1rvc - Revision history

OCA at 08:26, 14 February 2024

2024-02-14T08:26:14Z

←Older revision		Revision as of 08:26, 14 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 type II restriction endonuclease EcoRV was crystallized as a complex with the substrate DNA undecamer AAAGATATCTT (recognition sequence underlined). These crystals diffract to much better resolution (2 A) than was the case for the previously reported complex with the decamer GGGATATCCC [Winkler, F. K., Banner, D. W., Oefner, C., Tsernoglou, D., Brown, R. S., Heathman, S. P., Bryan, R. K., Martin, P. D., Petratos, K., & Wilson, K. S. (1993) EMBO J. 12, 1781-1795]. The crystal structure contains one dimer complex in the asymmetric unit and was solved by molecular replacement. The same kinked DNA conformation characteristic for enzyme-bound cognate DNA is observed. Crystals, soaked with Mg2+, show the essential cofactor bound at only one active site of the dimer, and the DNA is not cleaved. The Mg2+ has one oxygen from the scissile phosphodiester group and two carboxylate oxygens, one form Asp74 and one from Asp90, in its octahedral ligand sphere. The scissile phosphodiester group is pulled by 1 A toward the Mg2+. After substrate cleavage in solution, isomorphous crystals containing the enzyme--product--Mg2+ complex were obtained. In this structure, each of the 5'-phosphate groups is bound to two Mg2+. The kinked DNA conformation is essentially maintained, but the two central adenines, 3' to the cleavage sites, form an unusual cross-strand base stacking. The structures have been refined to R factors of 0.16 at 2.1-2.0 A resolution maintaining very good stereochemistry. On the basis of these structures and inspired by recent kinetic data [Vipond, I. B., & Halford, S. E. (1994) Biochemistry (second paper of three in this issue)], we have constructed a transition state model with two metals bound to the scissile phosphorane group.
-
-	Mg2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 A resolution.,Kostrewa D, Winkler FK Biochemistry. 1995 Jan 17;34(2):683-96. PMID:7819264<ref>PMID:7819264</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1rvc" 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 21:34, 28 June 2023

2023-06-28T21:34:44Z

←Older revision		Revision as of 21:34, 28 June 2023
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	<StructureSection load='1rvc' size='340' side='right'caption='[[1rvc]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1rvc' size='340' side='right'caption='[[1rvc]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1rvc]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. The August 2000 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Restriction Enzymes'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2000_8 10.2210/rcsb_pdb/mom_2000_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RVC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1rvc]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The August 2000 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Restriction Enzymes'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2000_8 10.2210/rcsb_pdb/mom_2000_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RVC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.1Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1rvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvc OCA], [https://pdbe.org/1rvc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rvc RCSB], [https://www.ebi.ac.uk/pdbsum/1rvc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rvc 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=1rvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvc OCA], [https://pdbe.org/1rvc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rvc RCSB], [https://www.ebi.ac.uk/pdbsum/1rvc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rvc 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 25:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Restriction Enzymes]]		[[Category: Restriction Enzymes]]
-	[[Category: Kostrewa, D]]	+	[[Category: Kostrewa D]]
-	[[Category: Winkler~~, F K]]~~	+	[[Category: Winkler FK]]
-	~~[[Category: Hydrolase-dna complex]]~~	+
-	~~[[Category: Protein-dna complex~~]]	+

OCA at 07:22, 22 September 2021

2021-09-22T07:22:41Z

←Older revision		Revision as of 07:22, 22 September 2021
Line 3:		Line 3:
	<StructureSection load='1rvc' size='340' side='right'caption='[[1rvc]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1rvc' size='340' side='right'caption='[[1rvc]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1rvc]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. The August 2000 RCSB PDB [~~http~~://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Restriction Enzymes'' by David S. Goodsell is [~~http~~://dx.doi.org/10.2210/rcsb_pdb/mom_2000_8 10.2210/rcsb_pdb/mom_2000_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1RVC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1rvc]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. The August 2000 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Restriction Enzymes'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2000_8 10.2210/rcsb_pdb/mom_2000_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RVC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=1rvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvc OCA], [~~http~~://pdbe.org/1rvc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1rvc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1rvc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1rvc 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=1rvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvc OCA], [https://pdbe.org/1rvc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rvc RCSB], [https://www.ebi.ac.uk/pdbsum/1rvc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rvc 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 19:04, 11 December 2019

