3gsm - Revision history

OCA at 07:11, 6 September 2023

OCA — Wed, 06 Sep 2023 07:11:48 GMT

←Older revision		Revision as of 07:11, 6 September 2023
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	<StructureSection load='3gsm' size='340' side='right'caption='[[3gsm]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3gsm' size='340' side='right'caption='[[3gsm]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gsm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillo_virgola_del_koch"_trevisan_1884 "bacillo virgola del koch" trevisan 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GSM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GSM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gsm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GSM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GSM FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=VPU:[[(3R,4R,5S,6R)~~-4,~~5-DIHYDROXY-6-(HYDROXYMETHYL)-3-(PENTANOYLAMINO)OXAN-2-YLIDENE]AMINO]+N-PHENYLCARBAMATE'>VPU</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]] 2.4Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[2oxn\|2oxn]], [[3gs6\|3gs6]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=VPU:[[(3R,4R,5S,6R)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)-3-(PENTANOYLAMINO)OXAN-2-YLIDENE]AMINO]+N-PHENYLCARBAMATE'>VPU</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>family 3 glycoside hydrolase NagZ, nagZ, VC_0692 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~666~~ "~~Bacillo virgola del Koch~~" ~~Trevisan 1884])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>~~[~~https://en.wikipedia.org/wiki/Beta~~-N-~~acetylhexosaminidase Beta~~-N-~~acetylhexosaminidase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=3gsm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gsm OCA], [https://pdbe.org/3gsm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gsm RCSB], [https://www.ebi.ac.uk/pdbsum/3gsm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gsm 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=3gsm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gsm OCA], [https://pdbe.org/3gsm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gsm RCSB], [https://www.ebi.ac.uk/pdbsum/3gsm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gsm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NAGZ_VIBCH NAGZ_VIBCH]] 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. Plays a role in beta-lactam antibiotic resistance via its role in generating anhydro-N-acetylmuramic acid-linked peptides; these peptides function as signaling molecules that induce high-level expression of the beta-lactamase AmpC.<ref>PMID:24009110</ref> <ref>PMID:17439950</ref> <ref>PMID:19499593</ref>	+	[https://www.uniprot.org/uniprot/NAGZ_VIBCH NAGZ_VIBCH] 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. Plays a role in beta-lactam antibiotic resistance via its role in generating anhydro-N-acetylmuramic acid-linked peptides; these peptides function as signaling molecules that induce high-level expression of the beta-lactamase AmpC.<ref>PMID:24009110</ref> <ref>PMID:17439950</ref> <ref>PMID:19499593</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillo virgola del koch trevisan 1884]]
-	[[Category: Beta-N-acetylhexosaminidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Balcewich, M D~~]]	+	[[Category: Vibrio cholerae]]
-	[[Category: ~~Mark, B L~~]]	+	[[Category: Balcewich MD]]
-	[[Category: ~~Cell cycle]]~~	+	[[Category: Mark BL]]
-	~~[[Category: Cell division]]~~	+
-	~~[[Category: Cell shape]]~~	+
-	~~[[Category: Cell wall biogenesis/degradation]]~~	+
-	~~[[Category: Glycosidase]]~~	+
-	~~[[Category: Glycoside hydrolase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Peptidoglycan synthesis~~]]	+

