5jp6 - Revision history

OCA at 19:01, 20 September 2023

2023-09-20T19:01:33Z

←Older revision		Revision as of 19:01, 20 September 2023
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	<StructureSection load='5jp6' size='340' side='right'caption='[[5jp6]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='5jp6' size='340' side='right'caption='[[5jp6]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jp6]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bdeba Bdeba~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JP6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JP6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jp6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bdellovibrio_bacteriovorus_HD100 Bdellovibrio bacteriovorus HD100]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JP6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JP6 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~~>, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.5Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=PXU:2-HYDROXY-L-PROLINE'>PXU</scene><~~/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>, <scene name='pdbligand=PXU:2-HYDROXY-L-PROLINE'>PXU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">Bd3279 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=264462 BDEBA])~~</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=5jp6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jp6 OCA], [https://pdbe.org/5jp6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jp6 RCSB], [https://www.ebi.ac.uk/pdbsum/5jp6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jp6 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=5jp6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jp6 OCA], [~~http~~://pdbe.org/5jp6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jp6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jp6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jp6 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q6MI90_BDEBA Q6MI90_BDEBA]
	<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: ~~Bdeba~~]]	+	[[Category: Bdellovibrio bacteriovorus HD100]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Lovering~~, A L]]~~	+	[[Category: Lovering AL]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Peptidoglycan deacetylase ce-4 carbohydrate esterase 4~~]]	+

OCA at 06:09, 10 July 2019

2019-07-10T06:09:55Z

←Older revision		Revision as of 06:09, 10 July 2019
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	==Bdellovibrio bacteriovorus peptidoglycan deacetylase Bd3279==		==Bdellovibrio bacteriovorus peptidoglycan deacetylase Bd3279==
-	<StructureSection load='5jp6' size='340' side='right' caption='[[5jp6]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='5jp6' size='340' side='right'caption='[[5jp6]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5jp6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bdeba Bdeba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JP6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JP6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5jp6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bdeba Bdeba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JP6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JP6 FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Bdeba]]		[[Category: Bdeba]]
		+	[[Category: Large Structures]]
	[[Category: Lovering, A L]]		[[Category: Lovering, A L]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Peptidoglycan deacetylase ce-4 carbohydrate esterase 4]]		[[Category: Peptidoglycan deacetylase ce-4 carbohydrate esterase 4]]

OCA at 07:13, 21 February 2019

2019-02-21T07:13:30Z

←Older revision		Revision as of 07:13, 21 February 2019
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	<StructureSection load='5jp6' size='340' side='right' caption='[[5jp6]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='5jp6' size='340' side='right' caption='[[5jp6]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jp6]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JP6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JP6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jp6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bdeba Bdeba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JP6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JP6 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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PXU:2-HYDROXY-L-PROLINE'>PXU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PXU:2-HYDROXY-L-PROLINE'>PXU</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=5jp6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jp6 OCA], [http://pdbe.org/5jp6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jp6 RCSB], [http://www.ebi.ac.uk/pdbsum/5jp6 PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Bd3279 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=264462 BDEBA])</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=5jp6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jp6 OCA], [http://pdbe.org/5jp6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jp6 RCSB], [http://www.ebi.ac.uk/pdbsum/5jp6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jp6 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bdeba]]
	[[Category: Lovering, A L]]		[[Category: Lovering, A L]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Peptidoglycan deacetylase ce-4 carbohydrate esterase 4]]		[[Category: Peptidoglycan deacetylase ce-4 carbohydrate esterase 4]]

OCA at 15:38, 1 June 2016

2016-06-01T15:38:04Z

←Older revision		Revision as of 15:38, 1 June 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5jp6 is ~~ON HOLD~~	+	==Bdellovibrio bacteriovorus peptidoglycan deacetylase Bd3279==
		+	<StructureSection load='5jp6' size='340' side='right' caption='[[5jp6]], [[Resolution\|resolution]] 1.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5jp6]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JP6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JP6 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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PXU:2-HYDROXY-L-PROLINE'>PXU</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=5jp6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jp6 OCA], [http://pdbe.org/5jp6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jp6 RCSB], [http://www.ebi.ac.uk/pdbsum/5jp6 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The peptidoglycan wall, located in the periplasm between the inner and outer membranes of the cell envelope in Gram-negative bacteria, maintains cell shape and endows osmotic robustness. Predatory Bdellovibrio bacteria invade the periplasm of other bacterial prey cells, usually crossing the peptidoglycan layer, forming transient structures called bdelloplasts within which the predators replicate. Prey peptidoglycan remains intact for several hours, but is modified and then degraded by escaping predators. Here we show predation is altered by deleting two Bdellovibrio N-acetylglucosamine (GlcNAc) deacetylases, one of which we show to have a unique two domain structure with a novel regulatory"plug". Deleting the deacetylases limits peptidoglycan degradation and rounded prey cell "ghosts" persist after mutant-predator exit. Mutant predators can replicate unusually in the periplasmic region between the peptidoglycan wall and the outer membrane rather than between wall and inner-membrane, yet still obtain nutrients from the prey cytoplasm. Deleting two further genes encoding DacB/PBP4 family proteins, known to decrosslink and round prey peptidoglycan, results in a quadruple mutant Bdellovibrio which leaves prey-shaped ghosts upon predation. The resultant bacterial ghosts contain cytoplasmic membrane within bacteria-shaped peptidoglycan surrounded by outer membrane material which could have promise as "bacterial skeletons" for housing artificial chromosomes.

-	~~Authors: Lovering~~, A.L.	+	Interrupting peptidoglycan deacetylation during Bdellovibrio predator-prey interaction prevents ultimate destruction of prey wall, liberating bacterial-ghosts.,Lambert C, Lerner TR, Bui NK, Somers H, Aizawa S, Liddell S, Clark A, Vollmer W, Lovering AL, Sockett RE Sci Rep. 2016 May 23;6:26010. doi: 10.1038/srep26010. PMID:27211869<ref>PMID:27211869</ref>

-	~~Description~~: ~~Bdellovibrio bacteriovorus peptidoglycan deacetylase Bd3279~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Lovering, A.L~~]]	+	<div class="pdbe-citations 5jp6" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Lovering, A L]]
		+	[[Category: Hydrolase]]
		+	[[Category: Peptidoglycan deacetylase ce-4 carbohydrate esterase 4]]

OCA: Protected "5jp6" [edit=sysop:move=sysop]

2016-05-15T15:41:48Z

Protected "5jp6" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:41, 15 May 2016

OCA: New page: '''Unreleased structure''' The entry 5jp6 is ON HOLD Authors: Lovering, A.L. Description: Bdellovibrio bacteriovorus peptidoglycan deacetylase Bd3279 [[Category: Unreleased Structures]...

2016-05-15T15:41:47Z

New page: '''Unreleased structure''' The entry 5jp6 is ON HOLD Authors: Lovering, A.L. Description: Bdellovibrio bacteriovorus peptidoglycan deacetylase Bd3279 [[Category: Unreleased Structures]...

New page

'''Unreleased structure'''

The entry 5jp6 is ON HOLD

Authors: Lovering, A.L.

Description: Bdellovibrio bacteriovorus peptidoglycan deacetylase Bd3279
[[Category: Unreleased Structures]]
[[Category: Lovering, A.L]]