7nsy - Revision history

OCA at 12:39, 1 February 2024

OCA — Thu, 01 Feb 2024 12:39:15 GMT

←Older revision		Revision as of 12:39, 1 February 2024
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	<StructureSection load='7nsy' size='340' side='right'caption='[[7nsy]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='7nsy' size='340' side='right'caption='[[7nsy]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7nsy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Drome Drome~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NSY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NSY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7nsy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NSY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NSY FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>PGRP-LB, CG14704 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=7227 DROME])</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]] 1.4Å</td></tr>
-	~~<tr id='activity'><td class~~="~~sblockLbl~~">~~<b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/N~~-~~acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase]~~, ~~with EC number~~ [~~https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.~~1.~~28 3.5.1.28] </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=7nsy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nsy OCA], [https://pdbe.org/7nsy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nsy RCSB], [https://www.ebi.ac.uk/pdbsum/7nsy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nsy 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=7nsy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nsy OCA], [https://pdbe.org/7nsy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nsy RCSB], [https://www.ebi.ac.uk/pdbsum/7nsy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nsy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PGPLB_DROME PGPLB_DROME]] N-acetylmuramyl-L-alanine amidase involved in innate immunity by degrading bacterial peptidoglycans (PGN). Probably plays a scavenger role by digesting biologically active PGN into biologically inactive fragments. Has no direct bacteriolytic activity.<ref>PMID:12845326</ref>	+	[https://www.uniprot.org/uniprot/PGPLB_DROME PGPLB_DROME] N-acetylmuramyl-L-alanine amidase involved in innate immunity by degrading bacterial peptidoglycans (PGN). Probably plays a scavenger role by digesting biologically active PGN into biologically inactive fragments. Has no direct bacteriolytic activity.<ref>PMID:12845326</ref>
	<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: ~~Drome~~]]	+	[[Category: Drosophila melanogaster]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: N-acetylmuramoyl-L-alanine amidase]]~~	+	[[Category: Aller P]]
-	[[Category: Aller, P]]	+	[[Category: Da Silva P]]
-	[[Category: ~~Orlans, J]]~~	+	[[Category: Orlans J]]
-	~~[[Category:~~ Silva, P Da]]	+
-	[[Category: ~~Drosophila]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Peptidoglycan recognition protein]]~~	+
-	~~[[Category: Pgrp]]~~	+
-	~~[[Category: Pgrp-lb~~]]	+

OCA at 15:02, 17 June 2021

OCA — Thu, 17 Jun 2021 15:02:24 GMT

←Older revision		Revision as of 15:02, 17 June 2021
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	==Drosophila PGRP-LB C160S mutant==		==Drosophila PGRP-LB C160S mutant==
-	<StructureSection load='7nsy' size='340' side='right'caption='[[7nsy]]' scene=''>	+	<StructureSection load='7nsy' size='340' side='right'caption='[[7nsy]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NSY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NSY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7nsy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NSY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NSY FirstGlance]. <br>
-	</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=7nsy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nsy OCA], [https://pdbe.org/7nsy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nsy RCSB], [https://www.ebi.ac.uk/pdbsum/7nsy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nsy ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PGRP-LB, CG14704 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] </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=7nsy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nsy OCA], [https://pdbe.org/7nsy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nsy RCSB], [https://www.ebi.ac.uk/pdbsum/7nsy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nsy ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/PGPLB_DROME PGPLB_DROME]] N-acetylmuramyl-L-alanine amidase involved in innate immunity by degrading bacterial peptidoglycans (PGN). Probably plays a scavenger role by digesting biologically active PGN into biologically inactive fragments. Has no direct bacteriolytic activity.<ref>PMID:12845326</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Peptidoglycan recognition proteins (PGRPs) are ubiquitous among animals and play pivotal functions in insect immunity. Non-catalytic PGRPs are involved in the activation of immune pathways by binding to the peptidoglycan (PGN), whereas amidase PGRPs are capable of cleaving the PGN into non-immunogenic compounds. Drosophila PGRP-LB belongs to the amidase PGRPs and downregulates the immune deficiency (IMD) pathway by cleaving meso-2,6-diaminopimelic (meso-DAP or DAP)-type PGN. While the recognition process is well analyzed for the non-catalytic PGRPs, little is known about the enzymatic mechanism for the amidase PGRPs, despite their essential function in immune homeostasis. Here, we analyzed the specific activity of different isoforms of Drosophila PGRP-LB towards various PGN substrates to understand their specificity and role in Drosophila immunity. We show that these isoforms have similar activity towards the different compounds. To analyze the mechanism of the amidase activity, we performed site directed mutagenesis and solved the X-ray structures of wild-type Drosophila PGRP-LB and its mutants, with one of these structures presenting a protein complexed with the tracheal cytotoxin (TCT), a muropeptide derived from the PGN. Only the Y78F mutation abolished the PGN cleavage while other mutations reduced the activity solely. Together, our findings suggest the dynamic role of the residue Y78 in the amidase mechanism by nucleophilic attack through a water molecule to the carbonyl group of the amide function destabilized by Zn(2+).
		+
		+	PGRP-LB: An Inside View into the Mechanism of the Amidase Reaction.,Orlans J, Vincent-Monegat C, Rahioui I, Sivignon C, Butryn A, Soulere L, Zaidman-Remy A, Orville AM, Heddi A, Aller P, Da Silva P Int J Mol Sci. 2021 May 7;22(9). pii: ijms22094957. doi: 10.3390/ijms22094957. PMID:34066955<ref>PMID:34066955</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7nsy" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Drome]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Aller P]]	+	[[Category: N-acetylmuramoyl-L-alanine amidase]]
-	[[Category: Da Silva P]]	+	[[Category: Aller, P]]
-	[[Category: ~~Orlans J~~]]	+	[[Category: Orlans, J]]
		+	[[Category: Silva, P Da]]
		+	[[Category: Drosophila]]
		+	[[Category: Immune system]]
		+	[[Category: Peptidoglycan recognition protein]]
		+	[[Category: Pgrp]]
		+	[[Category: Pgrp-lb]]

OCA at 10:11, 19 May 2021

OCA — Wed, 19 May 2021 10:11:27 GMT

←Older revision		Revision as of 10:11, 19 May 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7nsy is ~~ON HOLD until Paper Publication~~	+	==Drosophila PGRP-LB C160S mutant==
-		+	<StructureSection load='7nsy' size='340' side='right'caption='[[7nsy]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NSY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NSY FirstGlance]. <br>
-	~~Description~~:	+	</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=7nsy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nsy OCA], [https://pdbe.org/7nsy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nsy RCSB], [https://www.ebi.ac.uk/pdbsum/7nsy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nsy ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Aller P]]
		+	[[Category: Da Silva P]]
		+	[[Category: Orlans J]]

OCA at 09:30, 31 March 2021

OCA — Wed, 31 Mar 2021 09:30:56 GMT

←Older revision		Revision as of 09:30, 31 March 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7nsy is ON HOLD	+	The entry 7nsy is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7nsy" [edit=sysop:move=sysop]

OCA — Wed, 17 Mar 2021 05:35:11 GMT

Protected "7nsy" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:35, 17 March 2021

OCA: New page: '''Unreleased structure''' The entry 7nsy is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 17 Mar 2021 05:35:10 GMT

New page: '''Unreleased structure''' The entry 7nsy is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7nsy is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]