6pkg - Revision history

OCA at 08:14, 17 October 2024

2024-10-17T08:14:01Z

← Older revision		Revision as of 08:14, 17 October 2024
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	<StructureSection load='6pkg' size='340' side='right'caption='[[6pkg]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='6pkg' size='340' side='right'caption='[[6pkg]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6pkg]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Brachidanio_rerio Brachidanio~~ rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PKG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6PKG FirstGlance]. <br>		<table><tr><td colspan='2'>[[6pkg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PKG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=I2I:MOLECULAR+IODINE'>I2I</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</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]] 2.8Å</td></tr>
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nagpa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=I2I:MOLECULAR+IODINE'>I2I</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></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=6pkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pkg OCA], [~~http~~://pdbe.org/6pkg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6pkg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6pkg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6pkg 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=6pkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pkg OCA], [https://pdbe.org/6pkg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pkg RCSB], [https://www.ebi.ac.uk/pdbsum/6pkg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pkg ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Brachidanio~~ rerio]]		[[Category: Danio rerio]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Gorelik, A]]		[[Category: Gorelik A]]
	[[Category: Illes, K]]		[[Category: Illes K]]
	[[Category: Nagar, B]]		[[Category: Nagar B]]
	~~[[Category: Glycosidase]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Mannose 6-phosphate]]~~
	~~[[Category: Pro-peptide]]~~
	~~[[Category: Uncovering enzyme~~]]

OCA at 07:14, 15 April 2020

2020-04-15T07:14:59Z

← Older revision		Revision as of 07:14, 15 April 2020
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	<StructureSection load='6pkg' size='340' side='right'caption='[[6pkg]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='6pkg' size='340' side='right'caption='[[6pkg]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6pkg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PKG OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6PKG FirstGlance]. <br>		<table><tr><td colspan='2'>[[6pkg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PKG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PKG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=I2I:MOLECULAR+IODINE'>I2I</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=I2I:MOLECULAR+IODINE'>I2I</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nagpa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nagpa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</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=6pkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pkg OCA], [http://pdbe.org/6pkg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pkg RCSB], [http://www.ebi.ac.uk/pdbsum/6pkg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pkg ProSAT]</span></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=6pkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pkg OCA], [http://pdbe.org/6pkg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pkg RCSB], [http://www.ebi.ac.uk/pdbsum/6pkg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pkg ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:58, 11 March 2020

2020-03-11T07:58:27Z

← Older revision		Revision as of 07:58, 11 March 2020
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	<StructureSection load='6pkg' size='340' side='right'caption='[[6pkg]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='6pkg' size='340' side='right'caption='[[6pkg]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6pkg]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PKG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PKG FirstGlance]. <br>		<table><tr><td colspan='2'>[[6pkg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PKG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PKG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=I2I:MOLECULAR+IODINE'>I2I</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=I2I:MOLECULAR+IODINE'>I2I</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nagpa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</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=6pkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pkg OCA], [http://pdbe.org/6pkg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pkg RCSB], [http://www.ebi.ac.uk/pdbsum/6pkg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pkg 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=6pkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pkg OCA], [http://pdbe.org/6pkg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pkg RCSB], [http://www.ebi.ac.uk/pdbsum/6pkg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pkg ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Most lysosomal hydrolytic enzymes reach their destination via the mannose-6-phosphate (M6P) pathway. The enzyme N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA, or "uncovering enzyme") catalyzes the second step in the M6P tag formation, namely the removal of the masking N-acetylglucosamine (GlcNAc) portion. Defects in this protein are associated with non-syndromic stuttering. To gain a better understanding of the function and regulation of this enzyme, we determined its crystal structure. The propeptide binds in a groove on the globular catalytic domain, blocking active site access. High-affinity substrate binding is enabled by a conformational switch in an active site loop. The protein recognizes the GlcNAc and phosphate portions of its substrate, but not the mannose moiety of the glycan. Based on enzymatic and (1)H-NMR analysis, a catalytic mechanism is proposed. Crystallographic and solution scattering analyses suggest that the C-terminal domain forms a long flexible stem that extends the enzyme away from the Golgi membrane.

			Crystal Structure of the Mannose-6-Phosphate Uncovering Enzyme.,Gorelik A, Illes K, Nagar B Structure. 2020 Feb 25. pii: S0969-2126(20)30042-3. doi:, 10.1016/j.str.2020.02.001. PMID:32109365<ref>PMID:32109365</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6pkg" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Brachidanio rerio]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Gorelik, A]]		[[Category: Gorelik, A]]

OCA at 06:25, 19 February 2020

2020-02-19T06:25:39Z

← Older revision		Revision as of 06:25, 19 February 2020
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	~~'''Unreleased structure'''~~

	~~The entry~~ 6pkg is ~~ON HOLD until Paper Publication~~		==Zebrafish N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA) catalytic domain auto-inhibited by pro-peptide==
			<StructureSection load='6pkg' size='340' side='right'caption='[[6pkg]], [[Resolution\|resolution]] 2.80Å' scene=''>
	~~Authors~~:		== Structural highlights ==
			<table><tr><td colspan='2'>[[6pkg]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PKG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PKG FirstGlance]. <br>
	~~Description~~:		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=I2I:MOLECULAR+IODINE'>I2I</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr>
	[[Category: ~~Unreleased Structures~~]]		<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=6pkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pkg OCA], [http://pdbe.org/6pkg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pkg RCSB], [http://www.ebi.ac.uk/pdbsum/6pkg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pkg ProSAT]</span></td></tr>
			</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Gorelik, A]]
			[[Category: Illes, K]]
			[[Category: Nagar, B]]
			[[Category: Glycosidase]]
			[[Category: Hydrolase]]
			[[Category: Mannose 6-phosphate]]
			[[Category: Pro-peptide]]
			[[Category: Uncovering enzyme]]

OCA at 13:43, 28 August 2019

2019-08-28T13:43:34Z

← Older revision		Revision as of 13:43, 28 August 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6pkg is ON HOLD		The entry 6pkg is ON HOLD until Paper Publication

	Authors:		Authors:

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

2019-07-10T04:11:18Z

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

← Older revision	Revision as of 04:11, 10 July 2019
(No difference)

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

2019-07-10T04:11:17Z

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

New page

'''Unreleased structure'''

The entry 6pkg is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]