6zl6 - Revision history

OCA at 11:54, 1 February 2024

OCA — Thu, 01 Feb 2024 11:54:03 GMT

←Older revision		Revision as of 11:54, 1 February 2024
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	<StructureSection load='6zl6' size='340' side='right'caption='[[6zl6]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='6zl6' size='340' side='right'caption='[[6zl6]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6zl6]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacillus_cereus_hua2~~-4 Bacillus cereus ~~hua2~~-4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZL6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6ZL6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6zl6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus_HuA2-4 Bacillus cereus HuA2-4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZL6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZL6 FirstGlance]. <br>
-	</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=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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]] 1.7Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~IG7_05634 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id=1053203 Bacillus cereus HuA2~~-~~4])~~</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=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6zl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zl6 OCA], [~~http~~://pdbe.org/6zl6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6zl6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6zl6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6zl6 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=6zl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zl6 OCA], [https://pdbe.org/6zl6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zl6 RCSB], [https://www.ebi.ac.uk/pdbsum/6zl6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zl6 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus cereus ~~hua2~~-4]]	+	[[Category: Bacillus cereus HuA2-4]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Iacovino~~, L G~~]]	+	[[Category: Iacovino LG]]
-	[[Category: Mattevi, A]]	+	[[Category: Mattevi A]]
-	~~[[Category: Epimerase]]~~	+
-	~~[[Category: Nad]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Udp]]~~	+
-	~~[[Category: Udp-sugar binding protein~~]]	+

OCA at 10:02, 9 September 2020

OCA — Wed, 09 Sep 2020 10:02:36 GMT

←Older revision		Revision as of 10:02, 9 September 2020
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	==Crystal Structure of UDP-Glucuronic acid 4-epimerase from Bacillus cereus in complex with UDP and NAD==		==Crystal Structure of UDP-Glucuronic acid 4-epimerase from Bacillus cereus in complex with UDP and NAD==
-	<StructureSection load='6zl6' size='340' side='right'caption='[[6zl6]]' scene=''>	+	<StructureSection load='6zl6' size='340' side='right'caption='[[6zl6]], [[Resolution\|resolution]] 1.70Å' 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=6ZL6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZL6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6zl6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus_hua2-4 Bacillus cereus hua2-4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZL6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZL6 FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6zl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zl6 OCA], [http://pdbe.org/6zl6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zl6 RCSB], [http://www.ebi.ac.uk/pdbsum/6zl6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zl6 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=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IG7_05634 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1053203 Bacillus cereus HuA2-4])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6zl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zl6 OCA], [http://pdbe.org/6zl6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zl6 RCSB], [http://www.ebi.ac.uk/pdbsum/6zl6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zl6 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	UDP-glucuronic acid is converted to UDP-galacturonic acid en route to a variety of sugar-containing metabolites. This reaction is performed by a NAD(+)-dependent epimerase belonging to the short-chain dehydrogenase/reductase family. We present several high-resolution crystal structures of the UDP-glucuronic acid epimerase from Bacillus cereus The geometry of the substrate-NAD(+) interactions is finely arranged to promote hydride transfer. The exquisite complementarity between glucuronic acid and its binding site is highlighted by the observation that the unligated cavity is occupied by a cluster of ordered waters whose positions overlap the polar groups of the sugar substrate. Co-crystallization experiments led to a structure where substrate- and product-bound enzymes coexist within the same crystal. This equilibrium structure reveals the basis for a "swing & flip" rotation of the pro-chiral 4-keto-hexose-uronic acid intermediate that results from glucuronic acid oxidation, placing the C4' atom in position for receiving a hydride ion on the opposite side of the sugar ring. The product-bound active site is almost identical to that of the substrate-bound structure and satisfies all hydrogen-bonding requirements of the ligand. The structure of the apo-enzyme together with kinetic isotope effect and mutagenesis experiments further outlines a few flexible loops that exist in discrete conformations, imparting structural malleability required for ligand rotation while avoiding leakage of the catalytic intermediate and/or side-reactions. These data highlight the double nature of the enzymatic mechanism: the active site features a high degree of precision in substrate recognition combined with the flexibility required for intermediate rotation.
		+
		+	Crystallographic snapshots of UDP-glucuronic acid 4-epimeraseligand binding, rotation and reduction.,Iacovino LG, Savino S, Borg AJE, Binda C, Nidetzky B, Mattevi A J Biol Chem. 2020 Jul 13. pii: RA120.014692. doi: 10.1074/jbc.RA120.014692. PMID:32661196<ref>PMID:32661196</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6zl6" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus cereus hua2-4]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Iacovino LG]]	+	[[Category: Iacovino, L G]]
-	[[Category: Mattevi A]]	+	[[Category: Mattevi, A]]
		+	[[Category: Epimerase]]
		+	[[Category: Nad]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Udp]]
		+	[[Category: Udp-sugar binding protein]]

OCA at 11:13, 29 July 2020

OCA — Wed, 29 Jul 2020 11:13:14 GMT

←Older revision		Revision as of 11:13, 29 July 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6zl6 ~~is ON HOLD until Paper Publication~~	+	==Crystal Structure of UDP-Glucuronic acid 4-epimerase from Bacillus cereus in complex with UDP and NAD==
-		+	<StructureSection load='6zl6' size='340' side='right'caption='[[6zl6]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZL6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZL6 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6zl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zl6 OCA], [http://pdbe.org/6zl6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zl6 RCSB], [http://www.ebi.ac.uk/pdbsum/6zl6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zl6 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Iacovino LG]]
		+	[[Category: Mattevi A]]

OCA: Protected "6zl6" [edit=sysop:move=sysop]

OCA — Wed, 08 Jul 2020 11:17:29 GMT

Protected "6zl6" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:17, 8 July 2020

OCA: New page: '''Unreleased structure''' The entry 6zl6 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 08 Jul 2020 11:17:27 GMT

New page: '''Unreleased structure''' The entry 6zl6 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6zl6 is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]