5ya8 - Revision history

OCA at 08:25, 22 November 2023

OCA — Wed, 22 Nov 2023 08:25:18 GMT

←Older revision		Revision as of 08:25, 22 November 2023
Line 1:		Line 1:

	==Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity complexed with myo-inositol==		==Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity complexed with myo-inositol==
-	<StructureSection load='5ya8' size='340' side='right' caption='[[5ya8]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5ya8' size='340' side='right'caption='[[5ya8]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ya8]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Dsm_100094 Dsm 100094~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YA8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YA8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ya8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_laeviglucosivorans Paracoccus laeviglucosivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YA8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YA8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=INS:1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE'>INS</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 2.3Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lgdA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1197861 DSM 100094])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=INS:1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE'>INS</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></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=5ya8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ya8 OCA], [~~http~~://pdbe.org/5ya8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ya8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ya8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ya8 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=5ya8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ya8 OCA], [https://pdbe.org/5ya8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ya8 RCSB], [https://www.ebi.ac.uk/pdbsum/5ya8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ya8 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/K7ZP76_9RHOB K7ZP76_9RHOB]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Dsm 100094~~]]	+	[[Category: Large Structures]]
-	[[Category: Fukano, K]]	+	[[Category: Paracoccus laeviglucosivorans]]
-	[[Category: Nakamura, A]]	+	[[Category: Fukano K]]
-	[[Category: Sasaki, Y]]	+	[[Category: Nakamura A]]
-	[[Category: Shimizu, T]]	+	[[Category: Sasaki Y]]
-	[[Category: Yajima, S]]	+	[[Category: Shimizu T]]
-	~~[[Category: Homotetramer]]~~	+	[[Category: Yajima S]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rossmann fold]]~~	+
-	~~[[Category: Sugar metabolism~~]]	+

OCA at 08:05, 14 June 2018

OCA — Thu, 14 Jun 2018 08:05:00 GMT

←Older revision		Revision as of 08:05, 14 June 2018
Line 8:		Line 8:
	<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=5ya8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ya8 OCA], [http://pdbe.org/5ya8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ya8 RCSB], [http://www.ebi.ac.uk/pdbsum/5ya8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ya8 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=5ya8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ya8 OCA], [http://pdbe.org/5ya8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ya8 RCSB], [http://www.ebi.ac.uk/pdbsum/5ya8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ya8 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	For about 70 years, L-glucose had been considered non-metabolizable by either mammalian or bacterial cells. Recently, however, an L-glucose catabolic pathway has been discovered in Paracoccus laeviglucosivorans, and the genes responsible cloned. Scyllo-inositol dehydrogenase is involved in the first step in the pathway that oxidizes L-glucose to produce L-glucono-1,5-lactone with concomitant reduction of NAD+ dependent manner. Here, we report the crystal structure of the ternary complex of scyllo-inositol dehydrogenase with NAD+ and L-glucono-1,5-lactone at 1.8 A resolution. The enzyme adopts a homo-tetrameric structure, similar to those of the inositol dehydrogenase family, and the electron densities of the bound sugar was clearly observed, allowing identification of the residues responsible for interaction with the substrate in the catalytic site. In addition to the conserved catalytic residues (Lys106, Asp191, and His195), another residue, His318, located in the loop region of the adjacent subunit, is involved in substrate recognition. Site-directed mutagenesis confirmed the role of these residues in catalytic activity. We also report the complex structures of the enzyme with myo-inositol and scyllo-inosose. The Arg178 residue located in the flexible loop at the entrance of the catalytic site is also involved in substrate recognition, and plays an important role in accepting both L-glucose and inositols as substrates. On the basis of these structural features, which have not been identified in the known inositol dehydrogenases, and a phylogenetic analysis of IDH family enzymes, we suggest a novel subfamily of the GFO/IDH/MocA family. Since many enzymes in this family have not biochemically characterized, our results could promote to find their activities with various substrates.
		+
		+	Structural basis of L-glucose oxidation by scyllo-inositol dehydrogenase: Implications for a novel enzyme subfamily classification.,Fukano K, Ozawa K, Kokubu M, Shimizu T, Ito S, Sasaki Y, Nakamura A, Yajima S PLoS One. 2018 May 25;13(5):e0198010. doi: 10.1371/journal.pone.0198010., eCollection 2018. PMID:29799855<ref>PMID:29799855</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ya8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:16, 6 June 2018

