6rpc - Revision history

OCA at 12:25, 24 January 2024

2024-01-24T12:25:39Z

←Older revision		Revision as of 12:25, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6rpc' size='340' side='right'caption='[[6rpc]], [[Resolution\|resolution]] 1.69Å' scene=''>		<StructureSection load='6rpc' size='340' side='right'caption='[[6rpc]], [[Resolution\|resolution]] 1.69Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6rpc]] is a 1 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=6RPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RPC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6rpc]] is a 1 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=6RPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RPC FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</scene>~~, ~~<scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.69Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~alpha-Man-IIa, GmII, CG18802 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=7227 DROME])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[https://en.wikipedia.org/wiki/Mannosyl-oligosaccharide_1,3-1,6-alpha-mannosidase Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.114 3.2.1.114] </~~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=6rpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rpc OCA], [https://pdbe.org/6rpc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rpc RCSB], [https://www.ebi.ac.uk/pdbsum/6rpc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rpc 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=6rpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rpc OCA], [https://pdbe.org/6rpc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rpc RCSB], [https://www.ebi.ac.uk/pdbsum/6rpc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rpc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/MAN2_DROME MAN2_DROME]] Catalyzes the first committed step in the biosynthesis of complex N-glycans. It controls conversion of high mannose to complex N-glycans; the final hydrolytic step in the N-glycan maturation pathway (By similarity).	+	[https://www.uniprot.org/uniprot/MAN2_DROME MAN2_DROME] Catalyzes the first committed step in the biosynthesis of complex N-glycans. It controls conversion of high mannose to complex N-glycans; the final hydrolytic step in the N-glycan maturation pathway (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Drome~~]]	+	[[Category: Drosophila melanogaster]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase]]~~	+	[[Category: Aerts JMFG]]
-	[[Category: Aerts~~, J M.F G~~]]	+	[[Category: Armstrong Z]]
-	[[Category: Armstrong, Z]]	+	[[Category: Beenakker TJM]]
-	[[Category: Beenakker~~, T J.M]]~~	+	[[Category: Codee JDC]]
-	~~[[Category: Boer, C de~~]]	+	[[Category: Davies GJ]]
-	[[Category: Codee~~, J D.C~~]]	+	[[Category: Debets M]]
-	[[Category: Davies~~, G J~~]]	+	[[Category: Johnson R]]
-	[[Category: Debets, M]]	+	[[Category: Kuo CL]]
-	[[Category: Johnson, R]]	+	[[Category: Lahav D]]
-	[[Category: Kuo~~, C L~~]]	+	[[Category: Overkleeft HS]]
-	[[Category: Lahav, D]]	+	[[Category: Wong CS]]
-	[[Category: Overkleeft~~, H S]]~~	+	[[Category: Wu L]]
-	~~[[Category: Stelt, M van der~~]]	+	[[Category: De Boer C]]
-	[[Category: Wong~~, C S~~]]	+	[[Category: Van der Stelt M]]
-	[[Category: Wu, L]]	+
-	[[Category: ~~Glycoside hydrolase~~]]	+
-	[[Category: ~~Hydrolase]]~~	+
-	~~[[Category: Mannosidase~~]]	+

