6bw5 - Revision history

OCA at 14:51, 4 October 2023

OCA — Wed, 04 Oct 2023 14:51:22 GMT

←Older revision		Revision as of 14:51, 4 October 2023
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	<StructureSection load='6bw5' size='340' side='right'caption='[[6bw5]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='6bw5' size='340' side='right'caption='[[6bw5]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bw5]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BW5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6BW5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bw5]] is a 4 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=6BW5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BW5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PGW:(1R)-2-{[(S)-{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(HEXADECANOYLOXY)METHYL]ETHYL+(9Z)-OCTADEC-9-ENOATE'>PGW</scene>, <scene name='pdbligand=TUM:TUNICAMYCIN'>TUM</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]] 3.1Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DPAGT1, DPAGT2 ([http://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=PGW:(1R)-2-{[(S)-{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(HEXADECANOYLOXY)METHYL]ETHYL+(9Z)-OCTADEC-9-ENOATE'>PGW</scene>, <scene name='pdbligand=TUM:TUNICAMYCIN'>TUM</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylglucosamine--dolichyl-phosphate_N-acetylglucosaminephosphotransferase UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.8.15 2.7.8.15] </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=6bw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bw5 OCA], [https://pdbe.org/6bw5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bw5 RCSB], [https://www.ebi.ac.uk/pdbsum/6bw5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bw5 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=6bw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bw5 OCA], [~~http~~://pdbe.org/6bw5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6bw5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6bw5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6bw5 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/GPT_HUMAN GPT_HUMAN]] DPAGT1-CDG;Congenital myasthenic syndromes with glycosylation defect. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.	+	[https://www.uniprot.org/uniprot/GPT_HUMAN GPT_HUMAN] DPAGT1-CDG;Congenital myasthenic syndromes with glycosylation defect. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GPT_HUMAN GPT_HUMAN]] Catalyzes the initial step in the synthesis of dolichol-P-P-oligosaccharides.	+	[https://www.uniprot.org/uniprot/GPT_HUMAN GPT_HUMAN] Catalyzes the initial step in the synthesis of dolichol-P-P-oligosaccharides.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase]]~~	+	[[Category: Kuk ACY]]
-	[[Category: Kuk~~, A C.Y~~]]	+	[[Category: Lee S-Y]]
-	[[Category: Lee, S Y]]	+	[[Category: Mashalidis EH]]
-	[[Category: Mashalidis~~, E H~~]]	+	[[Category: Yoo J]]
-	[[Category: Yoo, J]]	+
-	~~[[Category: Endoplasmic reticulum]]~~	+
-	~~[[Category: N-linked glycosylation]]~~	+
-	~~[[Category: Natural product]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Transferase-antibiotic complex]]~~	+
-	~~[[Category: Tunicamycin~~]]	+

OCA at 09:24, 18 December 2019

OCA — Wed, 18 Dec 2019 09:24:31 GMT

←Older revision		Revision as of 09:24, 18 December 2019
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	==Human GPT (DPAGT1) in complex with tunicamycin==		==Human GPT (DPAGT1) in complex with tunicamycin==
-	<StructureSection load='6bw5' size='340' side='right' caption='[[6bw5]], [[Resolution\|resolution]] 3.10Å' scene=''>	+	<StructureSection load='6bw5' size='340' side='right'caption='[[6bw5]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6bw5]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BW5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BW5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6bw5]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BW5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BW5 FirstGlance]. <br>
Line 27:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase]]		[[Category: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase]]
	[[Category: Kuk, A C.Y]]		[[Category: Kuk, A C.Y]]

OCA at 07:04, 14 March 2018

OCA — Wed, 14 Mar 2018 07:04:04 GMT

←Older revision		Revision as of 07:04, 14 March 2018
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/GPT_HUMAN GPT_HUMAN]] Catalyzes the initial step in the synthesis of dolichol-P-P-oligosaccharides.		[[http://www.uniprot.org/uniprot/GPT_HUMAN GPT_HUMAN]] Catalyzes the initial step in the synthesis of dolichol-P-P-oligosaccharides.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	N-linked glycosylation is a predominant post-translational modification of protein in eukaryotes, and its dysregulation is the etiology of several human disorders. The enzyme UDP-N-acetylglucosamine:dolichyl-phosphate N-acetylglucosaminephosphotransferase (GlcNAc-1-P-transferase or GPT) catalyzes the first and committed step of N-linked glycosylation in the endoplasmic reticulum membrane, and it is the target of the natural product tunicamycin. Tunicamycin has potent antibacterial activity, inhibiting the bacterial cell wall synthesis enzyme MraY, but its usefulness as an antibiotic is limited by off-target inhibition of human GPT. Our understanding of how tunicamycin inhibits N-linked glycosylation and efforts to selectively target MraY are hampered by a lack of structural information. Here we present crystal structures of human GPT in complex with tunicamycin. Structural and functional analyses reveal the difference between GPT and MraY in their mechanisms of inhibition by tunicamycin. We demonstrate that this difference could be exploited to design MraY-specific inhibitors as potential antibiotics.
		+
		+	GlcNAc-1-P-transferase-tunicamycin complex structure reveals basis for inhibition of N-glycosylation.,Yoo J, Mashalidis EH, Kuk ACY, Yamamoto K, Kaeser B, Ichikawa S, Lee SY Nat Struct Mol Biol. 2018 Mar;25(3):217-224. doi: 10.1038/s41594-018-0031-y. Epub, 2018 Feb 19. PMID:29459785<ref>PMID:29459785</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6bw5" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:16, 28 February 2018