OCA — Wed, 06 Jun 2018 06:16:33 GMT

←Older revision		Revision as of 06:16, 6 June 2018
Line 3:		Line 3:
	<StructureSection load='5ya8' size='340' side='right' caption='[[5ya8]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5ya8' size='340' side='right' caption='[[5ya8]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ya8]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YA8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YA8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ya8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Dsm_100094 Dsm 100094]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YA8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YA8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=INS:1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE'>INS</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=INS:1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE'>INS</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lgdA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1197861 DSM 100094])</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=5ya8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ya8 OCA], [http://pdbe.org/5ya8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ya8 RCSB], [http://www.ebi.ac.uk/pdbsum/5ya8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ya8 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=5ya8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ya8 OCA], [http://pdbe.org/5ya8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ya8 RCSB], [http://www.ebi.ac.uk/pdbsum/5ya8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ya8 ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Dsm 100094]]
	[[Category: Fukano, K]]		[[Category: Fukano, K]]
	[[Category: Nakamura, A]]		[[Category: Nakamura, A]]

OCA at 07:16, 23 May 2018

OCA — Wed, 23 May 2018 07:16:55 GMT

←Older revision		Revision as of 07:16, 23 May 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5ya8 is ON HOLD until Paper Publication~~	+	==Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity complexed with myo-inositol==
-		+	<StructureSection load='5ya8' size='340' side='right' caption='[[5ya8]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~Authors: Fukano, K., Shimizu, T., Sasaki, Y., Nakamura, A., Yajima, S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ya8]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YA8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YA8 FirstGlance]. <br>
-	~~Description:~~ Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity complexed with myo-inositol	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=INS:1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE'>INS</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	[[~~Category: Unreleased Structures~~]]	+	<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=5ya8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ya8 OCA], [http://pdbe.org/5ya8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ya8 RCSB], [http://www.ebi.ac.uk/pdbsum/5ya8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ya8 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Yajima, S~~]]	+	</table>
-	[[~~Category~~: ~~Shimizu, T~~]]	+	__TOC__
-	[[~~Category~~: ~~Sasaki~~, Y]]	+	</StructureSection>
	[[Category: Fukano, K]]		[[Category: Fukano, K]]
	[[Category: Nakamura, A]]		[[Category: Nakamura, A]]
		+	[[Category: Sasaki, Y]]
		+	[[Category: Shimizu, T]]
		+	[[Category: Yajima, S]]
		+	[[Category: Homotetramer]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Rossmann fold]]
		+	[[Category: Sugar metabolism]]

OCA: Protected "5ya8" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 16:19:50 GMT

Protected "5ya8" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:19, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5ya8 is ON HOLD until Paper Publication Authors: Fukano, K., Shimizu, T., Sasaki, Y., Nakamura, A., Yajima, S. Description: Crystal structure of sc...

OCA — Wed, 27 Sep 2017 16:19:49 GMT

New page: '''Unreleased structure''' The entry 5ya8 is ON HOLD until Paper Publication Authors: Fukano, K., Shimizu, T., Sasaki, Y., Nakamura, A., Yajima, S. Description: Crystal structure of sc...

New page

'''Unreleased structure'''

The entry 5ya8 is ON HOLD until Paper Publication

Authors: Fukano, K., Shimizu, T., Sasaki, Y., Nakamura, A., Yajima, S.

Description: Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity complexed with myo-inositol
[[Category: Unreleased Structures]]
[[Category: Yajima, S]]
[[Category: Shimizu, T]]
[[Category: Sasaki, Y]]
[[Category: Fukano, K]]
[[Category: Nakamura, A]]