6mag - Revision history

OCA at 06:27, 11 October 2023

OCA — Wed, 11 Oct 2023 06:27:24 GMT

←Older revision		Revision as of 06:27, 11 October 2023
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	<StructureSection load='6mag' size='340' side='right'caption='[[6mag]], [[Resolution\|resolution]] 2.07Å' scene=''>		<StructureSection load='6mag' size='340' side='right'caption='[[6mag]], [[Resolution\|resolution]] 2.07Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mag]] is a 3 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=6MAG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6MAG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mag]] is a 3 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=6MAG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MAG FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ACT:ACETATE+ION'>ACT</scene~~>, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.07Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[6eg7\|6eg7]], [[6m9g\|6m9g]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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'>[https://proteopedia.org/fgij/fg.htm?mol=6mag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mag OCA], [https://pdbe.org/6mag PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mag RCSB], [https://www.ebi.ac.uk/pdbsum/6mag PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mag 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=6mag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mag OCA], [~~http~~://pdbe.org/6mag PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6mag RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6mag PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6mag ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5D6Y4_BREBE Q5D6Y4_BREBE]
	<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: ~~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 10:50, 18 December 2019

OCA — Wed, 18 Dec 2019 10:50:41 GMT

←Older revision		Revision as of 10:50, 18 December 2019
Line 1:		Line 1:

	==native BbvCI B2 dimer in space group C222==		==native BbvCI B2 dimer in space group C222==
-	<StructureSection load='6mag' size='340' side='right' caption='[[6mag]], [[Resolution\|resolution]] 2.07Å' scene=''>	+	<StructureSection load='6mag' size='340' side='right'caption='[[6mag]], [[Resolution\|resolution]] 2.07Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mag]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MAG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MAG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mag]] is a 3 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=6MAG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MAG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6eg7\|6eg7]], [[6m9g\|6m9g]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6eg7\|6eg7]], [[6m9g\|6m9g]]</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=6mag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mag OCA], [http://pdbe.org/6mag PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mag RCSB], [http://www.ebi.ac.uk/pdbsum/6mag PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mag 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=6mag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mag OCA], [http://pdbe.org/6mag PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mag RCSB], [http://www.ebi.ac.uk/pdbsum/6mag PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mag 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 6mag" 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 08:22, 14 November 2018

OCA — Wed, 14 Nov 2018 08:22:09 GMT

←Older revision		Revision as of 08:22, 14 November 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6mag ~~is ON HOLD~~	+	==native BbvCI B2 dimer in space group C222==
-		+	<StructureSection load='6mag' size='340' side='right' caption='[[6mag]], [[Resolution\|resolution]] 2.07Å' scene=''>
-	~~Authors~~: ~~Shen, B~~.W.~~, Stoddard, B~~.L.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6mag]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MAG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MAG FirstGlance]. <br>
-	~~Description~~: ~~native BbvCI B2 dimer in space group C222~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6eg7\|6eg7]], [[6m9g\|6m9g]]</td></tr>
-	[[Category: Shen, B.W]]	+	<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=6mag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mag OCA], [http://pdbe.org/6mag PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mag RCSB], [http://www.ebi.ac.uk/pdbsum/6mag PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mag ProSAT]</span></td></tr>
-	[[Category: Stoddard, B.L]]	+	</table>
		+	__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 "6mag" [edit=sysop:move=sysop]

OCA — Wed, 05 Sep 2018 08:53:09 GMT

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

←Older revision

Revision as of 08:53, 5 September 2018

OCA: New page: '''Unreleased structure''' The entry 6mag is ON HOLD Authors: Shen, B.W., Stoddard, B.L. Description: native BbvCI B2 dimer in space group C222 Category: Unreleased Structures [[Ca...

OCA — Wed, 05 Sep 2018 08:53:07 GMT

New page: '''Unreleased structure''' The entry 6mag is ON HOLD Authors: Shen, B.W., Stoddard, B.L. Description: native BbvCI B2 dimer in space group C222 Category: Unreleased Structures [[Ca...

New page

'''Unreleased structure'''

The entry 6mag is ON HOLD

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

Description: native BbvCI B2 dimer in space group C222
[[Category: Unreleased Structures]]
[[Category: Shen, B.W]]
[[Category: Stoddard, B.L]]