2019-12-11T19:04:12Z

←Older revision		Revision as of 19:04, 11 December 2019
Line 1:		Line 1:

	==MG2+ BINDING TO THE ACTIVE SITE OF ECO RV ENDONUCLEASE: A CRYSTALLOGRAPHIC STUDY OF COMPLEXES WITH SUBSTRATE AND PRODUCT DNA AT 2 ANGSTROMS RESOLUTION==		==MG2+ BINDING TO THE ACTIVE SITE OF ECO RV ENDONUCLEASE: A CRYSTALLOGRAPHIC STUDY OF COMPLEXES WITH SUBSTRATE AND PRODUCT DNA AT 2 ANGSTROMS RESOLUTION==
-	<StructureSection load='1rvc' size='340' side='right' caption='[[1rvc]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='1rvc' size='340' side='right'caption='[[1rvc]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rvc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. The August 2000 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Restriction Enzymes'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2000_8 10.2210/rcsb_pdb/mom_2000_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVC FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rvc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. The August 2000 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Restriction Enzymes'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2000_8 10.2210/rcsb_pdb/mom_2000_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVC 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: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Restriction Enzymes]]		[[Category: Restriction Enzymes]]

OCA at 06:36, 8 March 2018

2018-03-08T06:36:02Z

←Older revision		Revision as of 06:36, 8 March 2018
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		+
	==MG2+ BINDING TO THE ACTIVE SITE OF ECO RV ENDONUCLEASE: A CRYSTALLOGRAPHIC STUDY OF COMPLEXES WITH SUBSTRATE AND PRODUCT DNA AT 2 ANGSTROMS RESOLUTION==		==MG2+ BINDING TO THE ACTIVE SITE OF ECO RV ENDONUCLEASE: A CRYSTALLOGRAPHIC STUDY OF COMPLEXES WITH SUBSTRATE AND PRODUCT DNA AT 2 ANGSTROMS RESOLUTION==
	<StructureSection load='1rvc' size='340' side='right' caption='[[1rvc]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1rvc' size='340' side='right' caption='[[1rvc]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1rvc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. The August 2000 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Restriction Enzymes'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2000_8 10.2210/rcsb_pdb/mom_2000_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVC FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rvc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. The August 2000 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Restriction Enzymes'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2000_8 10.2210/rcsb_pdb/mom_2000_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=1rvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvc OCA], [http://pdbe.org/1rvc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rvc RCSB], [http://www.ebi.ac.uk/pdbsum/1rvc 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=1rvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvc OCA], [http://pdbe.org/1rvc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rvc RCSB], [http://www.ebi.ac.uk/pdbsum/1rvc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rvc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 21:32, 11 September 2015

2015-09-11T21:32:55Z

←Older revision

Revision as of 21:32, 11 September 2015

OCA at 19:59, 25 December 2014

2014-12-25T19:59:14Z

←Older revision		Revision as of 19:59, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rvc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The August 2000 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Restriction Enzymes'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2000_8 10.2210/rcsb_pdb/mom_2000_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVC FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rvc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The August 2000 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Restriction Enzymes'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2000_8 10.2210/rcsb_pdb/mom_2000_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVC FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=1rvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rvc RCSB], [http://www.ebi.ac.uk/pdbsum/1rvc 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=1rvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rvc RCSB], [http://www.ebi.ac.uk/pdbsum/1rvc 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 24:		Line 26:
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Restriction Enzymes]]		[[Category: Restriction Enzymes]]
-	[[Category: Kostrewa, D.]]	+	[[Category: Kostrewa, D]]
-	[[Category: Winkler, F K.]]	+	[[Category: Winkler, F K]]
	[[Category: Hydrolase-dna complex]]		[[Category: Hydrolase-dna complex]]
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]

