3e42 - Revision history

OCA at 09:44, 21 February 2024

OCA — Wed, 21 Feb 2024 09:44:31 GMT

←Older revision		Revision as of 09:44, 21 February 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/T2C2_HAEIF T2C2_HAEIF] Recognizes the double-stranded sequence GTYRAC and cleaves after Y-3.		[https://www.uniprot.org/uniprot/T2C2_HAEIF T2C2_HAEIF] Recognizes the double-stranded sequence GTYRAC and cleaves after Y-3.
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Five new structures of the Q138F HincII enzyme bound to a total of three different DNA sequences and three different metal ions (Ca(2+), Mg(2+), and Mn(2+)) are presented. While previous structures were produced from soaking Ca(2+) into preformed Q138F HincII/DNA crystals, the new structures are derived from cocrystallization with Ca(2+), Mg(2+), or Mn(2+). The Mn(2)(+)-bound structure provides the first view of a product complex of Q138F HincII with cleaved DNA. Binding studies and a crystal structure show how Ca(2+) allows trapping of a Q138F HincII complex with noncognate DNA in a catalytically incompetent conformation. Many Q138F HincII/DNA structures show asymmetry, despite the binding of a symmetric substrate by a symmetric enzyme. The various complexes are fit into a model describing the different conformations of the DNA-bound enzyme and show how DNA conformational energetics determine DNA-cleavage rates by the Q138F HincII enzyme.
-
-	DNA distortion and specificity in a sequence-specific endonuclease.,Babic AC, Little EJ, Manohar VM, Bitinaite J, Horton NC J Mol Biol. 2008 Oct 31;383(1):186-204. Epub 2008 Aug 22. PMID:18762194<ref>PMID:18762194</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3e42" 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 13:12, 26 July 2023

OCA — Wed, 26 Jul 2023 13:12:56 GMT

←Older revision		Revision as of 13:12, 26 July 2023
Line 3:		Line 3:
	<StructureSection load='3e42' size='340' side='right'caption='[[3e42]], [[Resolution\|resolution]] 2.68Å' scene=''>		<StructureSection load='3e42' size='340' side='right'caption='[[3e42]], [[Resolution\|resolution]] 2.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3e42]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium~~ influenzae~~" lehmann and neumann 1896~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E42 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E42 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3e42]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E42 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E42 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>~~, ~~<scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.68Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[3e41\|3e41]], [[2gih\|2gih]], [[3e3y\|3e3y]], [[3e40\|3e40]], [[3e43\|3e43]], [[3e44\|3e44]], [[3e45\|3e45]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>hindIIR, HI0512 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~727~~ "~~Bacterium influenzae~~" ~~Lehmann and Neumann 1896])</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=3e42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e42 OCA], [https://pdbe.org/3e42 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e42 RCSB], [https://www.ebi.ac.uk/pdbsum/3e42 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e42 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=3e42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e42 OCA], [https://pdbe.org/3e42 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e42 RCSB], [https://www.ebi.ac.uk/pdbsum/3e42 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e42 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~T2D2_HAEIN T2D2_HAEIN]~~] Recognizes the double-stranded sequence GTYRAC and cleaves after Y-3.	+	[https://www.uniprot.org/uniprot/T2C2_HAEIF T2C2_HAEIF] Recognizes the double-stranded sequence GTYRAC and cleaves after Y-3.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 28:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacterium~~ influenzae ~~lehmann and neumann 1896~~]]	+	[[Category: Haemophilus influenzae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Type II site-specific deoxyribonuclease]]~~	+	[[Category: Babic AC]]
-	[[Category: Babic~~, A C~~]]	+	[[Category: Horton NC]]
-	[[Category: Horton~~, N C~~]]	+	[[Category: Little EJ]]
-	[[Category: Little~~, E J~~]]	+	[[Category: Manohar VM]]
-	[[Category: Manohar~~, V M]]~~	+
-	~~[[Category: Endonuclease]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase-dna complex]]~~	+
-	~~[[Category: Indirect readout]]~~	+
-	~~[[Category: Nuclease]]~~	+
-	~~[[Category: Protein-dna interaction]]~~	+
-	~~[[Category: Restriction endonuclease]]~~	+
-	~~[[Category: Restriction system~~]]	+

