1rve - Revision history

OCA at 08:26, 14 February 2024

OCA — Wed, 14 Feb 2024 08:26:15 GMT

←Older revision		Revision as of 08:26, 14 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rve]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RVE FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rve]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RVE 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=1rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rve OCA], [https://pdbe.org/1rve PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rve RCSB], [https://www.ebi.ac.uk/pdbsum/1rve PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rve ProSAT]</span></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]] 2.5Å</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=1rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rve OCA], [https://pdbe.org/1rve PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rve RCSB], [https://www.ebi.ac.uk/pdbsum/1rve PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rve ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/T2E5_ECOLX T2E5_ECOLX] Recognizes the double-stranded sequence GATATC and cleaves after T-3.		[https://www.uniprot.org/uniprot/T2E5_ECOLX T2E5_ECOLX] Recognizes the double-stranded sequence GATATC and cleaves after T-3.
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The crystal structure of EcoRV endonuclease has been determined at 2.5 A resolution and that of its complexes with the cognate DNA decamer GGGATATCCC (recognition sequence underlined) and the non-cognate DNA octamer CGAGCTCG at 3.0 A resolution. Two octamer duplexes of the non-cognate DNA, stacked end-to-end, are bound to the dimeric enzyme in B-DNA-like conformations. The protein--DNA interactions of this complex are prototypic for non-specific DNA binding. In contrast, only one cognate decamer duplex is bound and deviates considerably from canonical B-form DNA. Most notably, a kink of approximately 50 degrees is observed at the central TA step with a concomitant compression of the major groove. Base-specific hydrogen bonds between the enzyme and the recognition base pairs occur exclusively in the major groove. These interactions appear highly co-operative as they are all made through one short surface loop comprising residues 182-186. Numerous contacts with the sugar phosphate backbone extending beyond the recognition sequence are observed in both types of complex. However, the total surface area buried on complex formation is > 1800 A2 larger in the case of cognate DNA binding. Two acidic side chains, Asp74 and Asp90, are close to the reactive phosphodiester group in the cognate complex and most probably provide oxygen ligands for binding the essential cofactor Mg2+. An important role is also indicated for Lys92, which together with the two acidic functions appears to be conserved in the otherwise unrelated structure of EcoRI endonuclease. The structural results give new insight into the physical basis of the remarkable sequence specificity of this enzyme.
-
-	The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments.,Winkler FK, Banner DW, Oefner C, Tsernoglou D, Brown RS, Heathman SP, Bryan RK, Martin PD, Petratos K, Wilson KS EMBO J. 1993 May;12(5):1781-95. PMID:8491171<ref>PMID:8491171</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1rve" 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 13:07, 22 February 2023

OCA — Wed, 22 Feb 2023 13:07:28 GMT

←Older revision		Revision as of 13:07, 22 February 2023
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	<StructureSection load='1rve' size='340' side='right'caption='[[1rve]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1rve' size='340' side='right'caption='[[1rve]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1rve]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RVE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1rve]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RVE FirstGlance]. <br>
-	</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>	+	</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=1rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rve OCA], [https://pdbe.org/1rve PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rve RCSB], [https://www.ebi.ac.uk/pdbsum/1rve PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rve 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=1rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rve OCA], [https://pdbe.org/1rve PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rve RCSB], [https://www.ebi.ac.uk/pdbsum/1rve PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rve ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/T2E5_ECOLX T2E5_ECOLX]] Recognizes the double-stranded sequence GATATC and cleaves after T-3.	+	[https://www.uniprot.org/uniprot/T2E5_ECOLX T2E5_ECOLX] Recognizes the double-stranded sequence GATATC and cleaves after T-3.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Type II site-specific deoxyribonuclease]]~~	+	[[Category: Winkler FK]]
-	[[Category: Winkler~~, F K]]~~	+
-	~~[[Category: Endonuclease~~]]	+

