6eg7 - Revision history

OCA at 14:41, 13 March 2024

2024-03-13T14:41:16Z

←Older revision		Revision as of 14:41, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6eg7' size='340' side='right'caption='[[6eg7]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='6eg7' size='340' side='right'caption='[[6eg7]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6eg7]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_8246 Atcc 8246~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EG7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6EG7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6eg7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Brevibacillus_brevis Brevibacillus brevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EG7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6EG7 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=I3C:5-AMINO-2,4,6-TRIIODOBENZENE-1,3-DICARBOXYLIC+ACID'>I3C</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 3Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bbvCIR-2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1393 ATCC 8246])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=I3C:5-AMINO-2,4,6-TRIIODOBENZENE-1,3-DICARBOXYLIC+ACID'>I3C</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=6eg7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eg7 OCA], [~~http~~://pdbe.org/6eg7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6eg7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6eg7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6eg7 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=6eg7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eg7 OCA], [https://pdbe.org/6eg7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6eg7 RCSB], [https://www.ebi.ac.uk/pdbsum/6eg7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6eg7 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q5D6Y4_BREBE Q5D6Y4_BREBE]
-	BbvCI, a Type IIT restriction endonuclease, recognizes and cleaves the seven base pair sequence 5'-CCTCAGC-3', generating 3-base, 5'-overhangs. BbvCI is composed of two protein subunits, each containing one catalytic site. Either site can be inactivated by mutation resulting in enzyme variants that nick DNA in a strand-specific manner. Here we demonstrate that the holoenzyme is labile, with the R1 subunit dissociating at low pH. Crystallization of the R2 subunit under such conditions revealed an elongated dimer with the two catalytic sites located on opposite sides. Subsequent crystallization at physiological pH revealed a tetramer comprising two copies of each subunit, with a pair of deep clefts each containing two catalytic sites appropriately positioned and oriented for DNA cleavage. This domain organization was further validated with single-chain protein constructs in which the two enzyme subunits were tethered via peptide linkers of variable length. We were unable to crystallize a DNA-bound complex; however, structural similarity to previously crystallized restriction endonucleases facilitated creation of an energy-minimized model bound to DNA, and identification of candidate residues responsible for target recognition. Mutation of residues predicted to recognize the central C:~~G base pair resulted in an altered enzyme that recognizes and cleaves CCTNAGC (N = any base).~~	+
-		+
-	Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI.,Shen BW, Doyle L, Bradley P, Heiter DF, Lunnen KD, Wilson GG, Stoddard BL Nucleic Acids Res. 2019 Jan 10;47(1):450-467. doi: 10.1093/~~nar~~/~~gky1059~~. ~~PMID:30395313<ref>PMID:30395313</ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.~~S. National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6eg7" 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>
-	[[Category: ~~Atcc 8246~~]]	+	[[Category: Brevibacillus brevis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Shen~~, B W~~]]	+	[[Category: Shen BW]]
-	[[Category: Stoddard~~, B L]]~~	+	[[Category: Stoddard BL]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Endonuclease]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Type iit restriction enzyme~~]]	+

OCA at 10:32, 18 December 2019

2019-12-18T10:32:35Z

←Older revision		Revision as of 10:32, 18 December 2019
Line 1:		Line 1:

