5ced - Revision history

OCA at 11:20, 10 January 2024

OCA — Wed, 10 Jan 2024 11:20:03 GMT

←Older revision		Revision as of 11:20, 10 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ced]] is a 2 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=5CED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CED FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ced]] is a 2 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=5CED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CED FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PNM:OPEN+FORM+-+PENICILLIN+G'>PNM</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]] 2.02Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PNM:OPEN+FORM+-+PENICILLIN+G'>PNM</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=5ced FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ced OCA], [https://pdbe.org/5ced PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ced RCSB], [https://www.ebi.ac.uk/pdbsum/5ced PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ced 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=5ced FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ced OCA], [https://pdbe.org/5ced PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ced RCSB], [https://www.ebi.ac.uk/pdbsum/5ced PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ced ProSAT]</span></td></tr>
	</table>		</table>

OCA at 12:01, 14 June 2023

OCA — Wed, 14 Jun 2023 12:01:22 GMT

←Older revision		Revision as of 12:01, 14 June 2023
Line 3:		Line 3:
	<StructureSection load='5ced' size='340' side='right'caption='[[5ced]], [[Resolution\|resolution]] 2.02Å' scene=''>		<StructureSection load='5ced' size='340' side='right'caption='[[5ced]], [[Resolution\|resolution]] 2.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ced]] is a 2 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=5CED OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5CED FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ced]] is a 2 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=5CED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CED FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PNM:OPEN+FORM+-+PENICILLIN+G'>PNM</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PNM:OPEN+FORM+-+PENICILLIN+G'>PNM</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Bd3459 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=264462 BDEBA]), Bd3460 ([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=5ced FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ced OCA], [https://pdbe.org/5ced PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ced RCSB], [https://www.ebi.ac.uk/pdbsum/5ced PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ced ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=5ced FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ced OCA], [~~http~~://pdbe.org/5ced PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ced RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ced PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ced ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q6MHT0_BDEBA Q6MHT0_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: Serine-type D-Ala-D-Ala carboxypeptidase]]~~	+	[[Category: Cadby IT]]
-	[[Category: Cadby~~, I T~~]]	+	[[Category: Lambert C]]
-	[[Category: Lambert, C]]	+	[[Category: Lovering AL]]
-	[[Category: Lovering~~, A L~~]]	+	[[Category: Sockett RE]]
-	[[Category: Sockett~~, R E]]~~	+
-	~~[[Category: Hydrolae]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Transpeptidase and ankyrin repeat~~]]	+

OCA at 11:35, 27 March 2020

OCA — Fri, 27 Mar 2020 11:35:00 GMT

←Older revision		Revision as of 11:35, 27 March 2020
Line 1:		Line 1:
		+
	==Penicillin G Acylated Bd3459 Predatory Endopeptidase from Bdellovibrio bacteriovorus in complex with immunity protein Bd3460==		==Penicillin G Acylated Bd3459 Predatory Endopeptidase from Bdellovibrio bacteriovorus in complex with immunity protein Bd3460==
-	<StructureSection load='5ced' size='340' side='right' caption='[[5ced]], [[Resolution\|resolution]] 2.02Å' scene=''>	+	<StructureSection load='5ced' size='340' side='right'caption='[[5ced]], [[Resolution\|resolution]] 2.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ced]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CED OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CED FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ced]] is a 2 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=5CED OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CED FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PNM:OPEN+FORM+-+PENICILLIN+G'>PNM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PNM:OPEN+FORM+-+PENICILLIN+G'>PNM</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Bd3459 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=264462 BDEBA]), Bd3460 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=264462 BDEBA])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=5ced FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ced OCA], [http://pdbe.org/5ced PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ced RCSB], [http://www.ebi.ac.uk/pdbsum/5ced 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=5ced FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ced OCA], [http://pdbe.org/5ced PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ced RCSB], [http://www.ebi.ac.uk/pdbsum/5ced PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ced ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bdeba]]
		+	[[Category: Large Structures]]
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
	[[Category: Cadby, I T]]		[[Category: Cadby, I T]]