OCA at 10:48, 19 May 2021

OCA — Wed, 19 May 2021 10:48:42 GMT

←Older revision		Revision as of 10:48, 19 May 2021
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	<StructureSection load='1rve' size='340' side='right'caption='[[1rve]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1rve' size='340' side='right'caption='[[1rve]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1rve]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1RVE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1rve]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RVE FirstGlance]. <br>
-	</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>	+	</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=1rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rve OCA], [~~http~~://pdbe.org/1rve PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1rve RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1rve PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1rve 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=1rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rve OCA], [https://pdbe.org/1rve PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rve RCSB], [https://www.ebi.ac.uk/pdbsum/1rve PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rve ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/T2E5_ECOLX T2E5_ECOLX]] Recognizes the double-stranded sequence GATATC and cleaves after T-3.	+	[[https://www.uniprot.org/uniprot/T2E5_ECOLX T2E5_ECOLX]] Recognizes the double-stranded sequence GATATC and cleaves after T-3.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 11:00, 17 July 2019

OCA — Wed, 17 Jul 2019 11:00:22 GMT

←Older revision		Revision as of 11:00, 17 July 2019
Line 1:		Line 1:

	==THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA FRAGMENTS==		==THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA FRAGMENTS==
-	<StructureSection load='1rve' size='340' side='right' caption='[[1rve]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='1rve' size='340' side='right'caption='[[1rve]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rve]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVE FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rve]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVE FirstGlance]. <br>
Line 20:		Line 20:

	==See Also==		==See Also==
-	*[[Endonuclease\|Endonuclease]]	+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 26:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Type II site-specific deoxyribonuclease]]		[[Category: Type II site-specific deoxyribonuclease]]
	[[Category: Winkler, F K]]		[[Category: Winkler, F K]]
	[[Category: Endonuclease]]		[[Category: Endonuclease]]

OCA at 07:08, 8 March 2018

OCA — Thu, 08 Mar 2018 07:08:34 GMT

←Older revision		Revision as of 07:08, 8 March 2018
Line 1:		Line 1:
		+
	==THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA FRAGMENTS==		==THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA FRAGMENTS==
	<StructureSection load='1rve' size='340' side='right' caption='[[1rve]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1rve' size='340' side='right' caption='[[1rve]], [[Resolution\|resolution]] 2.50Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1rve]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVE FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rve]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVE FirstGlance]. <br>
	</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>		</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=1rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rve OCA], [http://pdbe.org/1rve PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rve RCSB], [http://www.ebi.ac.uk/pdbsum/1rve 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=1rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rve OCA], [http://pdbe.org/1rve PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rve RCSB], [http://www.ebi.ac.uk/pdbsum/1rve PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rve ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 08:45, 11 September 2015

OCA — Fri, 11 Sep 2015 08:45:09 GMT

←Older revision		Revision as of 08:45, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1rve' size='340' side='right' caption='[[1rve]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1rve' size='340' side='right' caption='[[1rve]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1rve]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1rve]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVE FirstGlance]. <br>
	</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>		</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=1rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rve OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rve RCSB], [http://www.ebi.ac.uk/pdbsum/1rve 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=1rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rve OCA], [http://pdbe.org/1rve PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rve RCSB], [http://www.ebi.ac.uk/pdbsum/1rve PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~T2E5_ECOLI T2E5_ECOLI~~]] Recognizes the double-stranded sequence GATATC and cleaves after T-3.	+	[[http://www.uniprot.org/uniprot/T2E5_ECOLX T2E5_ECOLX]] Recognizes the double-stranded sequence GATATC and cleaves after T-3.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 16:		Line 16:
	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 1rve" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Type II site-specific deoxyribonuclease]]		[[Category: Type II site-specific deoxyribonuclease]]
	[[Category: Winkler, F K]]		[[Category: Winkler, F K]]
	[[Category: Endonuclease]]		[[Category: Endonuclease]]

