water-mediated hydrogen bonding. Interaction with the degenerate position is mediated by a purine-specific hydrogen bond to N7, ensuring specificity, and water-mediated H bonding to the purine N6/O6 and pyrimidine N4/O4, allowing degeneracy. In addition to the conserved active site residues of the DX(n)(E/D)ZK restriction enzyme motif, His253 is positioned to act as a general base. CONCLUSIONS: A catalytic mechanism employing His253 and two metal ions is proposed. If confirmed, this would be the first example of histidine-mediated catalysis in a restriction endonuclease. The structure also provides two novel examples of the role of water in protein-DNA interaction. Degenerate recognition may be mediated by employing water as a hydrogen bond donor or acceptor. The structure of DNA in the tunnel may also be influenced by the absence of bulk solvent.
-
-	Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis.,van der Woerd MJ, Pelletier JJ, Xu S, Friedman AM Structure. 2001 Feb 7;9(2):133-44. PMID:11250198<ref>PMID:11250198</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1dc1" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]		*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:36, 14 December 2022

OCA — Wed, 14 Dec 2022 10:36:06 GMT

←Older revision		Revision as of 10:36, 14 December 2022
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	<StructureSection load='1dc1' size='340' side='right'caption='[[1dc1]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1dc1' size='340' side='right'caption='[[1dc1]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dc1]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DC1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dc1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DC1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=1dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dc1 OCA], [https://pdbe.org/1dc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dc1 RCSB], [https://www.ebi.ac.uk/pdbsum/1dc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dc1 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=1dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dc1 OCA], [https://pdbe.org/1dc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dc1 RCSB], [https://www.ebi.ac.uk/pdbsum/1dc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dc1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/T2B1_GEOSE T2B1_GEOSE]] Recognizes the double-stranded sequence CYCGRG and cleaves after C-1.	+	[https://www.uniprot.org/uniprot/T2B1_GEOSE T2B1_GEOSE] Recognizes the double-stranded sequence CYCGRG and cleaves after C-1.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Geobacillus stearothermophilus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Type II site-specific deoxyribonuclease]]~~	+	[[Category: Friedman AM]]
-	[[Category: Friedman~~, A M~~]]	+	[[Category: Pelletier JJ]]
-	[[Category: Pelletier~~, J J]]~~	+	[[Category: Xu S-Y]]
-	~~[[Category: Woerd, M J.van der~~]]	+	[[Category: Van der Woerd MJ]]
-	[[Category: Xu, S Y]]	+
-	[[Category: ~~Degenerate dna recognition]]~~	+
-	~~[[Category: Hydrolase-dna complex]]~~	+
-	~~[[Category: Protein-dna complex]]~~	+
-	~~[[Category: Restriction endonuclease]]~~	+
-	~~[[Category: Thermophilic enzyme~~]]	+

OCA at 18:24, 10 March 2021

OCA — Wed, 10 Mar 2021 18:24:28 GMT

←Older revision		Revision as of 18:24, 10 March 2021
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	<StructureSection load='1dc1' size='340' side='right'caption='[[1dc1]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1dc1' size='340' side='right'caption='[[1dc1]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dc1]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1DC1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dc1]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DC1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</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'>[https://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [https://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=1dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dc1 OCA], [~~http~~://pdbe.org/1dc1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1dc1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1dc1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1dc1 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=1dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dc1 OCA], [https://pdbe.org/1dc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dc1 RCSB], [https://www.ebi.ac.uk/pdbsum/1dc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dc1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/T2B1_GEOSE T2B1_GEOSE]] Recognizes the double-stranded sequence CYCGRG and cleaves after C-1.	+	[[https://www.uniprot.org/uniprot/T2B1_GEOSE T2B1_GEOSE]] Recognizes the double-stranded sequence CYCGRG and cleaves after C-1.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:

	==See Also==		==See Also==
-	*[[Endonuclease\|Endonuclease]]	+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 00:21, 6 June 2019

OCA — Thu, 06 Jun 2019 00:21:15 GMT

←Older revision		Revision as of 00:21, 6 June 2019
Line 1:		Line 1:

	==RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD==		==RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD==
-	<StructureSection load='1dc1' size='340' side='right' caption='[[1dc1]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='1dc1' size='340' side='right'caption='[[1dc1]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1dc1]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DC1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1dc1]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DC1 FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Type II site-specific deoxyribonuclease]]		[[Category: Type II site-specific deoxyribonuclease]]
	[[Category: Friedman, A M]]		[[Category: Friedman, A M]]

OCA at 04:15, 30 August 2017

OCA — Wed, 30 Aug 2017 04:15:17 GMT

←Older revision		Revision as of 04:15, 30 August 2017
Line 1:		Line 1:
		+
	==RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD==		==RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD==
	<StructureSection load='1dc1' size='340' side='right' caption='[[1dc1]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1dc1' size='340' side='right' caption='[[1dc1]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dc1]] is a 4 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DC1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dc1]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DC1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</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=1dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dc1 OCA], [http://pdbe.org/1dc1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dc1 RCSB], [http://www.ebi.ac.uk/pdbsum/1dc1 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=1dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dc1 OCA], [http://pdbe.org/1dc1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dc1 RCSB], [http://www.ebi.ac.uk/pdbsum/1dc1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dc1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 25:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 12980]]
	[[Category: Type II site-specific deoxyribonuclease]]		[[Category: Type II site-specific deoxyribonuclease]]
	[[Category: Friedman, A M]]		[[Category: Friedman, A M]]

