3esw - Revision history

OCA at 06:32, 6 September 2023

OCA — Wed, 06 Sep 2023 06:32:46 GMT

←Older revision		Revision as of 06:32, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3esw' size='340' side='right'caption='[[3esw]], [[Resolution\|resolution]] 3.40Å' scene=''>		<StructureSection load='3esw' size='340' side='right'caption='[[3esw]], [[Resolution\|resolution]] 3.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3esw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ESW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ESW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3esw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ESW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ESW FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~, ~~<scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 3.4Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</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">PNG1~~, YPL096W ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), RAD23, SYGP-ORF29, YEL037C ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])<~~/td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[https://en.wikipedia.org/wiki/Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine_amidase Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.52 3.5.1.52] </~~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=3esw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3esw OCA], [https://pdbe.org/3esw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3esw RCSB], [https://www.ebi.ac.uk/pdbsum/3esw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3esw 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=3esw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3esw OCA], [https://pdbe.org/3esw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3esw RCSB], [https://www.ebi.ac.uk/pdbsum/3esw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3esw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PNG1_YEAST PNG1_YEAST]] Specifically deglycosylates the denatured form of N-linked glycoproteins in the cytoplasm and assists their proteasome-mediated degradation. Cleaves the beta-aspartyl-glucosamine (GlcNAc) of the glycan and the amide side chain of Asn, converting Asn to Asp. Prefers proteins containing high-mannose over those bearing complex type oligosaccharides. Can recognize misfolded proteins in the endoplasmic reticulum that are exported to the cytosol to be destroyed and deglycosylate them, while it has no activity toward native proteins. Deglycosylation is a prerequisite for subsequent proteasome-mediated degradation of some, but not all, misfolded glycoproteins. Involved in the formation of free oligosaccharide in cytosol.<ref>PMID:10831608</ref> <ref>PMID:12723970</ref> <ref>PMID:12606569</ref> <ref>PMID:14726951</ref> <ref>PMID:15670854</ref> <ref>PMID:16401726</ref> [[https://www.uniprot.org/uniprot/RAD23_YEAST RAD23_YEAST]] Plays a central role both in proteasomal degradation of misfolded proteins and DNA repair. Central component of a complex required to couple deglycosylation and proteasome-mediated degradation of misfolded proteins in the endoplasmic reticulum that are retrotranslocated in the cytosol. Involved in DNA excision repair. May play a part in DNA damage recognition and/or in altering chromatin structure to allow access by damage-processing enzymes.	+	[https://www.uniprot.org/uniprot/PNG1_YEAST PNG1_YEAST] Specifically deglycosylates the denatured form of N-linked glycoproteins in the cytoplasm and assists their proteasome-mediated degradation. Cleaves the beta-aspartyl-glucosamine (GlcNAc) of the glycan and the amide side chain of Asn, converting Asn to Asp. Prefers proteins containing high-mannose over those bearing complex type oligosaccharides. Can recognize misfolded proteins in the endoplasmic reticulum that are exported to the cytosol to be destroyed and deglycosylate them, while it has no activity toward native proteins. Deglycosylation is a prerequisite for subsequent proteasome-mediated degradation of some, but not all, misfolded glycoproteins. Involved in the formation of free oligosaccharide in cytosol.<ref>PMID:10831608</ref> <ref>PMID:12723970</ref> <ref>PMID:12606569</ref> <ref>PMID:14726951</ref> <ref>PMID:15670854</ref> <ref>PMID:16401726</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 39:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Lennarz~~, W J~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: Schindelin, H]]	+	[[Category: Lennarz WJ]]
-	[[Category: Zhao, G]]	+	[[Category: Schindelin H]]
-	[[Category: Zhou, X]]	+	[[Category: Zhao G]]
-	~~[[Category: Dna damage]]~~	+	[[Category: Zhou X]]
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Glycoproteins peptide:n-glycanase chitobiose]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Phosphoprotein]]~~	+
-	~~[[Category: Ubl conjugation pathway~~]]	+