OCA at 07:46, 16 December 2015

OCA — Wed, 16 Dec 2015 07:46:50 GMT

←Older revision		Revision as of 07:46, 16 December 2015
Line 7:		Line 7:
	<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=5ced FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ced OCA], [http://pdbe.org/5ced PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ced RCSB], [http://www.ebi.ac.uk/pdbsum/5ced 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=5ced FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ced OCA], [http://pdbe.org/5ced PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ced RCSB], [http://www.ebi.ac.uk/pdbsum/5ced PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Predatory Bdellovibrio bacteriovorus are natural antimicrobial organisms, killing other bacteria by whole-cell invasion. Self-protection against prey-metabolizing enzymes is important for the evolution of predation. Initial prey entry involves the predator's peptidoglycan DD-endopeptidases, which decrosslink cell walls and prevent wasteful entry by a second predator. Here we identify and characterize a self-protection protein from B. bacteriovorus, Bd3460, which displays an ankyrin-based fold common to intracellular pathogens of eukaryotes. Co-crystal structures reveal Bd3460 complexation of dual targets, binding a conserved epitope of each of the Bd3459 and Bd0816 endopeptidases. Complexation inhibits endopeptidase activity and cell wall decrosslinking in vitro. Self-protection is vital - DeltaBd3460 Bdellovibrio deleteriously decrosslink self-peptidoglycan upon invasion, adopt a round morphology, and lose predatory capacity and cellular integrity. Our analysis provides the first mechanistic examination of self-protection in Bdellovibrio, documents protection-multiplicity for products of two different genomic loci, and reveals an important evolutionary adaptation to an invasive predatory bacterial lifestyle.
		+
		+	Ankyrin-mediated self-protection during cell invasion by the bacterial predator Bdellovibrio bacteriovorus.,Lambert C, Cadby IT, Till R, Bui NK, Lerner TR, Hughes WS, Lee DJ, Alderwick LJ, Vollmer W, Sockett ER, Lovering AL Nat Commun. 2015 Dec 2;6:8884. doi: 10.1038/ncomms9884. PMID:26626559<ref>PMID:26626559</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ced" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 13:48, 9 December 2015

OCA — Wed, 09 Dec 2015 13:48:44 GMT

←Older revision		Revision as of 13:48, 9 December 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Penicillin G Acylated Bd3459 Predatory Endopeptidase from Bdellovibrio bacteriovorus in complex with immunity protein Bd3460==
-		+	<StructureSection load='5ced' size='340' side='right' caption='[[5ced]], [[Resolution\|resolution]] 2.02Å' scene=''>
-	~~The entry~~ 5ced is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ced]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CED OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CED FirstGlance]. <br>
-	~~Authors~~: ~~Lovering~~, A.L., ~~Cadby, I~~.T., ~~Lambert~~, C., ~~Sockett, R~~.E.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PNM:OPEN+FORM+-+PENICILLIN+G'>PNM</scene></td></tr>
-		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>
-	~~Description~~: ~~Penicillin G Acylated Bd3459 Predatory Endopeptidase from Bdellovibrio bacteriovorus in complex with immunity protein Bd3460~~	+	<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=5ced FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ced OCA], [http://pdbe.org/5ced PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ced RCSB], [http://www.ebi.ac.uk/pdbsum/5ced PDBsum]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
		+	[[Category: Cadby, I T]]
	[[Category: Lambert, C]]		[[Category: Lambert, C]]
-	[[Category: ~~Cadby~~, ~~I.T~~]]	+	[[Category: Lovering, A L]]
-	[[Category: ~~Lovering~~, ~~A.L~~]]	+	[[Category: Sockett, R E]]
-	[[Category: ~~Sockett, R.E~~]]	+	[[Category: Hydrolae]]
		+	[[Category: Hydrolase]]
		+	[[Category: Protein binding]]
		+	[[Category: Transpeptidase and ankyrin repeat]]

OCA at 13:20, 29 July 2015

OCA — Wed, 29 Jul 2015 13:20:02 GMT

←Older revision		Revision as of 13:20, 29 July 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ced is ON HOLD	+	The entry 5ced is ON HOLD until Paper Publication

	Authors: Lovering, A.L., Cadby, I.T., Lambert, C., Sockett, R.E.		Authors: Lovering, A.L., Cadby, I.T., Lambert, C., Sockett, R.E.

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

OCA — Wed, 15 Jul 2015 12:27:47 GMT

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

←Older revision

Revision as of 12:27, 15 July 2015

OCA: New page: '''Unreleased structure''' The entry 5ced is ON HOLD Authors: Lovering, A.L., Cadby, I.T., Lambert, C., Sockett, R.E. Description: Penicillin G Acylated Bd3459 Predatory Endopeptidase ...

OCA — Wed, 15 Jul 2015 12:27:45 GMT

New page: '''Unreleased structure''' The entry 5ced is ON HOLD Authors: Lovering, A.L., Cadby, I.T., Lambert, C., Sockett, R.E. Description: Penicillin G Acylated Bd3459 Predatory Endopeptidase ...

New page

'''Unreleased structure'''

The entry 5ced is ON HOLD

Authors: Lovering, A.L., Cadby, I.T., Lambert, C., Sockett, R.E.

Description: Penicillin G Acylated Bd3459 Predatory Endopeptidase from Bdellovibrio bacteriovorus in complex with immunity protein Bd3460
[[Category: Unreleased Structures]]
[[Category: Lambert, C]]
[[Category: Cadby, I.T]]
[[Category: Lovering, A.L]]
[[Category: Sockett, R.E]]