5utr - Revision history

OCA at 13:34, 4 October 2023

OCA — Wed, 04 Oct 2023 13:34:12 GMT

←Older revision		Revision as of 13:34, 4 October 2023
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	==Crystal structure of Burkholderia cenocepacia family 3 glycoside hydrolase (NagZ) bound to (3S,4R,5R,6S)-3-butyryl-4,5,6-trihydroxyazepane==		==Crystal structure of Burkholderia cenocepacia family 3 glycoside hydrolase (NagZ) bound to (3S,4R,5R,6S)-3-butyryl-4,5,6-trihydroxyazepane==
-	<StructureSection load='5utr' size='340' side='right' caption='[[5utr]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='5utr' size='340' side='right'caption='[[5utr]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5utr]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_baa-245 Atcc baa-245~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UTR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5UTR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5utr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_cenocepacia Burkholderia cenocepacia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UTR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UTR FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=8MP:N-[(3S,4R,5R,6S)-4,5,6-TRIHYDROXYAZEPAN-3-YL]BUTANAMIDE'>8MP</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]] 2.15Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mss\|4mss]]~~, [[~~4gnv~~\|~~4gnv]], [[4g6c\|4g6c~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8MP:N-[(3S,4R,5R,6S)-4,5,6-TRIHYDROXYAZEPAN-3-YL]BUTANAMIDE'>8MP</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>nagZ, A3203_21235, WL84_04775 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=95486 ATCC BAA-245])</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=5utr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5utr OCA], [https://pdbe.org/5utr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5utr RCSB], [https://www.ebi.ac.uk/pdbsum/5utr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5utr 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/Beta-~~N-~~acetylhexosaminidase Beta~~-~~N-acetylhexosaminidase]~~, ~~with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=~~3~~.2.1.52 3.2.1.52~~] </~~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=5utr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5utr OCA], [~~http~~://pdbe.org/5utr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5utr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5utr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5utr ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/A0A125HFC0_9BURK A0A125HFC0_9BURK]] Plays a role in peptidoglycan recycling by cleaving the terminal beta-1,4-linked N-acetylglucosamine (GlcNAc) from peptide-linked peptidoglycan fragments, giving rise to free GlcNAc, anhydro-N-acetylmuramic acid and anhydro-N-acetylmuramic acid-linked peptides.[HAMAP-Rule:MF_00364][SAAS:SAAS00634279]	+	[https://www.uniprot.org/uniprot/B4EA43_BURCJ B4EA43_BURCJ]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5utr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5utr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-Hexosaminidase\|Beta-Hexosaminidase]]
		+	*[[Beta-Hexosaminidase 3D structures\|Beta-Hexosaminidase 3D structures]]
		+	*[[Beta-N-acetylhexosaminidase 3D structures\|Beta-N-acetylhexosaminidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc baa-245~~]]	+	[[Category: Burkholderia cenocepacia]]
-	[[Category: ~~Beta-N-acetylhexosaminidase~~]]	+	[[Category: Large Structures]]
-	[[Category: Mark~~, B L~~]]	+	[[Category: Mark BL]]
-	[[Category: Vadlamani, G]]	+	[[Category: Vadlamani G]]
-	~~[[Category: Family 3]]~~	+
-	~~[[Category: Glycoside hydrolase]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex]]~~	+
-	~~[[Category: Nagz~~]]	+

OCA at 08:14, 17 January 2018

OCA — Wed, 17 Jan 2018 08:14:44 GMT

←Older revision		Revision as of 08:14, 17 January 2018
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	<StructureSection load='5utr' size='340' side='right' caption='[[5utr]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='5utr' size='340' side='right' caption='[[5utr]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5utr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UTR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5utr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_baa-245 Atcc baa-245]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UTR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8MP:N-[(3S,4R,5R,6S)-4,5,6-TRIHYDROXYAZEPAN-3-YL]BUTANAMIDE'>8MP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8MP:N-[(3S,4R,5R,6S)-4,5,6-TRIHYDROXYAZEPAN-3-YL]BUTANAMIDE'>8MP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mss\|4mss]], [[4gnv\|4gnv]], [[4g6c\|4g6c]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mss\|4mss]], [[4gnv\|4gnv]], [[4g6c\|4g6c]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nagZ, A3203_21235, WL84_04775 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=95486 ATCC BAA-245])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-N-acetylhexosaminidase Beta-N-acetylhexosaminidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.52 3.2.1.52] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-N-acetylhexosaminidase Beta-N-acetylhexosaminidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.52 3.2.1.52] </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=5utr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5utr OCA], [http://pdbe.org/5utr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5utr RCSB], [http://www.ebi.ac.uk/pdbsum/5utr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5utr 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=5utr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5utr OCA], [http://pdbe.org/5utr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5utr RCSB], [http://www.ebi.ac.uk/pdbsum/5utr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5utr ProSAT]</span></td></tr>
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc baa-245]]
	[[Category: Beta-N-acetylhexosaminidase]]		[[Category: Beta-N-acetylhexosaminidase]]
	[[Category: Mark, B L]]		[[Category: Mark, B L]]