OCA at 20:10, 20 October 2021

OCA — Wed, 20 Oct 2021 20:10:08 GMT

←Older revision		Revision as of 20:10, 20 October 2021
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	==Vibrio cholerae family 3 glycoside hydrolase (NagZ) bound to N-Valeryl-PUGNAc==		==Vibrio cholerae family 3 glycoside hydrolase (NagZ) bound to N-Valeryl-PUGNAc==
-	<StructureSection load='3gsm' size='340' side='right' caption='[[3gsm]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='3gsm' size='340' side='right'caption='[[3gsm]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gsm]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillo_virgola_del_koch"_trevisan_1884 "bacillo virgola del koch" trevisan 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GSM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3GSM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gsm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillo_virgola_del_koch"_trevisan_1884 "bacillo virgola del koch" trevisan 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GSM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GSM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=VPU:[[(3R,4R,5S,6R)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)-3-(PENTANOYLAMINO)OXAN-2-YLIDENE]AMINO]+N-PHENYLCARBAMATE'>VPU</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=VPU:[[(3R,4R,5S,6R)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)-3-(PENTANOYLAMINO)OXAN-2-YLIDENE]AMINO]+N-PHENYLCARBAMATE'>VPU</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2oxn\|2oxn]], [[3gs6\|3gs6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2oxn\|2oxn]], [[3gs6\|3gs6]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">family 3 glycoside hydrolase NagZ, nagZ, VC_0692 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=666 "Bacillo virgola del Koch" Trevisan 1884])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">family 3 glycoside hydrolase NagZ, nagZ, VC_0692 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=666 "Bacillo virgola del Koch" Trevisan 1884])</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'>[https://en.wikipedia.org/wiki/Beta-N-acetylhexosaminidase Beta-N-acetylhexosaminidase], with EC number [https://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=3gsm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gsm OCA], [~~http~~://pdbe.org/3gsm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3gsm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3gsm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3gsm 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=3gsm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gsm OCA], [https://pdbe.org/3gsm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gsm RCSB], [https://www.ebi.ac.uk/pdbsum/3gsm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gsm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/NAGZ_VIBCH NAGZ_VIBCH]] 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. Plays a role in beta-lactam antibiotic resistance via its role in generating anhydro-N-acetylmuramic acid-linked peptides; these peptides function as signaling molecules that induce high-level expression of the beta-lactamase AmpC.<ref>PMID:24009110</ref> <ref>PMID:17439950</ref> <ref>PMID:19499593</ref>	+	[[https://www.uniprot.org/uniprot/NAGZ_VIBCH NAGZ_VIBCH]] 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. Plays a role in beta-lactam antibiotic resistance via its role in generating anhydro-N-acetylmuramic acid-linked peptides; these peptides function as signaling molecules that induce high-level expression of the beta-lactamase AmpC.<ref>PMID:24009110</ref> <ref>PMID:17439950</ref> <ref>PMID:19499593</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	==See Also==		==See Also==
	*[[Beta-Hexosaminidase\|Beta-Hexosaminidase]]		*[[Beta-Hexosaminidase\|Beta-Hexosaminidase]]
		+	*[[Beta-Hexosaminidase 3D structures\|Beta-Hexosaminidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 40:		Line 41:
	[[Category: Bacillo virgola del koch trevisan 1884]]		[[Category: Bacillo virgola del koch trevisan 1884]]
	[[Category: Beta-N-acetylhexosaminidase]]		[[Category: Beta-N-acetylhexosaminidase]]
		+	[[Category: Large Structures]]
	[[Category: Balcewich, M D]]		[[Category: Balcewich, M D]]
	[[Category: Mark, B L]]		[[Category: Mark, B L]]

OCA at 06:07, 7 December 2018

OCA — Fri, 07 Dec 2018 06:07:41 GMT

←Older revision		Revision as of 06:07, 7 December 2018
Line 1:		Line 1:
		+
	==Vibrio cholerae family 3 glycoside hydrolase (NagZ) bound to N-Valeryl-PUGNAc==		==Vibrio cholerae family 3 glycoside hydrolase (NagZ) bound to N-Valeryl-PUGNAc==
	<StructureSection load='3gsm' size='340' side='right' caption='[[3gsm]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3gsm' size='340' side='right' caption='[[3gsm]], [[Resolution\|resolution]] 2.40Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">family 3 glycoside hydrolase NagZ, nagZ, VC_0692 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=666 "Bacillo virgola del Koch" Trevisan 1884])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">family 3 glycoside hydrolase NagZ, nagZ, VC_0692 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=666 "Bacillo virgola del Koch" Trevisan 1884])</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=3gsm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gsm OCA], [http://pdbe.org/3gsm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gsm RCSB], [http://www.ebi.ac.uk/pdbsum/3gsm 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=3gsm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gsm OCA], [http://pdbe.org/3gsm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gsm RCSB], [http://www.ebi.ac.uk/pdbsum/3gsm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3gsm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gs/3gsm_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gs/3gsm_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 21:27, 9 February 2016

