4m4k - Revision history

OCA at 16:31, 20 September 2023

OCA — Wed, 20 Sep 2023 16:31:40 GMT

←Older revision		Revision as of 16:31, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4m4k]] 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=4M4K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4M4K FirstGlance]. <br>		<table><tr><td colspan='2'>[[4m4k]] 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=4M4K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4M4K FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GDU:GALACTOSE-URIDINE-5-DIPHOSPHATE'>GDU</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PRD_900116:4beta-beta-xylobiose'>PRD_900116</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</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]] 2.2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GDU:GALACTOSE-URIDINE-5-DIPHOSPHATE'>GDU</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PRD_900116:4beta-beta-xylobiose'>PRD_900116</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></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=4m4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m4k OCA], [https://pdbe.org/4m4k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4m4k RCSB], [https://www.ebi.ac.uk/pdbsum/4m4k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4m4k 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=4m4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m4k OCA], [https://pdbe.org/4m4k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4m4k RCSB], [https://www.ebi.ac.uk/pdbsum/4m4k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4m4k ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:54, 21 December 2022

OCA — Wed, 21 Dec 2022 10:54:49 GMT

←Older revision		Revision as of 10:54, 21 December 2022
Line 1:		Line 1:

	==Crystal structure of the Drosphila beta,14galactosyltransferase 7 mutant D211N complex with manganese, UDP-Gal and xylobiose==		==Crystal structure of the Drosphila beta,14galactosyltransferase 7 mutant D211N complex with manganese, UDP-Gal and xylobiose==
-	<StructureSection load='4m4k' size='340' side='right' caption='[[4m4k]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='4m4k' size='340' side='right'caption='[[4m4k]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4m4k]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Drome Drome~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M4K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4M4K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4m4k]] 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=4M4K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4M4K FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GDU:GALACTOSE-URIDINE-5-DIPHOSPHATE'>GDU</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=~~XYP~~:~~BETA~~-D-~~XYLOPYRANOSE~~'>~~XYP~~</scene><~~/td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GDU:GALACTOSE-URIDINE-5-DIPHOSPHATE'>GDU</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PRD_900116:4beta-beta-xylobiose'>PRD_900116</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat">[[4lw3\|4lw3]], [[4lw6\|4lw6]]</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=4m4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m4k OCA], [https://pdbe.org/4m4k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4m4k RCSB], [https://www.ebi.ac.uk/pdbsum/4m4k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4m4k ProSAT]</span></td></tr>
-	~~<tr id='gene~~'>~~<td class="sblockLbl"><b>[[Gene\|Gene:]]~~</b></td><td class="sblockDat">4galactosyltransferase 7, beta-4GalT7, beta1, beta4GalT7, beta4GalT7-RA, CG11780, Dmel_CG11780 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</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=4m4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m4k OCA], [~~http~~://pdbe.org/4m4k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4m4k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4m4k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4m4k ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9VBZ9_DROME Q9VBZ9_DROME]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4m4k" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4m4k" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Glycosyltransferase 3D structures\|Glycosyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Drome~~]]	+	[[Category: Drosophila melanogaster]]
-	[[Category: ~~Qasba, P K~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Ramakrishnan, B~~]]	+	[[Category: Qasba PK]]
-	[[Category: ~~Golgi]]~~	+	[[Category: Ramakrishnan B]]
-	~~[[Category: Gt-a glycosyltransferase family]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Udp-gal and xylose~~]]	+