OCA at 09:15, 23 February 2022

OCA — Wed, 23 Feb 2022 09:15:28 GMT

←Older revision		Revision as of 09:15, 23 February 2022
Line 1:		Line 1:

	==Complex of yeast PNGase with GlcNAc2-IAc.==		==Complex of yeast PNGase with GlcNAc2-IAc.==
-	<StructureSection load='3esw' size='340' side='right' caption='[[3esw]], [[Resolution\|resolution]] 3.40Å' scene=''>	+	<StructureSection load='3esw' size='340' side='right'caption='[[3esw]], [[Resolution\|resolution]] 3.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3esw]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ESW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3ESW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3esw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ESW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ESW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~NAG~~:~~N-ACETYL-D-GLUCOSAMINE~~'>~~NAG~~</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" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PNG1, YPL096W ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), RAD23, SYGP-ORF29, YEL037C ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PNG1, YPL096W ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), RAD23, SYGP-ORF29, YEL037C ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine_amidase Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.52 3.5.1.52] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine_amidase Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.52 3.5.1.52] </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=3esw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3esw OCA], [~~http~~://pdbe.org/3esw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3esw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3esw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3esw 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=3esw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3esw OCA], [https://pdbe.org/3esw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3esw RCSB], [https://www.ebi.ac.uk/pdbsum/3esw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3esw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PNG1_YEAST PNG1_YEAST]] Specifically deglycosylates the denatured form of N-linked glycoproteins in the cytoplasm and assists their proteasome-mediated degradation. Cleaves the beta-aspartyl-glucosamine (GlcNAc) of the glycan and the amide side chain of Asn, converting Asn to Asp. Prefers proteins containing high-mannose over those bearing complex type oligosaccharides. Can recognize misfolded proteins in the endoplasmic reticulum that are exported to the cytosol to be destroyed and deglycosylate them, while it has no activity toward native proteins. Deglycosylation is a prerequisite for subsequent proteasome-mediated degradation of some, but not all, misfolded glycoproteins. Involved in the formation of free oligosaccharide in cytosol.<ref>PMID:10831608</ref> <ref>PMID:12723970</ref> <ref>PMID:12606569</ref> <ref>PMID:14726951</ref> <ref>PMID:15670854</ref> <ref>PMID:16401726</ref> [[~~http~~://www.uniprot.org/uniprot/RAD23_YEAST RAD23_YEAST]] Plays a central role both in proteasomal degradation of misfolded proteins and DNA repair. Central component of a complex required to couple deglycosylation and proteasome-mediated degradation of misfolded proteins in the endoplasmic reticulum that are retrotranslocated in the cytosol. Involved in DNA excision repair. May play a part in DNA damage recognition and/or in altering chromatin structure to allow access by damage-processing enzymes.	+	[[https://www.uniprot.org/uniprot/PNG1_YEAST PNG1_YEAST]] Specifically deglycosylates the denatured form of N-linked glycoproteins in the cytoplasm and assists their proteasome-mediated degradation. Cleaves the beta-aspartyl-glucosamine (GlcNAc) of the glycan and the amide side chain of Asn, converting Asn to Asp. Prefers proteins containing high-mannose over those bearing complex type oligosaccharides. Can recognize misfolded proteins in the endoplasmic reticulum that are exported to the cytosol to be destroyed and deglycosylate them, while it has no activity toward native proteins. Deglycosylation is a prerequisite for subsequent proteasome-mediated degradation of some, but not all, misfolded glycoproteins. Involved in the formation of free oligosaccharide in cytosol.<ref>PMID:10831608</ref> <ref>PMID:12723970</ref> <ref>PMID:12606569</ref> <ref>PMID:14726951</ref> <ref>PMID:15670854</ref> <ref>PMID:16401726</ref> [[https://www.uniprot.org/uniprot/RAD23_YEAST RAD23_YEAST]] Plays a central role both in proteasomal degradation of misfolded proteins and DNA repair. Central component of a complex required to couple deglycosylation and proteasome-mediated degradation of misfolded proteins in the endoplasmic reticulum that are retrotranslocated in the cytosol. Involved in DNA excision repair. May play a part in DNA damage recognition and/or in altering chromatin structure to allow access by damage-processing enzymes.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/es/3esw_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/es/3esw_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>
Line 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 3esw" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3esw" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Peptide N-glycanase\|Peptide N-glycanase]]
		+	*[[UV excision repair protein\|UV excision repair protein]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 40:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
		+	[[Category: Large Structures]]
	[[Category: Lennarz, W J]]		[[Category: Lennarz, W J]]
	[[Category: Schindelin, H]]		[[Category: Schindelin, H]]

