6k0i - Revision history

OCA at 10:23, 22 November 2023

OCA — Wed, 22 Nov 2023 10:23:56 GMT

←Older revision		Revision as of 10:23, 22 November 2023
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	<StructureSection load='6k0i' size='340' side='right'caption='[[6k0i]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6k0i' size='340' side='right'caption='[[6k0i]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k0i]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bifl2 Bifl2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K0I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6K0I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k0i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_longum_subsp._longum_JCM_1217 Bifidobacterium longum subsp. longum JCM 1217]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K0I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K0I FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=NAD:NICOTINAMIDE~~-~~ADENINE-DINUCLEOTIDE'>NAD</scene>~~, ~~<scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</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]] 1.8Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>galE, lnpD, BLLJ_1620 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~565042 BIFL2])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</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~~-~~glucose_4~~-~~epimerase UDP~~-~~glucose 4-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.2 5.1.3.2]~~ </~~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=6k0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0i OCA], [https://pdbe.org/6k0i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k0i RCSB], [https://www.ebi.ac.uk/pdbsum/6k0i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0i 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=6k0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0i OCA], [~~http~~://pdbe.org/6k0i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6k0i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6k0i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0i ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GALE_BIFL2 GALE_BIFL2]] Involved in the metabolism of galactose. Catalyzes the conversion of UDP-galactose (UDP-Gal) to UDP-glucose (UDP-Glc) through a mechanism involving the transient reduction of NAD. Can also epimerize UDP-GalNAc to UDP-GlcNAc. Involved in the lacto-N-biose I/galacto-N-biose (LNB/GNB) degradation pathway, which is important for host intestinal colonization by bifidobacteria.<ref>PMID:17720833</ref>	+	[https://www.uniprot.org/uniprot/GALE_BIFL2 GALE_BIFL2] Involved in the metabolism of galactose. Catalyzes the conversion of UDP-galactose (UDP-Gal) to UDP-glucose (UDP-Glc) through a mechanism involving the transient reduction of NAD. Can also epimerize UDP-GalNAc to UDP-GlcNAc. Involved in the lacto-N-biose I/galacto-N-biose (LNB/GNB) degradation pathway, which is important for host intestinal colonization by bifidobacteria.<ref>PMID:17720833</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6k0i" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6k0i" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[UDP-galactose 4-epimerase\|UDP-galactose 4-epimerase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bifl2~~]]	+	[[Category: Bifidobacterium longum subsp. longum JCM 1217]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: UDP-glucose 4-epimerase]]~~	+	[[Category: Arakawa T]]
-	[[Category: Arakawa, T]]	+	[[Category: Fushinobu S]]
-	[[Category: Fushinobu, S]]	+	[[Category: Kitaoka M]]
-	[[Category: Kitaoka, M]]	+	[[Category: Nam Y-W]]
-	[[Category: Nam, Y W]]	+	[[Category: Nishimoto M]]
-	[[Category: Nishimoto, M]]	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Rossmann fold~~]]	+