OCA at 16:49, 11 August 2016

OCA — Thu, 11 Aug 2016 16:49:31 GMT

←Older revision		Revision as of 16:49, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the Drosphila beta,14galactosyltransferase 7 mutant D211N complex with manganese, UDP-Gal and xylobiose==		==Crystal structure of the Drosphila beta,14galactosyltransferase 7 mutant D211N complex with manganese, UDP-Gal and xylobiose==
	<StructureSection load='4m4k' size='340' side='right' caption='[[4m4k]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='4m4k' size='340' side='right' caption='[[4m4k]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4lw3\|4lw3]], [[4lw6\|4lw6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4lw3\|4lw3]], [[4lw6\|4lw6]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">4galactosyltransferase 7, beta-4GalT7, beta1, beta4GalT7, beta4GalT7-RA, CG11780, Dmel_CG11780 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">4galactosyltransferase 7, beta-4GalT7, beta1, beta4GalT7, beta4GalT7-RA, CG11780, Dmel_CG11780 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</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=4m4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m4k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4m4k RCSB], [http://www.ebi.ac.uk/pdbsum/4m4k 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=4m4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m4k OCA], [http://pdbe.org/4m4k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4m4k RCSB], [http://www.ebi.ac.uk/pdbsum/4m4k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4m4k ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 4m4k" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:11, 5 January 2015

OCA — Mon, 05 Jan 2015 09:11:24 GMT

←Older revision		Revision as of 09:11, 5 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4m4k\| PDB=4m4k \| SCENE= }}~~	+	==Crystal structure of the Drosphila beta,14galactosyltransferase 7 mutant D211N complex with manganese, UDP-Gal and xylobiose==
-	===Crystal structure of the Drosphila beta,14galactosyltransferase 7 mutant D211N complex with manganese, UDP-Gal and xylobiose===	+	<StructureSection load='4m4k' size='340' side='right' caption='[[4m4k]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24052259}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4m4k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M4K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4M4K FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GDU:GALACTOSE-URIDINE-5-DIPHOSPHATE'>GDU</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4lw3\|4lw3]], [[4lw6\|4lw6]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">4galactosyltransferase 7, beta-4GalT7, beta1, beta4GalT7, beta4GalT7-RA, CG11780, Dmel_CG11780 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</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=4m4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m4k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4m4k RCSB], [http://www.ebi.ac.uk/pdbsum/4m4k PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The beta-1,4-galactosyltransferase 7 (beta4GalT7) enzyme is involved in proteoglycan synthesis. In the presence of a manganese ion, it transfers galactose from UDP-galactose to xylose on a proteoglycan acceptor substrate. We present here the crystal structures of human beta4GalT7 in open and closed conformations. A comparison of these crystal structures shows that, upon manganese and UDP or UDP-Gal binding, the enzyme undergoes conformational changes involving a small and a long loop. We also present the crystal structures of Drosophila wild-type beta4GalT7 and D211N beta4GalT7 mutant enzymes in the closed conformation in the presence of the acceptor substrate xylobiose and the donor substrate UDP-Gal, respectively. To understand the catalytic mechanism, we have crystallized the ternary complex of D211N beta4GalT7 mutant enzyme in the presence of manganese with the donor and the acceptor substrates together in the same crystal structure. The galactose moiety of the bound UDP-Gal molecule forms seven hydrogen bonds with the protein molecule. The nonreducing end of the xylose moiety of xylobiose binds to the hydrophobic acceptor sugar binding pocket created by the conformational changes, whereas its extended xylose moiety forms hydrophobic interactions with a Tyr residue. In the ternary complex crystal structure, the nucleophile O4 oxygen atom of the xylose molecule is found in close proximity to the C1 and O5 atoms of the galactose moiety. This is the first time that a Michaelis complex of a glycosyltransferase has been described, and it clearly suggests an SN2 type catalytic mechanism for the beta4GalT7 enzyme.

-	~~==About this Structure==~~	+	Crystal Structures of beta-1,4-Galactosyltransferase 7 Enzyme Reveal Conformational Changes and Substrate Binding.,Tsutsui Y, Ramakrishnan B, Qasba PK J Biol Chem. 2013 Nov 1;288(44):31963-70. doi: 10.1074/jbc.M113.509984. Epub 2013, Sep 19. PMID:24052259<ref>PMID:24052259</ref>
-	~~[[4m4k]] is a~~ 1 ~~chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Drome Drome]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.~~il/oca-bin/ocashort?id=4M4K OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024052259</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Drome]]		[[Category: Drome]]
-	[[Category: Qasba, P K.]]	+	[[Category: Qasba, P K]]
-	[[Category: Ramakrishnan, B.]]	+	[[Category: Ramakrishnan, B]]
	[[Category: Golgi]]		[[Category: Golgi]]
	[[Category: Gt-a glycosyltransferase family]]		[[Category: Gt-a glycosyltransferase family]]
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Udp-gal and xylose]]		[[Category: Udp-gal and xylose]]