OCA at 19:34, 20 October 2021

OCA — Wed, 20 Oct 2021 19:34:57 GMT

←Older revision		Revision as of 19:34, 20 October 2021
Line 1:		Line 1:

	==Q138F HincII bound to GTCGAC and Ca2+ (cocrystallized)==		==Q138F HincII bound to GTCGAC and Ca2+ (cocrystallized)==
-	<StructureSection load='3e42' size='340' side='right' caption='[[3e42]], [[Resolution\|resolution]] 2.68Å' scene=''>	+	<StructureSection load='3e42' size='340' side='right'caption='[[3e42]], [[Resolution\|resolution]] 2.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3e42]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E42 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3E42 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3e42]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E42 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E42 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e41\|3e41]], [[2gih\|2gih]], [[3e3y\|3e3y]], [[3e40\|3e40]], [[3e43\|3e43]], [[3e44\|3e44]], [[3e45\|3e45]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3e41\|3e41]], [[2gih\|2gih]], [[3e3y\|3e3y]], [[3e40\|3e40]], [[3e43\|3e43]], [[3e44\|3e44]], [[3e45\|3e45]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hindIIR, HI0512 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hindIIR, HI0512 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</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=3e42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e42 OCA], [~~http~~://pdbe.org/3e42 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3e42 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3e42 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3e42 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=3e42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e42 OCA], [https://pdbe.org/3e42 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e42 RCSB], [https://www.ebi.ac.uk/pdbsum/3e42 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e42 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/T2D2_HAEIN T2D2_HAEIN]] Recognizes the double-stranded sequence GTYRAC and cleaves after Y-3.	+	[[https://www.uniprot.org/uniprot/T2D2_HAEIN T2D2_HAEIN]] Recognizes the double-stranded sequence GTYRAC and cleaves after Y-3.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:

	==See Also==		==See Also==
-	*[[Endonuclease\|Endonuclease]]	+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Bacterium influenzae lehmann and neumann 1896]]		[[Category: Bacterium influenzae lehmann and neumann 1896]]
		+	[[Category: Large Structures]]
	[[Category: Type II site-specific deoxyribonuclease]]		[[Category: Type II site-specific deoxyribonuclease]]
	[[Category: Babic, A C]]		[[Category: Babic, A C]]

OCA at 11:06, 4 August 2016

OCA — Thu, 04 Aug 2016 11:06:16 GMT

←Older revision		Revision as of 11:06, 4 August 2016
Line 1:		Line 1:
		+
	==Q138F HincII bound to GTCGAC and Ca2+ (cocrystallized)==		==Q138F HincII bound to GTCGAC and Ca2+ (cocrystallized)==
	<StructureSection load='3e42' size='340' side='right' caption='[[3e42]], [[Resolution\|resolution]] 2.68Å' scene=''>		<StructureSection load='3e42' size='340' side='right' caption='[[3e42]], [[Resolution\|resolution]] 2.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3e42]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Haemophilus_influenzae Haemophilus~~ influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E42 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3e42]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E42 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e41\|3e41]], [[2gih\|2gih]], [[3e3y\|3e3y]], [[3e40\|3e40]], [[3e43\|3e43]], [[3e44\|3e44]], [[3e45\|3e45]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e41\|3e41]], [[2gih\|2gih]], [[3e3y\|3e3y]], [[3e40\|3e40]], [[3e43\|3e43]], [[3e44\|3e44]], [[3e45\|3e45]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hindIIR, HI0512 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 ~~Haemophilus~~ influenzae])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hindIIR, HI0512 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</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=3e42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e42 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e42 RCSB], [http://www.ebi.ac.uk/pdbsum/3e42 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=3e42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e42 OCA], [http://pdbe.org/3e42 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3e42 RCSB], [http://www.ebi.ac.uk/pdbsum/3e42 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3e42 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 3e42" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 26:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Haemophilus~~ influenzae]]	+	[[Category: Bacterium influenzae lehmann and neumann 1896]]
	[[Category: Type II site-specific deoxyribonuclease]]		[[Category: Type II site-specific deoxyribonuclease]]
	[[Category: Babic, A C]]		[[Category: Babic, A C]]

