7nuu - Revision history

OCA at 12:40, 1 February 2024

OCA — Thu, 01 Feb 2024 12:40:14 GMT

←Older revision		Revision as of 12:40, 1 February 2024
Line 3:		Line 3:
	<StructureSection load='7nuu' size='340' side='right'caption='[[7nuu]], [[Resolution\|resolution]] 1.84Å' scene=''>		<StructureSection load='7nuu' size='340' side='right'caption='[[7nuu]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7nuu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NUU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NUU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7nuu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NUU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NUU 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=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]] 1.836Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>AMDHD2, CGI-14 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9606 HUMAN])</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=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/N-acetylglucosamine-6-phosphate_deacetylase N-acetylglucosamine-6-phosphate deacetylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.25 3.5.1.25] </~~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=7nuu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nuu OCA], [https://pdbe.org/7nuu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nuu RCSB], [https://www.ebi.ac.uk/pdbsum/7nuu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nuu 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=7nuu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nuu OCA], [https://pdbe.org/7nuu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nuu RCSB], [https://www.ebi.ac.uk/pdbsum/7nuu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nuu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NAGA_HUMAN NAGA_HUMAN]] Hydrolyzes the N-glycolyl group from N-glycolylglucosamine 6-phosphate (GlcNGc-6-P) in the N-glycolylneuraminic acid (Neu5Gc) degradation pathway. Although human is not able to catalyze formation of Neu5Gc due to the inactive CMAHP enzyme, Neu5Gc is present in food and must be degraded.<ref>PMID:22692205</ref>	+	[https://www.uniprot.org/uniprot/NAGA_HUMAN NAGA_HUMAN] Hydrolyzes the N-glycolyl group from N-glycolylglucosamine 6-phosphate (GlcNGc-6-P) in the N-glycolylneuraminic acid (Neu5Gc) degradation pathway. Although human is not able to catalyze formation of Neu5Gc due to the inactive CMAHP enzyme, Neu5Gc is present in food and must be degraded.<ref>PMID:22692205</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: N-acetylglucosamine-6-phosphate deacetylase]]~~	+	[[Category: Baumann U]]
-	[[Category: Baumann, U]]	+	[[Category: Denzel MS]]
-	[[Category: Denzel~~, M S~~]]	+	[[Category: Kroef V]]
-	[[Category: Kroef, V]]	+	[[Category: Ruegenberg S]]
-	[[Category: Ruegenberg, S]]	+
-	~~[[Category: Amdhd2]]~~	+
-	~~[[Category: Amidohydrolase domain-containing protein 2]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Naga~~]]	+

OCA at 07:18, 16 March 2022

OCA — Wed, 16 Mar 2022 07:18:23 GMT

←Older revision		Revision as of 07:18, 16 March 2022
Line 3:		Line 3:
	<StructureSection load='7nuu' size='340' side='right'caption='[[7nuu]], [[Resolution\|resolution]] 1.84Å' scene=''>		<StructureSection load='7nuu' size='340' side='right'caption='[[7nuu]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7nuu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NUU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NUU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7nuu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NUU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NUU 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=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=GOL:GLYCEROL'>GOL</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">AMDHD2, CGI-14 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/N-acetylglucosamine-6-phosphate_deacetylase N-acetylglucosamine-6-phosphate deacetylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.25 3.5.1.25] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/N-acetylglucosamine-6-phosphate_deacetylase N-acetylglucosamine-6-phosphate deacetylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.25 3.5.1.25] </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=7nuu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nuu OCA], [https://pdbe.org/7nuu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nuu RCSB], [https://www.ebi.ac.uk/pdbsum/7nuu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nuu 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=7nuu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nuu OCA], [https://pdbe.org/7nuu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nuu RCSB], [https://www.ebi.ac.uk/pdbsum/7nuu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nuu ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/NAGA_HUMAN NAGA_HUMAN]] Hydrolyzes the N-glycolyl group from N-glycolylglucosamine 6-phosphate (GlcNGc-6-P) in the N-glycolylneuraminic acid (Neu5Gc) degradation pathway. Although human is not able to catalyze formation of Neu5Gc due to the inactive CMAHP enzyme, Neu5Gc is present in food and must be degraded.<ref>PMID:22692205</ref>		[[https://www.uniprot.org/uniprot/NAGA_HUMAN NAGA_HUMAN]] Hydrolyzes the N-glycolyl group from N-glycolylglucosamine 6-phosphate (GlcNGc-6-P) in the N-glycolylneuraminic acid (Neu5Gc) degradation pathway. Although human is not able to catalyze formation of Neu5Gc due to the inactive CMAHP enzyme, Neu5Gc is present in food and must be degraded.<ref>PMID:22692205</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The hexosamine biosynthetic pathway (HBP) produces the essential metabolite UDP-GlcNAc and plays a key role in metabolism, health, and aging. The HBP is controlled by its rate-limiting enzyme glutamine fructose-6-phosphate amidotransferase (GFPT/GFAT) that is directly inhibited by UDP-GlcNAc in a feedback loop. HBP regulation by GFPT is well studied but other HBP regulators have remained obscure. Elevated UDPGlcNAc levels counteract the glycosylation toxin tunicamycin (TM) and thus we screened for TM resistance in haploid mouse embryonic stem cells (mESCs) using random chemical mutagenesis to determine alternative HBP regulation. We identified the Nacetylglucosamine deacetylase AMDHD2 that catalyzes a reverse reaction in the HBP and its loss strongly elevated UDP-GlcNAc. To better understand AMDHD2, we solved the crystal structure and found that loss-of-function is caused by protein destabilization or interference with its catalytic activity. Finally, we show that mESCs express AMDHD2 together with GFPT2 instead of the more common paralog GFPT1. Compared with GFPT1, GFPT2 had a much lower sensitivity to UDP-GlcNAc inhibition, explaining how AMDHD2 loss-of-function resulted in HBP activation. This HBP configuration in which AMDHD2 serves to balance GFPT2 activity was also observed in other mESCs and, consistently, the GFPT2:GFPT1 ratio decreased with differentiation of human embryonic stem cells. Together, our data reveal a critical function of AMDHD2 in limiting UDPGlcNAc production in cells that use GFPT2 for metabolite entry into the HBP.
		+
		+	GFPT2/GFAT2 and AMDHD2 act in tandem to control the hexosamine pathway.,Kroef V, Ruegenberg S, Horn M, Allmeroth K, Ebert L, Bozkus S, Miethe S, Elling U, Schermer B, Baumann U, Denzel MS Elife. 2022 Mar 1;11. pii: 69223. doi: 10.7554/eLife.69223. PMID:35229715<ref>PMID:35229715</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7nuu" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: N-acetylglucosamine-6-phosphate deacetylase]]		[[Category: N-acetylglucosamine-6-phosphate deacetylase]]