OCA — Tue, 09 Feb 2016 21:27:04 GMT

←Older revision		Revision as of 21:27, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3gsm' size='340' side='right' caption='[[3gsm]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3gsm' size='340' side='right' caption='[[3gsm]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gsm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Vibrio_cholerae Vibrio cholerae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GSM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GSM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gsm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillo_virgola_del_koch"_trevisan_1884 "bacillo virgola del koch" trevisan 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GSM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GSM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=VPU:[[(3R,4R,5S,6R)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)-3-(PENTANOYLAMINO)OXAN-2-YLIDENE]AMINO]+N-PHENYLCARBAMATE'>VPU</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=VPU:[[(3R,4R,5S,6R)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)-3-(PENTANOYLAMINO)OXAN-2-YLIDENE]AMINO]+N-PHENYLCARBAMATE'>VPU</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2oxn\|2oxn]], [[3gs6\|3gs6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2oxn\|2oxn]], [[3gs6\|3gs6]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">family 3 glycoside hydrolase NagZ, nagZ, VC_0692 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=666 ~~Vibrio cholerae~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">family 3 glycoside hydrolase NagZ, nagZ, VC_0692 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=666 "Bacillo virgola del Koch" Trevisan 1884])</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=3gsm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gsm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gsm RCSB], [http://www.ebi.ac.uk/pdbsum/3gsm 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=3gsm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gsm OCA], [http://pdbe.org/3gsm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gsm RCSB], [http://www.ebi.ac.uk/pdbsum/3gsm PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3gsm ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3gsm" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillo virgola del koch trevisan 1884]]
	[[Category: Beta-N-acetylhexosaminidase]]		[[Category: Beta-N-acetylhexosaminidase]]
-	[[Category: Vibrio cholerae]]
	[[Category: Balcewich, M D]]		[[Category: Balcewich, M D]]
	[[Category: Mark, B L]]		[[Category: Mark, B L]]

OCA at 09:39, 25 December 2014

OCA — Thu, 25 Dec 2014 09:39:12 GMT

←Older revision		Revision as of 09:39, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3gsm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GSM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GSM FirstGlance]. <br>		<table><tr><td colspan='2'>[[3gsm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GSM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GSM FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=VPU:[[(3R,4R,5S,6R)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)-3-(PENTANOYLAMINO)OXAN-2-YLIDENE]AMINO]+N-PHENYLCARBAMATE'>VPU</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=VPU:[[(3R,4R,5S,6R)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)-3-(PENTANOYLAMINO)OXAN-2-YLIDENE]AMINO]+N-PHENYLCARBAMATE'>VPU</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2oxn\|2oxn]], [[3gs6\|3gs6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2oxn\|2oxn]], [[3gs6\|3gs6]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">family 3 glycoside hydrolase NagZ, nagZ, VC_0692 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=666 Vibrio cholerae])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">family 3 glycoside hydrolase NagZ, nagZ, VC_0692 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=666 Vibrio cholerae])</td></tr>
-	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3gsm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gsm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gsm RCSB], [http://www.ebi.ac.uk/pdbsum/3gsm 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=3gsm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gsm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gsm RCSB], [http://www.ebi.ac.uk/pdbsum/3gsm PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NAGZ_VIBCH NAGZ_VIBCH]] 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. Plays a role in beta-lactam antibiotic resistance via its role in generating anhydro-N-acetylmuramic acid-linked peptides; these peptides function as signaling molecules that induce high-level expression of the beta-lactamase AmpC.<ref>PMID:24009110</ref> <ref>PMID:17439950</ref> <ref>PMID:19499593</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: Beta-N-acetylhexosaminidase]]		[[Category: Beta-N-acetylhexosaminidase]]
	[[Category: Vibrio cholerae]]		[[Category: Vibrio cholerae]]
-	[[Category: Balcewich, M D.]]	+	[[Category: Balcewich, M D]]
-	[[Category: Mark, B L.]]	+	[[Category: Mark, B L]]
	[[Category: Cell cycle]]		[[Category: Cell cycle]]
	[[Category: Cell division]]		[[Category: Cell division]]