OCA at 09:19, 25 October 2017

OCA — Wed, 25 Oct 2017 09:19:01 GMT

←Older revision		Revision as of 09:19, 25 October 2017
Line 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 3esw" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3esw" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Peptide N-glycanase\|Peptide N-glycanase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:54, 5 August 2016

OCA — Fri, 05 Aug 2016 11:54:11 GMT

←Older revision		Revision as of 11:54, 5 August 2016
Line 1:		Line 1:
		+
	==Complex of yeast PNGase with GlcNAc2-IAc.==		==Complex of yeast PNGase with GlcNAc2-IAc.==
	<StructureSection load='3esw' size='340' side='right' caption='[[3esw]], [[Resolution\|resolution]] 3.40Å' scene=''>		<StructureSection load='3esw' size='340' side='right' caption='[[3esw]], [[Resolution\|resolution]] 3.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3esw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ESW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ESW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3esw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ESW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ESW FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PNG1, YPL096W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ~~Saccharomyces cerevisiae~~]), RAD23, SYGP-ORF29, YEL037C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ~~Saccharomyces cerevisiae~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PNG1, YPL096W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), RAD23, SYGP-ORF29, YEL037C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine_amidase Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.52 3.5.1.52] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine_amidase Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.52 3.5.1.52] </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=3esw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3esw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3esw RCSB], [http://www.ebi.ac.uk/pdbsum/3esw 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=3esw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3esw OCA], [http://pdbe.org/3esw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3esw RCSB], [http://www.ebi.ac.uk/pdbsum/3esw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3esw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	<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=3esw ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	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 3esw" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Peptide N-glycanase\|Peptide N-glycanase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Saccharomyces cerevisiae~~]]	+	[[Category: Atcc 18824]]
	[[Category: Lennarz, W J]]		[[Category: Lennarz, W J]]
	[[Category: Schindelin, H]]		[[Category: Schindelin, H]]

OCA at 18:35, 25 December 2014

OCA — Thu, 25 Dec 2014 18:35:57 GMT

←Older revision		Revision as of 18:35, 25 December 2014
Line 9:		Line 9:
	<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=3esw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3esw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3esw RCSB], [http://www.ebi.ac.uk/pdbsum/3esw 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=3esw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3esw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3esw RCSB], [http://www.ebi.ac.uk/pdbsum/3esw PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PNG1_YEAST PNG1_YEAST]] Specifically deglycosylates the denatured form of N-linked glycoproteins in the cytoplasm and assists their proteasome-mediated degradation. Cleaves the beta-aspartyl-glucosamine (GlcNAc) of the glycan and the amide side chain of Asn, converting Asn to Asp. Prefers proteins containing high-mannose over those bearing complex type oligosaccharides. Can recognize misfolded proteins in the endoplasmic reticulum that are exported to the cytosol to be destroyed and deglycosylate them, while it has no activity toward native proteins. Deglycosylation is a prerequisite for subsequent proteasome-mediated degradation of some, but not all, misfolded glycoproteins. Involved in the formation of free oligosaccharide in cytosol.<ref>PMID:10831608</ref> <ref>PMID:12723970</ref> <ref>PMID:12606569</ref> <ref>PMID:14726951</ref> <ref>PMID:15670854</ref> <ref>PMID:16401726</ref> [[http://www.uniprot.org/uniprot/RAD23_YEAST RAD23_YEAST]] Plays a central role both in proteasomal degradation of misfolded proteins and DNA repair. Central component of a complex required to couple deglycosylation and proteasome-mediated degradation of misfolded proteins in the endoplasmic reticulum that are retrotranslocated in the cytosol. Involved in DNA excision repair. May play a part in DNA damage recognition and/or in altering chromatin structure to allow access by damage-processing enzymes.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:41, 26 November 2014