	==BbvCI B2 dimer with I3C clusters==		==BbvCI B2 dimer with I3C clusters==
-	<StructureSection load='6eg7' size='340' side='right' caption='[[6eg7]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='6eg7' size='340' side='right'caption='[[6eg7]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6eg7]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EG7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EG7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6eg7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_8246 Atcc 8246]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EG7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EG7 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=I3C:5-AMINO-2,4,6-TRIIODOBENZENE-1,3-DICARBOXYLIC+ACID'>I3C</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=I3C:5-AMINO-2,4,6-TRIIODOBENZENE-1,3-DICARBOXYLIC+ACID'>I3C</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bbvCIR-2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1393 ATCC 8246])</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=6eg7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eg7 OCA], [http://pdbe.org/6eg7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6eg7 RCSB], [http://www.ebi.ac.uk/pdbsum/6eg7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6eg7 ProSAT]</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=6eg7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eg7 OCA], [http://pdbe.org/6eg7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6eg7 RCSB], [http://www.ebi.ac.uk/pdbsum/6eg7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6eg7 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BbvCI, a Type IIT restriction endonuclease, recognizes and cleaves the seven base pair sequence 5'-CCTCAGC-3', generating 3-base, 5'-overhangs. BbvCI is composed of two protein subunits, each containing one catalytic site. Either site can be inactivated by mutation resulting in enzyme variants that nick DNA in a strand-specific manner. Here we demonstrate that the holoenzyme is labile, with the R1 subunit dissociating at low pH. Crystallization of the R2 subunit under such conditions revealed an elongated dimer with the two catalytic sites located on opposite sides. Subsequent crystallization at physiological pH revealed a tetramer comprising two copies of each subunit, with a pair of deep clefts each containing two catalytic sites appropriately positioned and oriented for DNA cleavage. This domain organization was further validated with single-chain protein constructs in which the two enzyme subunits were tethered via peptide linkers of variable length. We were unable to crystallize a DNA-bound complex; however, structural similarity to previously crystallized restriction endonucleases facilitated creation of an energy-minimized model bound to DNA, and identification of candidate residues responsible for target recognition. Mutation of residues predicted to recognize the central C:G base pair resulted in an altered enzyme that recognizes and cleaves CCTNAGC (N = any base).
		+
		+	Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI.,Shen BW, Doyle L, Bradley P, Heiter DF, Lunnen KD, Wilson GG, Stoddard BL Nucleic Acids Res. 2019 Jan 10;47(1):450-467. doi: 10.1093/nar/gky1059. PMID:30395313<ref>PMID:30395313</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6eg7" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 8246]]
		+	[[Category: Large Structures]]
	[[Category: Shen, B W]]		[[Category: Shen, B W]]
	[[Category: Stoddard, B L]]		[[Category: Stoddard, B L]]

OCA at 08:17, 14 November 2018

2018-11-14T08:17:28Z

←Older revision		Revision as of 08:17, 14 November 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6eg7 ~~is ON HOLD~~	+	==BbvCI B2 dimer with I3C clusters==
-		+	<StructureSection load='6eg7' size='340' side='right' caption='[[6eg7]], [[Resolution\|resolution]] 3.00Å' scene=''>
-	~~Authors~~: ~~Shen, B~~.W.~~, Stoddard, B~~.L.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6eg7]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EG7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EG7 FirstGlance]. <br>
-	~~Description~~: ~~BbvCI B2 dimer with~~ I3C ~~clusters~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=I3C:5-AMINO-2,4,6-TRIIODOBENZENE-1,3-DICARBOXYLIC+ACID'>I3C</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=6eg7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eg7 OCA], [http://pdbe.org/6eg7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6eg7 RCSB], [http://www.ebi.ac.uk/pdbsum/6eg7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6eg7 ProSAT]</span></td></tr>
-	[[Category: Shen, B.W]]	+	</table>
-	[[Category: Stoddard, B.L]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Shen, B W]]
		+	[[Category: Stoddard, B L]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Endonuclease]]
		+	[[Category: Hydrolase]]
		+	[[Category: Type iit restriction enzyme]]

OCA: Protected "6eg7" [edit=sysop:move=sysop]

2018-08-29T05:46:01Z

Protected "6eg7" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:46, 29 August 2018

OCA: New page: '''Unreleased structure''' The entry 6eg7 is ON HOLD Authors: Shen, B.W., Stoddard, B.L. Description: BbvCI B2 dimer with I3C clusters Category: Unreleased Structures [[Category: S...

2018-08-29T05:46:00Z

New page: '''Unreleased structure''' The entry 6eg7 is ON HOLD Authors: Shen, B.W., Stoddard, B.L. Description: BbvCI B2 dimer with I3C clusters Category: Unreleased Structures [[Category: S...

New page

'''Unreleased structure'''

The entry 6eg7 is ON HOLD

Authors: Shen, B.W., Stoddard, B.L.

Description: BbvCI B2 dimer with I3C clusters
[[Category: Unreleased Structures]]
[[Category: Shen, B.W]]
[[Category: Stoddard, B.L]]