2rve - Revision history

OCA at 09:23, 21 February 2024

2024-02-21T09:23:43Z

←Older revision		Revision as of 09:23, 21 February 2024
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	== 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 2rve" 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 01:18, 28 December 2023

2023-12-28T01:18:31Z

←Older revision		Revision as of 01:18, 28 December 2023
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	<StructureSection load='2rve' size='340' side='right'caption='[[2rve]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2rve' size='340' side='right'caption='[[2rve]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rve]] is a 6 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=2RVE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RVE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rve]] is a 6 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=2RVE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RVE 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=2rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rve OCA], [https://pdbe.org/2rve PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rve RCSB], [https://www.ebi.ac.uk/pdbsum/2rve PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rve 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]] 3Å</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=2rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rve OCA], [https://pdbe.org/2rve PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rve RCSB], [https://www.ebi.ac.uk/pdbsum/2rve PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rve 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 ==
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Banner~~, D W~~]]	+	[[Category: Banner DW]]
-	[[Category: Brown~~, R S~~]]	+	[[Category: Brown RS]]
-	[[Category: Bryan~~, R K~~]]	+	[[Category: Bryan RK]]
-	[[Category: Heathman~~, S P~~]]	+	[[Category: Heathman SP]]
-	[[Category: Martin~~, P D~~]]	+	[[Category: Martin PD]]
-	[[Category: Oefner, C]]	+	[[Category: Oefner C]]
-	[[Category: Petratos, K]]	+	[[Category: Petratos K]]
-	[[Category: Tsernoglou, D]]	+	[[Category: Tsernoglou D]]
-	[[Category: Wilson~~, K S~~]]	+	[[Category: Wilson KS]]
-	[[Category: Winkler~~, F K]]~~	+	[[Category: Winkler FK]]
-	~~[[Category: Double helix]]~~	+
-	~~[[Category: Hydrolase-dna complex]]~~	+
-	~~[[Category: Protein-dna complex~~]]	+

OCA at 12:27, 23 March 2022

2022-03-23T12:27:18Z

←Older revision		Revision as of 12:27, 23 March 2022
Line 3:		Line 3:
	<StructureSection load='2rve' size='340' side='right'caption='[[2rve]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2rve' size='340' side='right'caption='[[2rve]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rve]] is a 6 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=2RVE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2RVE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rve]] is a 6 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=2RVE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RVE FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=2rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rve OCA], [~~http~~://pdbe.org/2rve PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2rve RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2rve PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2rve ProSAT]</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=2rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rve OCA], [https://pdbe.org/2rve PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rve RCSB], [https://www.ebi.ac.uk/pdbsum/2rve PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rve 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 11:06, 17 June 2020

2020-06-17T11:06:30Z

←Older revision		Revision as of 11:06, 17 June 2020
Line 1:		Line 1:

	==THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA SEGMENTS==		==THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA SEGMENTS==
-	<StructureSection load='2rve' size='340' side='right' caption='[[2rve]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='2rve' size='340' side='right'caption='[[2rve]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rve]] is a 6 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=2RVE OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2RVE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rve]] is a 6 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=2RVE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2RVE FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rve OCA], [http://pdbe.org/2rve PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rve RCSB], [http://www.ebi.ac.uk/pdbsum/2rve PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rve ProSAT]</span></td></tr>	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rve OCA], [http://pdbe.org/2rve PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rve RCSB], [http://www.ebi.ac.uk/pdbsum/2rve PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rve ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:

	==See Also==		==See Also==
-	*[[Endonuclease\|Endonuclease]]	+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Banner, D W]]		[[Category: Banner, D W]]
	[[Category: Brown, R S]]		[[Category: Brown, R S]]

OCA at 01:44, 5 August 2016

2016-08-05T01:44:24Z

←Older revision		Revision as of 01:44, 5 August 2016
Line 1:		Line 1:
		+
	==THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA SEGMENTS==		==THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA SEGMENTS==
	<StructureSection load='2rve' size='340' side='right' caption='[[2rve]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2rve' size='340' side='right' caption='[[2rve]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rve]] is a 6 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=2RVE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RVE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rve]] is a 6 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=2RVE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RVE FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rve OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rve RCSB], [http://www.ebi.ac.uk/pdbsum/2rve PDBsum]</span></td></tr>	+	</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=2rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rve OCA], [http://pdbe.org/2rve PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rve RCSB], [http://www.ebi.ac.uk/pdbsum/2rve PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rve ProSAT]</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 15:		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 2rve" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 22:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Banner, D W]]		[[Category: Banner, D W]]
	[[Category: Brown, R S]]		[[Category: Brown, R S]]