OCA — Wed, 28 Feb 2018 07:16:54 GMT

←Older revision		Revision as of 07:16, 28 February 2018
Line 3:		Line 3:
	<StructureSection load='6bw5' size='340' side='right' caption='[[6bw5]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='6bw5' size='340' side='right' caption='[[6bw5]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bw5]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BW5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BW5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bw5]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BW5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BW5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PGW:(1R)-2-{[(S)-{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(HEXADECANOYLOXY)METHYL]ETHYL+(9Z)-OCTADEC-9-ENOATE'>PGW</scene>, <scene name='pdbligand=TUM:TUNICAMYCIN'>TUM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PGW:(1R)-2-{[(S)-{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(HEXADECANOYLOXY)METHYL]ETHYL+(9Z)-OCTADEC-9-ENOATE'>PGW</scene>, <scene name='pdbligand=TUM:TUNICAMYCIN'>TUM</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DPAGT1, DPAGT2 ([http://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'>[http://en.wikipedia.org/wiki/UDP-N-acetylglucosamine--dolichyl-phosphate_N-acetylglucosaminephosphotransferase UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.8.15 2.7.8.15] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylglucosamine--dolichyl-phosphate_N-acetylglucosaminephosphotransferase UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.8.15 2.7.8.15] </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=6bw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bw5 OCA], [http://pdbe.org/6bw5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bw5 RCSB], [http://www.ebi.ac.uk/pdbsum/6bw5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bw5 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=6bw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bw5 OCA], [http://pdbe.org/6bw5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bw5 RCSB], [http://www.ebi.ac.uk/pdbsum/6bw5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bw5 ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase]]		[[Category: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase]]
	[[Category: Kuk, A C.Y]]		[[Category: Kuk, A C.Y]]

OCA at 07:28, 22 February 2018

OCA — Thu, 22 Feb 2018 07:28:37 GMT

←Older revision		Revision as of 07:28, 22 February 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6bw5 is ~~ON HOLD~~ ~~until Paper Publication~~	+	==Human GPT (DPAGT1) in complex with tunicamycin==
-		+	<StructureSection load='6bw5' size='340' side='right' caption='[[6bw5]], [[Resolution\|resolution]] 3.10Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6bw5]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BW5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BW5 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PGW:(1R)-2-{[(S)-{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(HEXADECANOYLOXY)METHYL]ETHYL+(9Z)-OCTADEC-9-ENOATE'>PGW</scene>, <scene name='pdbligand=TUM:TUNICAMYCIN'>TUM</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylglucosamine--dolichyl-phosphate_N-acetylglucosaminephosphotransferase UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.8.15 2.7.8.15] </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=6bw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bw5 OCA], [http://pdbe.org/6bw5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bw5 RCSB], [http://www.ebi.ac.uk/pdbsum/6bw5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bw5 ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/GPT_HUMAN GPT_HUMAN]] DPAGT1-CDG;Congenital myasthenic syndromes with glycosylation defect. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GPT_HUMAN GPT_HUMAN]] Catalyzes the initial step in the synthesis of dolichol-P-P-oligosaccharides.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase]]
		+	[[Category: Kuk, A C.Y]]
		+	[[Category: Lee, S Y]]
		+	[[Category: Mashalidis, E H]]
		+	[[Category: Yoo, J]]
		+	[[Category: Endoplasmic reticulum]]
		+	[[Category: N-linked glycosylation]]
		+	[[Category: Natural product]]
		+	[[Category: Transferase]]
		+	[[Category: Transferase-antibiotic complex]]
		+	[[Category: Tunicamycin]]

OCA at 07:18, 27 December 2017

OCA — Wed, 27 Dec 2017 07:18:57 GMT

←Older revision		Revision as of 07:18, 27 December 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6bw5 is ON HOLD	+	The entry 6bw5 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6bw5" [edit=sysop:move=sysop]

OCA — Wed, 20 Dec 2017 05:05:17 GMT

Protected "6bw5" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:05, 20 December 2017

OCA: New page: '''Unreleased structure''' The entry 6bw5 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 20 Dec 2017 05:05:16 GMT

New page: '''Unreleased structure''' The entry 6bw5 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6bw5 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]