OCA at 08:40, 25 December 2014

OCA — Thu, 25 Dec 2014 08:40:19 GMT

←Older revision		Revision as of 08:40, 25 December 2014
Line 9:		Line 9:
	<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=3e42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e42 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e42 RCSB], [http://www.ebi.ac.uk/pdbsum/3e42 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=3e42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e42 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e42 RCSB], [http://www.ebi.ac.uk/pdbsum/3e42 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/T2D2_HAEIN T2D2_HAEIN]] Recognizes the double-stranded sequence GTYRAC and cleaves after Y-3.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 13:22, 19 November 2014

OCA — Wed, 19 Nov 2014 13:22:52 GMT

←Older revision		Revision as of 13:22, 19 November 2014
Line 1:		Line 1:
-	[[~~Image:~~3e42.~~png~~\|~~left~~\|~~200px~~]]	+	==Q138F HincII bound to GTCGAC and Ca2+ (cocrystallized)==
		+	<StructureSection load='3e42' size='340' side='right' caption='[[3e42]], [[Resolution\|resolution]] 2.68Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3e42]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E42 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e41\|3e41]], [[2gih\|2gih]], [[3e3y\|3e3y]], [[3e40\|3e40]], [[3e43\|3e43]], [[3e44\|3e44]], [[3e45\|3e45]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hindIIR, HI0512 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 Haemophilus influenzae])</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=3e42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e42 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e42 RCSB], [http://www.ebi.ac.uk/pdbsum/3e42 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Five new structures of the Q138F HincII enzyme bound to a total of three different DNA sequences and three different metal ions (Ca(2+), Mg(2+), and Mn(2+)) are presented. While previous structures were produced from soaking Ca(2+) into preformed Q138F HincII/DNA crystals, the new structures are derived from cocrystallization with Ca(2+), Mg(2+), or Mn(2+). The Mn(2)(+)-bound structure provides the first view of a product complex of Q138F HincII with cleaved DNA. Binding studies and a crystal structure show how Ca(2+) allows trapping of a Q138F HincII complex with noncognate DNA in a catalytically incompetent conformation. Many Q138F HincII/DNA structures show asymmetry, despite the binding of a symmetric substrate by a symmetric enzyme. The various complexes are fit into a model describing the different conformations of the DNA-bound enzyme and show how DNA conformational energetics determine DNA-cleavage rates by the Q138F HincII enzyme.

-	~~{{STRUCTURE_3e42\| PDB=3e42 \| SCENE= }}~~	+	DNA distortion and specificity in a sequence-specific endonuclease.,Babic AC, Little EJ, Manohar VM, Bitinaite J, Horton NC J Mol Biol. 2008 Oct 31;383(1):186-204. Epub 2008 Aug 22. PMID:18762194<ref>PMID:18762194</ref>

-	~~===Q138F HincII bound to GTCGAC and Ca2+ (cocrystallized)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18762194}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3e42]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Haemophilus_influenzae Haemophilus influenzae]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3E42 OCA].~~	+

	==See Also==		==See Also==
	*[[Endonuclease\|Endonuclease]]		*[[Endonuclease\|Endonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018762194<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Haemophilus influenzae]]		[[Category: Haemophilus influenzae]]
	[[Category: Type II site-specific deoxyribonuclease]]		[[Category: Type II site-specific deoxyribonuclease]]
-	[[Category: Babic, A C.]]	+	[[Category: Babic, A C]]
-	[[Category: Horton, N C.]]	+	[[Category: Horton, N C]]
-	[[Category: Little, E J.]]	+	[[Category: Little, E J]]
-	[[Category: Manohar, V M.]]	+	[[Category: Manohar, V M]]
	[[Category: Endonuclease]]		[[Category: Endonuclease]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 14:44, 20 October 2012