OCA — Wed, 26 Nov 2014 08:41:38 GMT

←Older revision		Revision as of 08:41, 26 November 2014
Line 1:		Line 1:
-	[[~~Image:~~3esw.~~png~~\|~~left~~\|200px]]	+	==Complex of yeast PNGase with GlcNAc2-IAc.==
		+	<StructureSection load='3esw' size='340' side='right' caption='[[3esw]], [[Resolution\|resolution]] 3.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3esw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ESW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ESW FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PNG1, YPL096W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), RAD23, SYGP-ORF29, YEL037C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine_amidase Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.52 3.5.1.52] </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=3esw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3esw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3esw RCSB], [http://www.ebi.ac.uk/pdbsum/3esw 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/es/3esw_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 ==
		+	Peptide:N-glycanase (PNGase) is an important component of the endoplasmic reticulum-associated protein degradation pathway in which it de-glycosylates misfolded glycoproteins, thus facilitating their proteasomal degradation. PNGase belongs to the transglutaminase superfamily and features a Cys, His, and Asp catalytic triad, which is essential for its enzymatic activity. An elongated substrate-binding groove centered on the active site Cys191 was visualized in the crystal structure of apo-PNGase, whereas its complex with Z-VAD-fmk, a peptide-based inhibitor of PNGase, revealed that the inhibitor occupied one end of the substrate-binding groove while being covalently linked to the active site Cys. Recently, haloacetamidyl-containing carbohydrate-based inhibitors of PNGase were developed and shown to specifically label the active site Cys. In this study, we describe the crystal structure of yeast PNGase in complex with N,N'-diacetylchitobiose (chitobiose). We found that the chitobiose binds on the side opposite to the peptide binding site with the active site Cys191 being located approximately midway between the carbohydrate and peptide binding sites. Mutagenesis studies confirm the critical role of the chitobiose-interacting residues in substrate binding and suggest that efficient oligosaccharide binding is required for PNGase activity. In addition, the N-terminus of a symmetry-related PNGase was found to bind to the proposed peptide-binding site of PNGase. Together with the bound chitobiose, this enables us to propose a model for glycoprotein binding to PNGase. Finally, deleting the C-terminal residues of yeast PNGase, which are disordered in all structures of this enzyme, results in a significant reduction in enzyme activity, indicating that these residues might be involved in binding of the mannose residues of the glycan chain.

-	~~{{STRUCTURE_3esw\| PDB=3esw \| SCENE= }}~~	+	Structural and mutational studies on the importance of oligosaccharide binding for the activity of yeast PNGase.,Zhao G, Li G, Zhou X, Matsuo I, Ito Y, Suzuki T, Lennarz WJ, Schindelin H Glycobiology. 2009 Feb;19(2):118-25. Epub 2008 Oct 14. PMID:18854368<ref>PMID:18854368</ref>

-	~~===Complex~~ of ~~yeast PNGase with GlcNAc2-IAc~~.~~===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18854368}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3esw]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ESW OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018854368<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Lennarz, W J.]]	+	[[Category: Lennarz, W J]]
-	[[Category: Schindelin, H.]]	+	[[Category: Schindelin, H]]
-	[[Category: Zhao, G.]]	+	[[Category: Zhao, G]]
-	[[Category: Zhou, X.]]	+	[[Category: Zhou, X]]
	[[Category: Dna damage]]		[[Category: Dna damage]]
	[[Category: Dna repair]]		[[Category: Dna repair]]

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

OCA — Wed, 06 Feb 2013 13:24:16 GMT

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

←Older revision

Revision as of 13:24, 6 February 2013

OCA at 13:24, 6 February 2013

OCA — Wed, 06 Feb 2013 13:24:13 GMT

←Older revision		Revision as of 13:24, 6 February 2013
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-	{{Seed}}
	[[Image:3esw.png\|left\|200px]]		[[Image:3esw.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3esw", 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_3esw\| PDB=3esw \| SCENE= }}		{{STRUCTURE_3esw\| PDB=3esw \| SCENE= }}