OCA at 11:24, 29 September 2014

OCA — Mon, 29 Sep 2014 11:24:17 GMT

←Older revision		Revision as of 11:24, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3gsm.~~png~~\|~~left~~\|200px]]	+	==Vibrio cholerae family 3 glycoside hydrolase (NagZ) bound to N-Valeryl-PUGNAc==
		+	<StructureSection load='3gsm' size='340' side='right' caption='[[3gsm]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3gsm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GSM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GSM FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=VPU:[[(3R,4R,5S,6R)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)-3-(PENTANOYLAMINO)OXAN-2-YLIDENE]AMINO]+N-PHENYLCARBAMATE'>VPU</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2oxn\|2oxn]], [[3gs6\|3gs6]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">family 3 glycoside hydrolase NagZ, nagZ, VC_0692 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=666 Vibrio cholerae])</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3gsm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gsm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gsm RCSB], [http://www.ebi.ac.uk/pdbsum/3gsm PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gs/3gsm_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	NagZ is an exo-N-acetyl-beta-glucosaminidase, found within Gram-negative bacteria, that acts in the peptidoglycan recycling pathway to cleave N-acetylglucosamine residues off peptidoglycan fragments. This activity is required for resistance to cephalosporins mediated by inducible AmpC beta-lactamase. NagZ uses a catalytic mechanism involving a covalent glycosyl enzyme intermediate, unlike that of the human exo-N-acetyl-beta-glucosaminidases: O-GlcNAcase and the beta-hexosaminidase isoenzymes. These latter enzymes, which remove GlcNAc from glycoconjugates, use a neighboring-group catalytic mechanism that proceeds through an oxazoline intermediate. Exploiting these mechanistic differences we previously developed 2-N-acyl derivatives of O-(2-acetamido-2-deoxy-D-glucopyranosylidene)amino-N-phenylcarbamate (PUGNAc), which selectively inhibits NagZ over the functionally related human enzymes and attenuate antibiotic resistance in Gram-negatives that harbor inducible AmpC. To understand the structural basis for the selectivity of these inhibitors for NagZ, we have determined its crystallographic structure in complex with N-valeryl-PUGNAc, the most selective known inhibitor of NagZ over both the human beta-hexosaminidases and O-GlcNAcase. The selectivity stems from the five-carbon acyl chain of N-valeryl-PUGNAc, which we found ordered within the enzyme active site. In contrast, a structure determination of a human O-GlcNAcase homologue bound to a related inhibitor N-butyryl-PUGNAc, which bears a four-carbon chain and is selective for both NagZ and O-GlcNAcase over the human beta-hexosamnidases, reveals that this inhibitor induces several conformational changes in the active site of this O-GlcNAcase homologue. A comparison of these complexes, and with the human beta-hexosaminidases, reveals how selectivity for NagZ can be engineered by altering the 2-N-acyl substituent of PUGNAc to develop inhibitors that repress AmpC mediated beta-lactam resistance.