OCA at 05:13, 10 September 2015

OCA — Thu, 10 Sep 2015 05:13:15 GMT

←Older revision		Revision as of 05:13, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1dc1' size='340' side='right' caption='[[1dc1]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1dc1' size='340' side='right' caption='[[1dc1]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dc1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Geobacillus_stearothermophilus Geobacillus stearothermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DC1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dc1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DC1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</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=1dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dc1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dc1 RCSB], [http://www.ebi.ac.uk/pdbsum/1dc1 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=1dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dc1 OCA], [http://pdbe.org/1dc1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dc1 RCSB], [http://www.ebi.ac.uk/pdbsum/1dc1 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~T2B1_BACST T2B1_BACST~~]] Recognizes the double-stranded sequence CYCGRG and cleaves after C-1.	+	[[http://www.uniprot.org/uniprot/T2B1_GEOSE T2B1_GEOSE]] Recognizes the double-stranded sequence CYCGRG and cleaves after C-1.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		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>
		+	<div class="pdbe-citations 1dc1" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Geobacillus stearothermophilus~~]]	+	[[Category: Atcc 12980]]
	[[Category: Type II site-specific deoxyribonuclease]]		[[Category: Type II site-specific deoxyribonuclease]]
	[[Category: Friedman, A M]]		[[Category: Friedman, A M]]

OCA at 18:25, 24 December 2014

OCA — Wed, 24 Dec 2014 18:25:53 GMT

←Older revision		Revision as of 18:25, 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=1dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dc1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dc1 RCSB], [http://www.ebi.ac.uk/pdbsum/1dc1 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=1dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dc1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dc1 RCSB], [http://www.ebi.ac.uk/pdbsum/1dc1 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/T2B1_BACST T2B1_BACST]] Recognizes the double-stranded sequence CYCGRG and cleaves after C-1.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 19:56, 22 December 2014

OCA — Mon, 22 Dec 2014 19:56:20 GMT

←Older revision		Revision as of 19:56, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1dc1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DC1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1dc1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DC1 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</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=1dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dc1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dc1 RCSB], [http://www.ebi.ac.uk/pdbsum/1dc1 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=1dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dc1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dc1 RCSB], [http://www.ebi.ac.uk/pdbsum/1dc1 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: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Type II site-specific deoxyribonuclease]]		[[Category: Type II site-specific deoxyribonuclease]]
-	[[Category: Friedman, A M.]]	+	[[Category: Friedman, A M]]
-	[[Category: Pelletier, J J.]]	+	[[Category: Pelletier, J J]]
-	[[Category: Woerd, M J.van der.]]	+	[[Category: Woerd, M J.van der]]
-	[[Category: Xu, S Y.]]	+	[[Category: Xu, S Y]]
	[[Category: Degenerate dna recognition]]		[[Category: Degenerate dna recognition]]
	[[Category: Hydrolase-dna complex]]		[[Category: Hydrolase-dna complex]]

OCA at 06:46, 4 September 2014

OCA — Thu, 04 Sep 2014 06:46:02 GMT

←Older revision		Revision as of 06:46, 4 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1dc1.~~png~~\|~~left\|200px~~]]	+	==RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD==
		+	<StructureSection load='1dc1' size='340' side='right' caption='[[1dc1]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1dc1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DC1 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</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=1dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dc1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dc1 RCSB], [http://www.ebi.ac.uk/pdbsum/1dc1 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: Restriction endonucleases form a diverse family of proteins with substantial variation in sequence, structure, and interaction with recognition site DNA. BsoBI is a thermophilic restriction endonuclease that exhibits both base-specific and degenerate recognition within the sequence CPyCGPuG. RESULTS: The structure of BsoBI complexed to cognate DNA has been determined to 1.7 A resolution, revealing several unprecedented features. Each BsoBI monomer is formed by inserting a helical domain into an expanded EcoRI-type catalytic domain. DNA is completely encircled by a BsoBI dimer. Recognition sequence DNA lies within a 20 A long tunnel of protein that excludes bulk solvent. Interactions with the specific bases are made in both grooves through direct and water-mediated hydrogen bonding. Interaction with the degenerate position is mediated by a purine-specific hydrogen bond to N7, ensuring specificity, and water-mediated H bonding to the purine N6/O6 and pyrimidine N4/O4, allowing degeneracy. In addition to the conserved active site residues of the DX(n)(E/D)ZK restriction enzyme motif, His253 is positioned to act as a general base. CONCLUSIONS: A catalytic mechanism employing His253 and two metal ions is proposed. If confirmed, this would be the first example of histidine-mediated catalysis in a restriction endonuclease. The structure also provides two novel examples of the role of water in protein-DNA interaction. Degenerate recognition may be mediated by employing water as a hydrogen bond donor or acceptor. The structure of DNA in the tunnel may also be influenced by the absence of bulk solvent.

-	~~{{STRUCTURE_1dc1\| PDB=1dc1 \| SCENE= }}~~	+	Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis.,van der Woerd MJ, Pelletier JJ, Xu S, Friedman AM Structure. 2001 Feb 7;9(2):133-44. PMID:11250198<ref>PMID:11250198</ref>

-	~~===RESTRICTION ENZYME BSOBI~~/~~DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11250198}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1dc1]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA].~~	+

	==See Also==		==See Also==
	*[[Endonuclease\|Endonuclease]]		*[[Endonuclease\|Endonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:011250198<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Type II site-specific deoxyribonuclease]]		[[Category: Type II site-specific deoxyribonuclease]]

OCA at 07:56, 20 October 2012

OCA — Sat, 20 Oct 2012 07:56:35 GMT

←Older revision		Revision as of 07:56, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1dc1]] is a 4 chain structure ~~of [[Endonuclease]]~~ with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA].	+	[[1dc1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA].

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