OCA at 14:48, 25 December 2014

2014-12-25T14:48:13Z

←Older revision		Revision as of 14:48, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rve]] is a 6 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=2RVE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RVE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rve]] is a 6 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=2RVE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RVE FirstGlance]. <br>
-	</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=2rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rve OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rve RCSB], [http://www.ebi.ac.uk/pdbsum/2rve PDBsum]</span></td></tr>	+	</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=2rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rve OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rve RCSB], [http://www.ebi.ac.uk/pdbsum/2rve 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 21:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Banner, D W.]]	+	[[Category: Banner, D W]]
-	[[Category: Brown, R S.]]	+	[[Category: Brown, R S]]
-	[[Category: Bryan, R K.]]	+	[[Category: Bryan, R K]]
-	[[Category: Heathman, S P.]]	+	[[Category: Heathman, S P]]
-	[[Category: Martin, P D.]]	+	[[Category: Martin, P D]]
-	[[Category: Oefner, C.]]	+	[[Category: Oefner, C]]
-	[[Category: Petratos, K.]]	+	[[Category: Petratos, K]]
-	[[Category: Tsernoglou, D.]]	+	[[Category: Tsernoglou, D]]
-	[[Category: Wilson, K S.]]	+	[[Category: Wilson, K S]]
-	[[Category: Winkler, F K.]]	+	[[Category: Winkler, F K]]
	[[Category: Double helix]]		[[Category: Double helix]]
	[[Category: Hydrolase-dna complex]]		[[Category: Hydrolase-dna complex]]
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]

OCA at 01:03, 2 October 2014

2014-10-02T01:03:06Z

←Older revision		Revision as of 01:03, 2 October 2014
Line 1:		Line 1:
-	[[~~Image~~:2rve.~~png\|left\|200px~~]]	+	==THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA SEGMENTS==
		+	<StructureSection load='2rve' size='340' side='right' caption='[[2rve]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2rve]] is a 6 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=2RVE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RVE FirstGlance]. <br>
		+	</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=2rve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rve OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rve RCSB], [http://www.ebi.ac.uk/pdbsum/2rve 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_2rve\| PDB=2rve \| 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 SEGMENTS===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_8491171}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2rve]] is~~ a ~~6 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=2RVE OCA].~~	+

	==See Also==		==See Also==
	*[[Endonuclease\|Endonuclease]]		*[[Endonuclease\|Endonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:008491171<~~/~~ref~~><~~ref group="xtra">PMID:008969304</ref><references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Banner, D W.]]		[[Category: Banner, D W.]]

OCA at 17:59, 20 October 2012

2012-10-20T17:59:41Z

←Older revision		Revision as of 17:59, 20 October 2012
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	==About this Structure==		==About this Structure==
-	[[2rve]] is a 6 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=2RVE OCA].	+	[[2rve]] is a 6 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=2RVE OCA].

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

OCA: Protected "2rve" [edit=sysop:move=sysop]

2012-07-27T02:39:46Z

Protected "2rve" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:39, 27 July 2012

OCA at 02:39, 27 July 2012

2012-07-27T02:39:45Z

←Older revision		Revision as of 02:39, 27 July 2012
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-	{{Seed}}
	[[Image:2rve.png\|left\|200px]]		[[Image:2rve.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_2rve\| PDB=2rve \| SCENE= }}		{{STRUCTURE_2rve\| PDB=2rve \| SCENE= }}

	===THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA SEGMENTS===		===THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA SEGMENTS===

-
-	<!--
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	{{ABSTRACT_PUBMED_8491171}}		{{ABSTRACT_PUBMED_8491171}}

	==About this Structure==		==About this Structure==
-	~~2RVE is a~~ [[~~Single protein~~]] structure of 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=2RVE OCA].	+	[[2rve]] is a 6 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=2RVE OCA].
		+
		+	==See Also==
		+	*[[Endonuclease\|Endonuclease]]

	==Reference==		==Reference==
-	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:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~8491171 8491171]~~	+	<ref group="xtra">PMID:008491171</ref><ref group="xtra">PMID:008969304</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Banner, D W.]]		[[Category: Banner, D W.]]
	[[Category: Brown, R S.]]		[[Category: Brown, R S.]]
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	[[Category: Winkler, F K.]]		[[Category: Winkler, F K.]]
	[[Category: Double helix]]		[[Category: Double helix]]
		+	[[Category: Hydrolase-dna complex]]
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 03:13:14 2008''