-	~~{{STRUCTURE_3gsm\| PDB=3gsm \| SCENE= }}~~	+	Insight into a strategy for attenuating AmpC-mediated beta-lactam resistance: Structural basis for selective inhibition of the glycoside hydrolase NagZ.,Balcewich MD, Stubbs KA, He Y, James TW, Davies GJ, Vocadlo DJ, Mark BL Protein Sci. 2009 Apr 16. PMID:19499593<ref>PMID:19499593</ref>

-	~~===Vibrio cholerae family 3 glycoside hydrolase (NagZ) bound to N-Valeryl-PUGNAc===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19499593}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3gsm]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Vibrio_cholerae Vibrio cholerae]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3GSM OCA].~~	+

	==See Also==		==See Also==
	*[[Beta-Hexosaminidase\|Beta-Hexosaminidase]]		*[[Beta-Hexosaminidase\|Beta-Hexosaminidase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019499593<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Beta-N-acetylhexosaminidase]]		[[Category: Beta-N-acetylhexosaminidase]]
	[[Category: Vibrio cholerae]]		[[Category: Vibrio cholerae]]

OCA at 15:12, 20 October 2012

OCA — Sat, 20 Oct 2012 15:12:06 GMT

←Older revision		Revision as of 15:12, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3gsm]] is a 1 chain structure ~~of [[Beta-Hexosaminidase]]~~ with sequence from [http://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GSM OCA].	+	[[3gsm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GSM OCA].

	==See Also==		==See Also==

OCA: Protected "3gsm" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 17:36:44 GMT

Protected "3gsm" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:36, 26 July 2012

OCA at 17:36, 26 July 2012

OCA — Thu, 26 Jul 2012 17:36:43 GMT

←Older revision		Revision as of 17:36, 26 July 2012
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-	{{Seed}}
	[[Image:3gsm.png\|left\|200px]]		[[Image:3gsm.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3gsm", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3gsm\| PDB=3gsm \| SCENE= }}		{{STRUCTURE_3gsm\| PDB=3gsm \| SCENE= }}

	===Vibrio cholerae family 3 glycoside hydrolase (NagZ) bound to N-Valeryl-PUGNAc===		===Vibrio cholerae family 3 glycoside hydrolase (NagZ) bound to N-Valeryl-PUGNAc===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19499593}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19499593 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19499593}}		{{ABSTRACT_PUBMED_19499593}}

	==About this Structure==		==About this Structure==
-	~~3GSM~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GSM OCA].	+	[[3gsm]] is a 1 chain structure of [[Beta-Hexosaminidase]] with sequence from [http://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GSM OCA].
		+
		+	==See Also==
		+	*[[Beta-Hexosaminidase\|Beta-Hexosaminidase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19499593~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019499593</ref><references group="xtra"/>
	[[Category: Beta-N-acetylhexosaminidase]]		[[Category: Beta-N-acetylhexosaminidase]]
	[[Category: Vibrio cholerae]]		[[Category: Vibrio cholerae]]
Line 32:		Line 23:
	[[Category: Cell shape]]		[[Category: Cell shape]]
	[[Category: Cell wall biogenesis/degradation]]		[[Category: Cell wall biogenesis/degradation]]
-	[[Category: Cytoplasm]]
	[[Category: Glycosidase]]		[[Category: Glycosidase]]
	[[Category: Glycoside hydrolase]]		[[Category: Glycoside hydrolase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Peptidoglycan synthesis]]		[[Category: Peptidoglycan synthesis]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 22 21:31:40 2009''

OCA at 18:31, 22 July 2009

OCA — Wed, 22 Jul 2009 18:31:42 GMT

←Older revision		Revision as of 18:31, 22 July 2009
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	{{Seed}}		{{Seed}}
-	[[Image:3gsm.~~jpg~~\|left\|200px]]	+	[[Image:3gsm.png\|left\|200px]]

	<!--		<!--
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	[[Category: Peptidoglycan synthesis]]		[[Category: Peptidoglycan synthesis]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul ~~1 09~~:19:32 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 22 21:31:40 2009''