5zoi - Revision history

OCA at 10:28, 27 March 2024

OCA — Wed, 27 Mar 2024 10:28:46 GMT

←Older revision		Revision as of 10:28, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5zoi' size='340' side='right'caption='[[5zoi]], [[Resolution\|resolution]] 3.19Å' scene=''>		<StructureSection load='5zoi' size='340' side='right'caption='[[5zoi]], [[Resolution\|resolution]] 3.19Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zoi]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_43504 Atcc 43504~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZOI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZOI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zoi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZOI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZOI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C06:[[(2S,3R,4S,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2S,3S,4S,5R,6R)-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]+hydrogen+phosphate'>C06</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]] 3.19Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fucT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 ATCC 43504])</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C06:[[(2S,3R,4S,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2S,3S,4S,5R,6R)-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]+hydrogen+phosphate'>C06</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-galactosyl-N-acetylglucosaminide_3-alpha-L-fucosyltransferase 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.152 2.4.1.152] </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=5zoi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zoi OCA], [https://pdbe.org/5zoi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zoi RCSB], [https://www.ebi.ac.uk/pdbsum/5zoi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zoi 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=5zoi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zoi OCA], [~~http~~://pdbe.org/5zoi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zoi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zoi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zoi ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/FUCT_HELPX FUCT_HELPX]] Involved in the biosynthesis of the Lewis X (LeX) trisaccharide of the lipopolysaccharide (LPS) O-antigen. Catalyzes the addition of fucose in alpha 1-3 linkage to Gal-beta-1-4-GlcNAc-beta-O-R (LacNAc-R) type II acceptor.<ref>PMID:12676935</ref> <ref>PMID:16150700</ref> <ref>PMID:16800635</ref> <ref>PMID:17251184</ref> <ref>PMID:9261149</ref>	+	[https://www.uniprot.org/uniprot/FUCT_HELPX FUCT_HELPX] Involved in the biosynthesis of the Lewis X (LeX) trisaccharide of the lipopolysaccharide (LPS) O-antigen. Catalyzes the addition of fucose in alpha 1-3 linkage to Gal-beta-1-4-GlcNAc-beta-O-R (LacNAc-R) type II acceptor.<ref>PMID:12676935</ref> <ref>PMID:16150700</ref> <ref>PMID:16800635</ref> <ref>PMID:17251184</ref> <ref>PMID:9261149</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Fucosylated glycoconjugates are involved in a variety of physiological and pathological processes. However, economical production of fucosylated drugs and prebiotic supplements has been hampered by the poor catalytic efficiency of fucosyltransferases. Here, we developed a fluorescence-activated cell sorting system that enables the ultrahigh-throughput screening (>10(7) mutants/hour) of such enzymes and designed a companion strategy to assess the screening performance of the system. After three rounds of directed evolution, a mutant M32 of the alpha1,3-FucT from Helicobacter pylori was identified with 6- and 14-fold increases in catalytic efficiency (k cat/K m) for the synthesis of Lewis x and 3'-fucosyllactose, respectively. The structure of the M32 mutant revealed that the S45F mutation generates a clamp-like structure that appears to improve binding of the galactopyranose ring of the acceptor substrate. Moreover, molecular dynamic simulations reveal that helix alpha5, is more mobile in the M32 mutant, possibly explaining its high fucosylation activity.	+
-		+
-	Directed evolution of an alpha1,3-fucosyltransferase using a single-cell ultrahigh-throughput screening method.,Tan Y, Zhang Y, Han Y, Liu H, Chen H, Ma F, Withers SG, Feng Y, Yang G Sci Adv. 2019 Oct 9;5(10):eaaw8451. doi: 10.1126/sciadv.aaw8451. eCollection 2019, Oct. PMID:31633018<ref>PMID:31633018</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5zoi" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase]]~~	+	[[Category: Helicobacter pylori]]
-	~~[[Category: Atcc 43504~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Tan, Y]]	+	[[Category: Tan Y]]
-	[[Category: Yang, G]]	+	[[Category: Yang G]]
-	~~[[Category: Enzyme]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 16:30, 22 January 2020