OCA at 08:33, 27 November 2013

OCA — Wed, 27 Nov 2013 08:33:35 GMT

←Older revision		Revision as of 08:33, 27 November 2013
Line 1:		Line 1:
	{{STRUCTURE_4m4k\| PDB=4m4k \| SCENE= }}		{{STRUCTURE_4m4k\| PDB=4m4k \| SCENE= }}
	===Crystal structure of the Drosphila beta,14galactosyltransferase 7 mutant D211N complex with manganese, UDP-Gal and xylobiose===		===Crystal structure of the Drosphila beta,14galactosyltransferase 7 mutant D211N complex with manganese, UDP-Gal and xylobiose===
		+	{{ABSTRACT_PUBMED_24052259}}

	==About this Structure==		==About this Structure==
-	[[4m4k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Drosophila_melanogaster Drosophila melanogaster~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M4K OCA].	+	[[4m4k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M4K OCA].
-	[[Category: ~~Drosophila melanogaster~~]]	+
		+	==Reference==
		+	<ref group="xtra">PMID:024052259</ref><references group="xtra"/><references/>
		+	[[Category: Drome]]
	[[Category: Qasba, P K.]]		[[Category: Qasba, P K.]]
	[[Category: Ramakrishnan, B.]]		[[Category: Ramakrishnan, B.]]

OCA at 08:21, 29 September 2013

OCA — Sun, 29 Sep 2013 08:21:04 GMT

←Older revision		Revision as of 08:21, 29 September 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4m4k\| PDB=4m4k \| SCENE= }}
		+	===Crystal structure of the Drosphila beta,14galactosyltransferase 7 mutant D211N complex with manganese, UDP-Gal and xylobiose===

-	~~The entry~~ 4m4k is ~~ON HOLD~~	+	==About this Structure==
-		+	[[4m4k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M4K OCA].
-	~~Authors~~: ~~Ramakrishnan, B.,~~ Qasba, P.K.	+	[[Category: Drosophila melanogaster]]
-		+	[[Category: Qasba, P K.]]
-	~~Description~~: ~~Crystal structure of the Drosphila beta~~,~~14galactosyltransferase 7 mutant D211N complex with manganese, UDP~~-~~Gal~~ and ~~xylobiose~~	+	[[Category: Ramakrishnan, B.]]
		+	[[Category: Golgi]]
		+	[[Category: Gt-a glycosyltransferase family]]
		+	[[Category: Transferase]]
		+	[[Category: Udp-gal and xylose]]

OCA: Protected "4m4k" [edit=sysop:move=sysop]

OCA — Wed, 14 Aug 2013 07:26:14 GMT

Protected "4m4k" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:26, 14 August 2013

OCA: New page: '''Unreleased structure''' The entry 4m4k is ON HOLD Authors: Ramakrishnan, B., Qasba, P.K. Description: Crystal structure of the Drosphila beta,14galactosyltransferase 7 mutant D211N ...

OCA — Wed, 14 Aug 2013 07:26:13 GMT

New page: '''Unreleased structure''' The entry 4m4k is ON HOLD Authors: Ramakrishnan, B., Qasba, P.K. Description: Crystal structure of the Drosphila beta,14galactosyltransferase 7 mutant D211N ...

New page

'''Unreleased structure'''

The entry 4m4k is ON HOLD

Authors: Ramakrishnan, B., Qasba, P.K.

Description: Crystal structure of the Drosphila beta,14galactosyltransferase 7 mutant D211N complex with manganese, UDP-Gal and xylobiose