OCA at 17:23, 14 August 2019

OCA — Wed, 14 Aug 2019 17:23:14 GMT

←Older revision		Revision as of 17:23, 14 August 2019
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	<StructureSection load='6k0i' size='340' side='right'caption='[[6k0i]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6k0i' size='340' side='right'caption='[[6k0i]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k0i]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K0I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K0I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k0i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bifl2 Bifl2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K0I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K0I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">galE, lnpD, BLLJ_1620 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=565042 BIFL2])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-glucose_4-epimerase UDP-glucose 4-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.2 5.1.3.2] </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-glucose_4-epimerase UDP-glucose 4-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.2 5.1.3.2] </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=6k0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0i OCA], [http://pdbe.org/6k0i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k0i RCSB], [http://www.ebi.ac.uk/pdbsum/6k0i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0i 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=6k0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0i OCA], [http://pdbe.org/6k0i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k0i RCSB], [http://www.ebi.ac.uk/pdbsum/6k0i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0i ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/GALE_BIFL2 GALE_BIFL2]] Involved in the metabolism of galactose. Catalyzes the conversion of UDP-galactose (UDP-Gal) to UDP-glucose (UDP-Glc) through a mechanism involving the transient reduction of NAD. Can also epimerize UDP-GalNAc to UDP-GlcNAc. Involved in the lacto-N-biose I/galacto-N-biose (LNB/GNB) degradation pathway, which is important for host intestinal colonization by bifidobacteria.<ref>PMID:17720833</ref>		[[http://www.uniprot.org/uniprot/GALE_BIFL2 GALE_BIFL2]] Involved in the metabolism of galactose. Catalyzes the conversion of UDP-galactose (UDP-Gal) to UDP-glucose (UDP-Glc) through a mechanism involving the transient reduction of NAD. Can also epimerize UDP-GalNAc to UDP-GlcNAc. Involved in the lacto-N-biose I/galacto-N-biose (LNB/GNB) degradation pathway, which is important for host intestinal colonization by bifidobacteria.<ref>PMID:17720833</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Infant gut-associated bifidobacteria has a metabolic pathway that specifically utilizes lacto-N-biose I (Gal-beta1,3-GlcNAc) and galacto-N-biose (Gal-beta1,3-GalNAc) from human milk and mucin glycans. UDP-glucose 4-epimerase (GalE) from Bifidobacterium longum (bGalE) catalyzes epimerization reactions of UDP-Gal into UDP-Glc and UDP-GalNAc into UDP-GlcNAc with the same level of activity that is required to send galacto-hexoses into glycolysis. Here, we determined the crystal structures of bGalE in three ternary complex forms: NAD(+)/UDP, NAD(+)/UDP-GlcNAc, and NAD(+)/UDP-Glc. The broad specificity of bGalE was explained by structural features of the binding pocket for the N-acetyl or C2 hydroxy group of the substrate. Asn200 is located in a pocket of the C2 group, and its side chain adopts different conformations in the complex structures with UDP-Glc and UDP-GlcNAc. On the other side, Cys299 forms a large pocket for the C5 sugar ring atom. The flexible C2 pocket and the large C5 pocket of bGalE are suitable for accommodating both the hydroxy and N-acetyl groups of the substrate during sugar ring rotation in the catalytic cycle. The substrate specificity and active site structure of bGalE were distinct from those of Esherichia coli GalE but similar to those of human GalE.
		+
		+	Structural basis for broad substrate specificity of UDP-glucose 4-epimerase in the human milk oligosaccharide catabolic pathway of Bifidobacterium longum.,Nam YW, Nishimoto M, Arakawa T, Kitaoka M, Fushinobu S Sci Rep. 2019 Jul 31;9(1):11081. doi: 10.1038/s41598-019-47591-w. PMID:31366978<ref>PMID:31366978</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6k0i" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bifl2]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: UDP-glucose 4-epimerase]]		[[Category: UDP-glucose 4-epimerase]]

OCA at 05:52, 7 August 2019

OCA — Wed, 07 Aug 2019 05:52:12 GMT

←Older revision		Revision as of 05:52, 7 August 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6k0i is ~~ON HOLD until Paper Publication~~	+	==Crystal Structure of UDP-glucose 4-epimerase from Bifidobacterium longum in complex with NAD+ and UDP-Glc==
-		+	<StructureSection load='6k0i' size='340' side='right'caption='[[6k0i]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6k0i]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K0I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K0I FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</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-glucose_4-epimerase UDP-glucose 4-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.2 5.1.3.2] </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=6k0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0i OCA], [http://pdbe.org/6k0i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k0i RCSB], [http://www.ebi.ac.uk/pdbsum/6k0i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0i ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GALE_BIFL2 GALE_BIFL2]] Involved in the metabolism of galactose. Catalyzes the conversion of UDP-galactose (UDP-Gal) to UDP-glucose (UDP-Glc) through a mechanism involving the transient reduction of NAD. Can also epimerize UDP-GalNAc to UDP-GlcNAc. Involved in the lacto-N-biose I/galacto-N-biose (LNB/GNB) degradation pathway, which is important for host intestinal colonization by bifidobacteria.<ref>PMID:17720833</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: UDP-glucose 4-epimerase]]
		+	[[Category: Arakawa, T]]
		+	[[Category: Fushinobu, S]]
		+	[[Category: Kitaoka, M]]
		+	[[Category: Nam, Y W]]
		+	[[Category: Nishimoto, M]]
		+	[[Category: Hydrolase]]
		+	[[Category: Isomerase]]
		+	[[Category: Rossmann fold]]

OCA at 03:52, 22 May 2019

OCA — Wed, 22 May 2019 03:52:56 GMT

←Older revision		Revision as of 03:52, 22 May 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6k0i is ON HOLD	+	The entry 6k0i is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6k0i" [edit=sysop:move=sysop]

OCA — Tue, 21 May 2019 05:38:56 GMT

Protected "6k0i" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:38, 21 May 2019

OCA: New page: '''Unreleased structure''' The entry 6k0i is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Tue, 21 May 2019 05:38:54 GMT

New page: '''Unreleased structure''' The entry 6k0i is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6k0i is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]