	===Complex of yeast PNGase with GlcNAc2-IAc.===		===Complex of yeast PNGase with GlcNAc2-IAc.===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18854368}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18854368 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18854368}}		{{ABSTRACT_PUBMED_18854368}}

	==About this Structure==		==About this Structure==
-	~~3ESW~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ESW OCA].	+	[[3esw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ESW OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18854368~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018854368</ref><references group="xtra"/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Lennarz, W J.]]		[[Category: Lennarz, W J.]]
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	[[Category: Zhao, G.]]		[[Category: Zhao, G.]]
	[[Category: Zhou, X.]]		[[Category: Zhou, X.]]
-	[[Category: Cytoplasm]]
	[[Category: Dna damage]]		[[Category: Dna damage]]
	[[Category: Dna repair]]		[[Category: Dna repair]]
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	[[Category: Phosphoprotein]]		[[Category: Phosphoprotein]]
	[[Category: Ubl conjugation pathway]]		[[Category: Ubl conjugation pathway]]
-	[[Category: Zinc]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 02:40:20 2009''

OCA at 00:40, 18 February 2009

OCA — Wed, 18 Feb 2009 00:40:21 GMT

←Older revision		Revision as of 00:40, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3ESW is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ESW OCA].	+	3ESW is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ESW OCA].

	==Reference==		==Reference==
-	Structural and Mutational Studies on the Importance of Oligosaccharide Binding for the Activity of Yeast PNGase., Zhao G, Li G, Zhou X, Matsuo I, Ito Y, Suzuki T, Lennarz WJ, Schindelin H, Glycobiology. 2008 Oct 14. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18854368 18854368]~~	+	<ref group="xtra">PMID:18854368</ref><references group="xtra"/>
-	~~[[Category: Protein complex]]~~	+
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: ~~Pdbx_ordinal=~~, ~~<PDBx~~:~~audit_author~~.]]	+	[[Category: Lennarz, W J.]]
		+	[[Category: Schindelin, H.]]
		+	[[Category: Zhao, G.]]
		+	[[Category: Zhou, X.]]
	[[Category: Cytoplasm]]		[[Category: Cytoplasm]]
	[[Category: Dna damage]]		[[Category: Dna damage]]
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	[[Category: Zinc]]		[[Category: Zinc]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jan 14 20~~:03:46 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 02:40:20 2009''

OCA at 20:26, 15 January 2009

OCA — Thu, 15 Jan 2009 20:26:43 GMT

←Older revision		Revision as of 20:26, 15 January 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3ESW is a ~~2 chains~~ structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ESW OCA].	+	3ESW is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ESW OCA].

	==Reference==		==Reference==
	Structural and Mutational Studies on the Importance of Oligosaccharide Binding for the Activity of Yeast PNGase., Zhao G, Li G, Zhou X, Matsuo I, Ito Y, Suzuki T, Lennarz WJ, Schindelin H, Glycobiology. 2008 Oct 14. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18854368 18854368]		Structural and Mutational Studies on the Importance of Oligosaccharide Binding for the Activity of Yeast PNGase., Zhao G, Li G, Zhou X, Matsuo I, Ito Y, Suzuki T, Lennarz WJ, Schindelin H, Glycobiology. 2008 Oct 14. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18854368 18854368]
		+	[[Category: Protein complex]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: ~~Lennarz~~, ~~W J.]]~~	+	[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
-	~~[[Category~~: ~~Schindelin, H.]]~~	+
-	~~[[Category: Zhao, G.]]~~	+
-	~~[[Category: Zhou, X~~.]]	+
	[[Category: Cytoplasm]]		[[Category: Cytoplasm]]
	[[Category: Dna damage]]		[[Category: Dna damage]]
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	[[Category: Zinc]]		[[Category: Zinc]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 14 12:40:35 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 14 20:03:46 2009''