OCA at 10:40, 28 July 2021

2021-07-28T10:40:06Z

←Older revision		Revision as of 10:40, 28 July 2021
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	==GOLGI ALPHA-MANNOSIDASE II==		==GOLGI ALPHA-MANNOSIDASE II==
-	<StructureSection load='6rpc' size='340' side='right'caption='[[6rpc]]' scene=''>	+	<StructureSection load='6rpc' size='340' side='right'caption='[[6rpc]], [[Resolution\|resolution]] 1.69Å' 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=6RPC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6RPC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6rpc]] is a 1 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=6RPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RPC FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6rpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rpc OCA], [~~http~~://pdbe.org/6rpc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6rpc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6rpc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6rpc ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</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">alpha-Man-IIa, GmII, CG18802 ([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/Mannosyl-oligosaccharide_1,3-1,6-alpha-mannosidase Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.114 3.2.1.114] </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=6rpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rpc OCA], [https://pdbe.org/6rpc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rpc RCSB], [https://www.ebi.ac.uk/pdbsum/6rpc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rpc ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/MAN2_DROME MAN2_DROME]] Catalyzes the first committed step in the biosynthesis of complex N-glycans. It controls conversion of high mannose to complex N-glycans; the final hydrolytic step in the N-glycan maturation pathway (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Golgi mannosidase II (GMII) catalyzes the sequential hydrolysis of two mannosyl residues from GlcNAcMan5GlcNAc2 to produce GlcNAcMan3GlcNAc2, the precursor for all complex N-glycans, including the branched N-glycans associated with cancer. Inhibitors of GMII are potential cancer therapeutics, but their usefulness is limited by off-target effects, which produce alpha-mannosidosis-like symptoms. Despite many structural and mechanistic studies of GMII, we still lack a potent and selective inhibitor of this enzyme. Here, we synthesized manno-epi-cyclophellitol epoxide and aziridines and demonstrate their covalent modification and time-dependent inhibition of GMII. Application of fluorescent manno-epi-cyclophellitol aziridine derivatives enabled activity-based protein profiling of alpha-mannosidases from both human cell lysate and mouse tissue extracts. Synthesized probes also facilitated a fluorescence polarization-based screen for dGMII inhibitors. We identified seven previously unknown inhibitors of GMII from a library of over 350 iminosugars and investigated their binding modalities through X-ray crystallography. Our results reveal previously unobserved inhibitor binding modes and promising scaffolds for the generation of selective GMII inhibitors.
		+
		+	Manno-epi-cyclophellitols Enable Activity-Based Protein Profiling of Human alpha-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors.,Armstrong Z, Kuo CL, Lahav D, Liu B, Johnson R, Beenakker TJM, de Boer C, Wong CS, van Rijssel ER, Debets MF, Florea BI, Hissink C, Boot RG, Geurink PP, Ovaa H, van der Stelt M, van der Marel GM, Codee JDC, Aerts JMFG, Wu L, Overkleeft HS, Davies GJ J Am Chem Soc. 2020 Jul 29;142(30):13021-13029. doi: 10.1021/jacs.0c03880. Epub, 2020 Jul 16. PMID:32605368<ref>PMID:32605368</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6rpc" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Mannosidase 3D structures\|Mannosidase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Drome]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Aerts ~~JMFG~~]]	+	[[Category: Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase]]
-	[[Category: Armstrong Z]]	+	[[Category: Aerts, J M.F G]]
-	[[Category: Beenakker ~~TJM~~]]	+	[[Category: Armstrong, Z]]
-	[[Category: Codee ~~JDC~~]]	+	[[Category: Beenakker, T J.M]]
-	[[Category: Davies GJ]]	+	[[Category: Boer, C de]]
-	[[Category: Debets M]]	+	[[Category: Codee, J D.C]]
-	[[Category: Johnson R]]	+	[[Category: Davies, G J]]
-	[[Category: Kuo CL]]	+	[[Category: Debets, M]]
-	[[Category: Lahav D]]	+	[[Category: Johnson, R]]
-	[[Category: Overkleeft HS]]	+	[[Category: Kuo, C L]]
-	[[Category: Wong CS]]	+	[[Category: Lahav, D]]
-	[[Category: Wu L]]	+	[[Category: Overkleeft, H S]]
-	[[Category: ~~De Boer C~~]]	+	[[Category: Stelt, M van der]]
-	[[Category: ~~Van der Stelt M~~]]	+	[[Category: Wong, C S]]
		+	[[Category: Wu, L]]
		+	[[Category: Glycoside hydrolase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Mannosidase]]

OCA at 14:01, 8 July 2020

2020-07-08T14:01:51Z

←Older revision		Revision as of 14:01, 8 July 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6rpc is ~~ON HOLD until Paper Publication~~	+	==GOLGI ALPHA-MANNOSIDASE II==
-		+	<StructureSection load='6rpc' size='340' side='right'caption='[[6rpc]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RPC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6RPC FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6rpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rpc OCA], [http://pdbe.org/6rpc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rpc RCSB], [http://www.ebi.ac.uk/pdbsum/6rpc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rpc ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Aerts JMFG]]
		+	[[Category: Armstrong Z]]
		+	[[Category: Beenakker TJM]]
		+	[[Category: Codee JDC]]
		+	[[Category: Davies GJ]]
		+	[[Category: Debets M]]
		+	[[Category: Johnson R]]
		+	[[Category: Kuo CL]]
		+	[[Category: Lahav D]]
		+	[[Category: Overkleeft HS]]
		+	[[Category: Wong CS]]
		+	[[Category: Wu L]]
		+	[[Category: De Boer C]]
		+	[[Category: Van der Stelt M]]

OCA at 04:41, 29 May 2019

2019-05-29T04:41:47Z

←Older revision		Revision as of 04:41, 29 May 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6rpc is ON HOLD	+	The entry 6rpc is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6rpc" [edit=sysop:move=sysop]

2019-05-22T04:18:56Z

Protected "6rpc" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:18, 22 May 2019

OCA: New page: '''Unreleased structure''' The entry 6rpc is ON HOLD Authors: Description: Category: Unreleased Structures

2019-05-22T04:18:55Z

New page: '''Unreleased structure''' The entry 6rpc is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6rpc is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]