OCA at 13:04, 19 April 2017

OCA — Wed, 19 Apr 2017 13:04:35 GMT

←Older revision		Revision as of 13:04, 19 April 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5utr is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Burkholderia cenocepacia family 3 glycoside hydrolase (NagZ) bound to (3S,4R,5R,6S)-3-butyryl-4,5,6-trihydroxyazepane==
		+	<StructureSection load='5utr' size='340' side='right' caption='[[5utr]], [[Resolution\|resolution]] 2.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5utr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UTR FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8MP:N-[(3S,4R,5R,6S)-4,5,6-TRIHYDROXYAZEPAN-3-YL]BUTANAMIDE'>8MP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mss\|4mss]], [[4gnv\|4gnv]], [[4g6c\|4g6c]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-N-acetylhexosaminidase Beta-N-acetylhexosaminidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.52 3.2.1.52] </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=5utr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5utr OCA], [http://pdbe.org/5utr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5utr RCSB], [http://www.ebi.ac.uk/pdbsum/5utr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5utr ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0A125HFC0_9BURK A0A125HFC0_9BURK]] Plays a role in peptidoglycan recycling by cleaving the terminal beta-1,4-linked N-acetylglucosamine (GlcNAc) from peptide-linked peptidoglycan fragments, giving rise to free GlcNAc, anhydro-N-acetylmuramic acid and anhydro-N-acetylmuramic acid-linked peptides.[HAMAP-Rule:MF_00364][SAAS:SAAS00634279]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	NagZ is an N-acetyl-beta-d-glucosaminidase that participates in the peptidoglycan (PG) recycling pathway of Gram-negative bacteria by removing N-acetyl-glucosamine (GlcNAc) from PG fragments that have been excised from the cell wall during growth. The 1,6-anhydromuramoyl-peptide products generated by NagZ activate beta-lactam resistance in many Gram-negative bacteria by inducing the expression of AmpC beta-lactamase. Blocking NagZ activity can thereby suppress beta-lactam antibiotic resistance in these bacteria. The NagZ active site is dynamic and it accommodates distortion of the glycan substrate during catalysis using a mobile catalytic loop that carries a histidine residue which serves as the active site general acid/base catalyst. Here, we show that flexibility of this catalytic loop also accommodates structural differences in small molecule inhibitors of NagZ, which could be exploited to improve inhibitor specificity. X-ray structures of NagZ bound to the potent yet non-selective N-acetyl-beta-glucosaminidase inhibitor PUGNAc (O-(2-acetamido-2-deoxy-d-glucopyranosylidene) amino-N-phenylcarbamate), and two NagZ-selective inhibitors - EtBuPUG, a PUGNAc derivative bearing a 2-N-ethylbutyryl group, and MM-156, a 3-N-butyryl trihydroxyazepane, revealed that the phenylcarbamate moiety of PUGNAc and EtBuPUG completely displaces the catalytic loop from the NagZ active site to yield a catalytically incompetent form of the enzyme. In contrast, the catalytic loop was found positioned in the catalytically active conformation within the NagZ active site when bound to MM-156, which lacks the phenylcarbamate extension. Displacement of the catalytic loop by PUGNAc and its N-acyl derivative EtBuPUG alters the active site conformation of NagZ, which presents an additional strategy to improve the potency and specificity of NagZ inhibitors.

-	~~Authors~~:	+	Conformational flexibility of the glycosidase NagZ allows it to bind structurally diverse inhibitors to suppress beta-lactam antibiotic resistance.,Vadlamani G, Stubbs KA, Desire J, Bleriot Y, Vocadlo DJ, Mark BL Protein Sci. 2017 Mar 28. doi: 10.1002/pro.3166. PMID:28370529<ref>PMID:28370529</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5utr" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-N-acetylhexosaminidase]]
		+	[[Category: Mark, B L]]
		+	[[Category: Vadlamani, G]]
		+	[[Category: Family 3]]
		+	[[Category: Glycoside hydrolase]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]
		+	[[Category: Nagz]]

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

OCA — Thu, 09 Mar 2017 14:55:29 GMT

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

←Older revision

Revision as of 14:55, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5utr is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Thu, 09 Mar 2017 14:55:28 GMT

New page: '''Unreleased structure''' The entry 5utr is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5utr is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]