OCA — Sat, 20 Oct 2012 14:44:00 GMT

←Older revision		Revision as of 14:44, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3e42]] is a 4 chain structure ~~of [[Endonuclease]]~~ with sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E42 OCA].	+	[[3e42]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E42 OCA].

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

OCA: Protected "3e42" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 16:04:11 GMT

Protected "3e42" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:04, 26 July 2012

OCA at 16:04, 26 July 2012

OCA — Thu, 26 Jul 2012 16:04:08 GMT

←Older revision		Revision as of 16:04, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3e42.png\|left\|200px]]		[[Image:3e42.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3e42", 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),
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	{{STRUCTURE_3e42\| PDB=3e42 \| SCENE= }}		{{STRUCTURE_3e42\| PDB=3e42 \| SCENE= }}

	===Q138F HincII bound to GTCGAC and Ca2+ (cocrystallized)===		===Q138F HincII bound to GTCGAC and Ca2+ (cocrystallized)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18762194}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18762194 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_18762194}}		{{ABSTRACT_PUBMED_18762194}}

	==About this Structure==		==About this Structure==
-	~~3E42~~ is a 4 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E42 OCA].	+	[[3e42]] is a 4 chain structure of [[Endonuclease]] with sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E42 OCA].
		+
		+	==See Also==
		+	*[[Endonuclease\|Endonuclease]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18762194~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018762194</ref><references group="xtra"/>
	[[Category: Haemophilus influenzae]]		[[Category: Haemophilus influenzae]]
	[[Category: Type II site-specific deoxyribonuclease]]		[[Category: Type II site-specific deoxyribonuclease]]
Line 32:		Line 23:
	[[Category: Endonuclease]]		[[Category: Endonuclease]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
-	[[Category: Hydrolase/dna complex]]	+	[[Category: Hydrolase-dna complex]]
	[[Category: Indirect readout]]		[[Category: Indirect readout]]
	[[Category: Nuclease]]		[[Category: Nuclease]]
Line 38:		Line 29:
	[[Category: Restriction endonuclease]]		[[Category: Restriction endonuclease]]
	[[Category: Restriction system]]		[[Category: Restriction system]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 11:29:43 2010''

OCA at 08:20, 22 September 2010

OCA — Wed, 22 Sep 2010 08:20:45 GMT

←Older revision		Revision as of 08:20, 22 September 2010
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3E42 is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E42 OCA].	+	3E42 is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E42 OCA].

	==Reference==		==Reference==
-	~~DNA distortion and specificity in a sequence-specific endonuclease., Babic AC, Little EJ, Manohar VM, Bitinaite J, Horton NC, J Mol Biol. 2008 Oct 31;383(1):186-204. Epub 2008 Aug 22.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18762194 18762194]~~	+	<ref group="xtra">PMID:18762194</ref><references group="xtra"/>
	[[Category: Haemophilus influenzae]]		[[Category: Haemophilus influenzae]]
-	[[Category: Protein complex]]
	[[Category: Type II site-specific deoxyribonuclease]]		[[Category: Type II site-specific deoxyribonuclease]]
-	[[Category: ~~Pdbx_ordinal=~~, ~~<PDBx~~:~~audit_author~~.]]	+	[[Category: Babic, A C.]]
		+	[[Category: Horton, N C.]]
		+	[[Category: Little, E J.]]
		+	[[Category: Manohar, V M.]]
	[[Category: Endonuclease]]		[[Category: Endonuclease]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
Line 37:		Line 39:
	[[Category: Restriction system]]		[[Category: Restriction system]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jan 21 20~~:33:~~20 2009~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 11:29:43 2010''