OCA at 14:02, 25 December 2014

OCA — Thu, 25 Dec 2014 14:02:17 GMT

←Older revision		Revision as of 14:02, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rve]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVE FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rve]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVE FirstGlance]. <br>
-	</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>	+	</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=1rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rve OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rve RCSB], [http://www.ebi.ac.uk/pdbsum/1rve 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=1rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rve OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rve RCSB], [http://www.ebi.ac.uk/pdbsum/1rve PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/T2E5_ECOLI T2E5_ECOLI]] Recognizes the double-stranded sequence GATATC and cleaves after T-3.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 25:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Type II site-specific deoxyribonuclease]]		[[Category: Type II site-specific deoxyribonuclease]]
-	[[Category: Winkler, F K.]]	+	[[Category: Winkler, F K]]
	[[Category: Endonuclease]]		[[Category: Endonuclease]]

OCA at 23:00, 28 September 2014

OCA — Sun, 28 Sep 2014 23:00:30 GMT

←Older revision		Revision as of 23:00, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1rve.~~png\|left\|200px~~]]	+	==THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA FRAGMENTS==
		+	<StructureSection load='1rve' size='340' side='right' caption='[[1rve]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1rve]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVE FirstGlance]. <br>
		+	</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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rve OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rve RCSB], [http://www.ebi.ac.uk/pdbsum/1rve PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structure of EcoRV endonuclease has been determined at 2.5 A resolution and that of its complexes with the cognate DNA decamer GGGATATCCC (recognition sequence underlined) and the non-cognate DNA octamer CGAGCTCG at 3.0 A resolution. Two octamer duplexes of the non-cognate DNA, stacked end-to-end, are bound to the dimeric enzyme in B-DNA-like conformations. The protein--DNA interactions of this complex are prototypic for non-specific DNA binding. In contrast, only one cognate decamer duplex is bound and deviates considerably from canonical B-form DNA. Most notably, a kink of approximately 50 degrees is observed at the central TA step with a concomitant compression of the major groove. Base-specific hydrogen bonds between the enzyme and the recognition base pairs occur exclusively in the major groove. These interactions appear highly co-operative as they are all made through one short surface loop comprising residues 182-186. Numerous contacts with the sugar phosphate backbone extending beyond the recognition sequence are observed in both types of complex. However, the total surface area buried on complex formation is > 1800 A2 larger in the case of cognate DNA binding. Two acidic side chains, Asp74 and Asp90, are close to the reactive phosphodiester group in the cognate complex and most probably provide oxygen ligands for binding the essential cofactor Mg2+. An important role is also indicated for Lys92, which together with the two acidic functions appears to be conserved in the otherwise unrelated structure of EcoRI endonuclease. The structural results give new insight into the physical basis of the remarkable sequence specificity of this enzyme.

-	~~{{STRUCTURE_1rve\| PDB=1rve \| SCENE= }}~~	+	The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments.,Winkler FK, Banner DW, Oefner C, Tsernoglou D, Brown RS, Heathman SP, Bryan RK, Martin PD, Petratos K, Wilson KS EMBO J. 1993 May;12(5):1781-95. PMID:8491171<ref>PMID:8491171</ref>

-	~~===THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA FRAGMENTS===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_8491171}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1rve]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1RVE OCA].~~	+

	==See Also==		==See Also==
	*[[Endonuclease\|Endonuclease]]		*[[Endonuclease\|Endonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:008491171<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Type II site-specific deoxyribonuclease]]		[[Category: Type II site-specific deoxyribonuclease]]
	[[Category: Winkler, F K.]]		[[Category: Winkler, F K.]]
	[[Category: Endonuclease]]		[[Category: Endonuclease]]

OCA at 17:34, 20 October 2012

OCA — Sat, 20 Oct 2012 17:34:44 GMT

←Older revision		Revision as of 17:34, 20 October 2012
Line 8:		Line 8:

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

	==See Also==		==See Also==
Line 14:		Line 14:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:008491171~~</ref><ref group="xtra">PMID:012215419~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:008491171</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Type II site-specific deoxyribonuclease]]		[[Category: Type II site-specific deoxyribonuclease]]
	[[Category: Winkler, F K.]]		[[Category: Winkler, F K.]]
	[[Category: Endonuclease]]		[[Category: Endonuclease]]

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

OCA — Fri, 27 Jul 2012 01:22:28 GMT

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

←Older revision

Revision as of 01:22, 27 July 2012