OCA at 09:16, 5 May 2021

OCA — Wed, 05 May 2021 09:16:03 GMT

←Older revision		Revision as of 09:16, 5 May 2021
Line 1:		Line 1:

	==Crystal structure of human AMDHD2 in complex with Zn==		==Crystal structure of human AMDHD2 in complex with Zn==
-	<StructureSection load='7nuu' size='340' side='right'caption='[[7nuu]]' scene=''>	+	<StructureSection load='7nuu' size='340' side='right'caption='[[7nuu]], [[Resolution\|resolution]] 1.84Å' 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=7NUU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NUU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7nuu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NUU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NUU FirstGlance]. <br>
-	</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=7nuu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nuu OCA], [https://pdbe.org/7nuu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nuu RCSB], [https://www.ebi.ac.uk/pdbsum/7nuu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nuu 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=GOL:GLYCEROL'>GOL</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/N-acetylglucosamine-6-phosphate_deacetylase N-acetylglucosamine-6-phosphate deacetylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.25 3.5.1.25] </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=7nuu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nuu OCA], [https://pdbe.org/7nuu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nuu RCSB], [https://www.ebi.ac.uk/pdbsum/7nuu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nuu ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/NAGA_HUMAN NAGA_HUMAN]] Hydrolyzes the N-glycolyl group from N-glycolylglucosamine 6-phosphate (GlcNGc-6-P) in the N-glycolylneuraminic acid (Neu5Gc) degradation pathway. Although human is not able to catalyze formation of Neu5Gc due to the inactive CMAHP enzyme, Neu5Gc is present in food and must be degraded.<ref>PMID:22692205</ref>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Baumann U]]	+	[[Category: N-acetylglucosamine-6-phosphate deacetylase]]
-	[[Category: Denzel MS]]	+	[[Category: Baumann, U]]
-	[[Category: Kroef V]]	+	[[Category: Denzel, M S]]
-	[[Category: Ruegenberg S]]	+	[[Category: Kroef, V]]
		+	[[Category: Ruegenberg, S]]
		+	[[Category: Amdhd2]]
		+	[[Category: Amidohydrolase domain-containing protein 2]]
		+	[[Category: Hydrolase]]
		+	[[Category: Naga]]

OCA at 05:22, 28 April 2021

OCA — Wed, 28 Apr 2021 05:22:37 GMT

←Older revision		Revision as of 05:22, 28 April 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7nuu is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of human AMDHD2 in complex with Zn==
-		+	<StructureSection load='7nuu' size='340' side='right'caption='[[7nuu]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NUU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NUU FirstGlance]. <br>
-	~~Description~~:	+	</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=7nuu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nuu OCA], [https://pdbe.org/7nuu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nuu RCSB], [https://www.ebi.ac.uk/pdbsum/7nuu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nuu ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Baumann U]]
		+	[[Category: Denzel MS]]
		+	[[Category: Kroef V]]
		+	[[Category: Ruegenberg S]]

OCA: Protected "7nuu" [edit=sysop:move=sysop]

OCA — Wed, 24 Mar 2021 05:38:48 GMT

Protected "7nuu" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:38, 24 March 2021

OCA: New page: '''Unreleased structure''' The entry 7nuu is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 24 Mar 2021 05:38:47 GMT

New page: '''Unreleased structure''' The entry 7nuu is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7nuu is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]