OCA — Wed, 22 Jan 2020 16:30:24 GMT

←Older revision		Revision as of 16:30, 22 January 2020
Line 3:		Line 3:
	<StructureSection load='5zoi' size='340' side='right'caption='[[5zoi]], [[Resolution\|resolution]] 3.19Å' scene=''>		<StructureSection load='5zoi' size='340' side='right'caption='[[5zoi]], [[Resolution\|resolution]] 3.19Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zoi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZOI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZOI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zoi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43504 Atcc 43504]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZOI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZOI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C06:[[(2S,3R,4S,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2S,3S,4S,5R,6R)-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]+hydrogen+phosphate'>C06</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C06:[[(2S,3R,4S,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2S,3S,4S,5R,6R)-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]+hydrogen+phosphate'>C06</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fucT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 ATCC 43504])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-galactosyl-N-acetylglucosaminide_3-alpha-L-fucosyltransferase 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.152 2.4.1.152] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-galactosyl-N-acetylglucosaminide_3-alpha-L-fucosyltransferase 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.152 2.4.1.152] </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=5zoi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zoi OCA], [http://pdbe.org/5zoi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zoi RCSB], [http://www.ebi.ac.uk/pdbsum/5zoi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zoi 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=5zoi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zoi OCA], [http://pdbe.org/5zoi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zoi RCSB], [http://www.ebi.ac.uk/pdbsum/5zoi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zoi ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/FUCT_HELPX FUCT_HELPX]] Involved in the biosynthesis of the Lewis X (LeX) trisaccharide of the lipopolysaccharide (LPS) O-antigen. Catalyzes the addition of fucose in alpha 1-3 linkage to Gal-beta-1-4-GlcNAc-beta-O-R (LacNAc-R) type II acceptor.<ref>PMID:12676935</ref> <ref>PMID:16150700</ref> <ref>PMID:16800635</ref> <ref>PMID:17251184</ref> <ref>PMID:9261149</ref>		[[http://www.uniprot.org/uniprot/FUCT_HELPX FUCT_HELPX]] Involved in the biosynthesis of the Lewis X (LeX) trisaccharide of the lipopolysaccharide (LPS) O-antigen. Catalyzes the addition of fucose in alpha 1-3 linkage to Gal-beta-1-4-GlcNAc-beta-O-R (LacNAc-R) type II acceptor.<ref>PMID:12676935</ref> <ref>PMID:16150700</ref> <ref>PMID:16800635</ref> <ref>PMID:17251184</ref> <ref>PMID:9261149</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Fucosylated glycoconjugates are involved in a variety of physiological and pathological processes. However, economical production of fucosylated drugs and prebiotic supplements has been hampered by the poor catalytic efficiency of fucosyltransferases. Here, we developed a fluorescence-activated cell sorting system that enables the ultrahigh-throughput screening (>10(7) mutants/hour) of such enzymes and designed a companion strategy to assess the screening performance of the system. After three rounds of directed evolution, a mutant M32 of the alpha1,3-FucT from Helicobacter pylori was identified with 6- and 14-fold increases in catalytic efficiency (k cat/K m) for the synthesis of Lewis x and 3'-fucosyllactose, respectively. The structure of the M32 mutant revealed that the S45F mutation generates a clamp-like structure that appears to improve binding of the galactopyranose ring of the acceptor substrate. Moreover, molecular dynamic simulations reveal that helix alpha5, is more mobile in the M32 mutant, possibly explaining its high fucosylation activity.
		+
		+	Directed evolution of an alpha1,3-fucosyltransferase using a single-cell ultrahigh-throughput screening method.,Tan Y, Zhang Y, Han Y, Liu H, Chen H, Ma F, Withers SG, Feng Y, Yang G Sci Adv. 2019 Oct 9;5(10):eaaw8451. doi: 10.1126/sciadv.aaw8451. eCollection 2019, Oct. PMID:31633018<ref>PMID:31633018</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5zoi" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 15:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase]]		[[Category: 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase]]
		+	[[Category: Atcc 43504]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Tan, Y]]		[[Category: Tan, Y]]