OCA at 20:46, 28 September 2014

2014-09-28T20:46:10Z

←Older revision		Revision as of 20:46, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1rvc.~~png~~\|~~left\|200px~~]]	+	==MG2+ BINDING TO THE ACTIVE SITE OF ECO RV ENDONUCLEASE: A CRYSTALLOGRAPHIC STUDY OF COMPLEXES WITH SUBSTRATE AND PRODUCT DNA AT 2 ANGSTROMS RESOLUTION==
		+	<StructureSection load='1rvc' size='340' side='right' caption='[[1rvc]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1rvc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The August 2000 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Restriction Enzymes'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2000_8 10.2210/rcsb_pdb/mom_2000_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVC FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<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=1rvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rvc RCSB], [http://www.ebi.ac.uk/pdbsum/1rvc PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The type II restriction endonuclease EcoRV was crystallized as a complex with the substrate DNA undecamer AAAGATATCTT (recognition sequence underlined). These crystals diffract to much better resolution (2 A) than was the case for the previously reported complex with the decamer GGGATATCCC [Winkler, F. K., Banner, D. W., Oefner, C., Tsernoglou, D., Brown, R. S., Heathman, S. P., Bryan, R. K., Martin, P. D., Petratos, K., & Wilson, K. S. (1993) EMBO J. 12, 1781-1795]. The crystal structure contains one dimer complex in the asymmetric unit and was solved by molecular replacement. The same kinked DNA conformation characteristic for enzyme-bound cognate DNA is observed. Crystals, soaked with Mg2+, show the essential cofactor bound at only one active site of the dimer, and the DNA is not cleaved. The Mg2+ has one oxygen from the scissile phosphodiester group and two carboxylate oxygens, one form Asp74 and one from Asp90, in its octahedral ligand sphere. The scissile phosphodiester group is pulled by 1 A toward the Mg2+. After substrate cleavage in solution, isomorphous crystals containing the enzyme--product--Mg2+ complex were obtained. In this structure, each of the 5'-phosphate groups is bound to two Mg2+. The kinked DNA conformation is essentially maintained, but the two central adenines, 3' to the cleavage sites, form an unusual cross-strand base stacking. The structures have been refined to R factors of 0.16 at 2.1-2.0 A resolution maintaining very good stereochemistry. On the basis of these structures and inspired by recent kinetic data [Vipond, I. B., & Halford, S. E. (1994) Biochemistry (second paper of three in this issue)], we have constructed a transition state model with two metals bound to the scissile phosphorane group.

-	~~{{STRUCTURE_1rvc\| PDB=1rvc \| SCENE= }}~~	+	Mg2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 A resolution.,Kostrewa D, Winkler FK Biochemistry. 1995 Jan 17;34(2):683-96. PMID:7819264<ref>PMID:7819264</ref>

-	~~===MG2+ BINDING TO THE ACTIVE SITE OF ECO RV ENDONUCLEASE: A CRYSTALLOGRAPHIC STUDY OF COMPLEXES WITH SUBSTRATE AND PRODUCT DNA AT 2 ANGSTROMS RESOLUTION===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_7819264}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1rvc]] is~~ a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The August 2000 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the ~~Month] feature on ''Restriction Enzymes'' by David~~ S. ~~Goodsell is [http://dx~~.~~doi.org~~/~~10.2210/rcsb_pdb/mom_2000_8 10.2210/rcsb_pdb/mom_2000_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVC OCA].~~	+

	==See Also==		==See Also==
	*[[Endonuclease\|Endonuclease]]		*[[Endonuclease\|Endonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:007819264<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]

OCA at 20:51, 20 October 2012

2012-10-20T20:51:19Z

←Older revision		Revision as of 20:51, 20 October 2012
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	==About this Structure==		==About this Structure==
-	[[1rvc]] is a 6 chain structure ~~of [[Endonuclease]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The August 2000 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Restriction Enzymes'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2000_8 10.2210/rcsb_pdb/mom_2000_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVC OCA].	+	[[1rvc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The August 2000 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Restriction Enzymes'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2000_8 10.2210/rcsb_pdb/mom_2000_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVC OCA].

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

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

2012-07-27T11:50:18Z

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

←Older revision

Revision as of 11:50, 27 July 2012