OCA at 06:41, 26 June 2019

OCA — Wed, 26 Jun 2019 06:41:41 GMT

←Older revision		Revision as of 06:41, 26 June 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zoi is ~~ON HOLD until Jun 22 2020~~	+	==Crystal Structure of alpha1,3-Fucosyltransferase==
-		+	<StructureSection load='5zoi' size='340' side='right'caption='[[5zoi]], [[Resolution\|resolution]] 3.19Å' scene=''>
-	~~Authors~~: ~~Tan~~, Y., ~~Yang~~, G.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5zoi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZOI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZOI FirstGlance]. <br>
-	~~Description~~: ~~Crystal Structure~~ of ~~alpha1,~~3-~~Fucosyltransferase~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C06:[[(2S,3R,4S,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2S,3S,4S,5R,6R)-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]+hydrogen+phosphate'>C06</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/4-galactosyl-N-acetylglucosaminide_3-alpha-L-fucosyltransferase 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.152 2.4.1.152] </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=5zoi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zoi OCA], [http://pdbe.org/5zoi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zoi RCSB], [http://www.ebi.ac.uk/pdbsum/5zoi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zoi ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/FUCT_HELPX FUCT_HELPX]] Involved in the biosynthesis of the Lewis X (LeX) trisaccharide of the lipopolysaccharide (LPS) O-antigen. Catalyzes the addition of fucose in alpha 1-3 linkage to Gal-beta-1-4-GlcNAc-beta-O-R (LacNAc-R) type II acceptor.<ref>PMID:12676935</ref> <ref>PMID:16150700</ref> <ref>PMID:16800635</ref> <ref>PMID:17251184</ref> <ref>PMID:9261149</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase]]
		+	[[Category: Large Structures]]
	[[Category: Tan, Y]]		[[Category: Tan, Y]]
	[[Category: Yang, G]]		[[Category: Yang, G]]
		+	[[Category: Enzyme]]
		+	[[Category: Transferase]]

OCA at 20:52, 5 June 2019

OCA — Wed, 05 Jun 2019 20:52:45 GMT

←Older revision		Revision as of 20:52, 5 June 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zoi is ON HOLD	+	The entry 5zoi is ON HOLD until Jun 22 2020

	Authors: Tan, Y., Yang, G.		Authors: Tan, Y., Yang, G.

OCA at 03:51, 25 April 2018

OCA — Wed, 25 Apr 2018 03:51:23 GMT

←Older revision		Revision as of 03:51, 25 April 2018
Line 3:		Line 3:
	The entry 5zoi is ON HOLD		The entry 5zoi is ON HOLD

-	Authors: ~~Yumeng~~, T., ~~Guangyu~~, Y.	+	Authors: Tan, Y., Yang, G.

	Description: Crystal Structure of alpha1,3-Fucosyltransferase		Description: Crystal Structure of alpha1,3-Fucosyltransferase
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Guangyu~~, Y]]	+	[[Category: Tan, Y]]
-	[[Category: ~~Yumeng~~, T]]	+	[[Category: Yang, G]]

OCA: Protected "5zoi" [edit=sysop:move=sysop]

OCA — Wed, 18 Apr 2018 04:08:02 GMT

Protected "5zoi" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:08, 18 April 2018

OCA: New page: '''Unreleased structure''' The entry 5zoi is ON HOLD Authors: Yumeng, T., Guangyu, Y. Description: Crystal Structure of alpha1,3-Fucosyltransferase Category: Unreleased Structures ...

OCA — Wed, 18 Apr 2018 04:08:01 GMT

New page: '''Unreleased structure''' The entry 5zoi is ON HOLD Authors: Yumeng, T., Guangyu, Y. Description: Crystal Structure of alpha1,3-Fucosyltransferase Category: Unreleased Structures ...

New page

'''Unreleased structure'''

The entry 5zoi is ON HOLD

Authors: Yumeng, T., Guangyu, Y.

Description: Crystal Structure of alpha1,3-Fucosyltransferase
[[Category: Unreleased Structures]]
[[Category: Guangyu, Y]]
[[Category: Yumeng, T]]