6ktk - Revision history

OCA at 10:43, 22 November 2023

OCA — Wed, 22 Nov 2023 10:43:24 GMT

←Older revision		Revision as of 10:43, 22 November 2023
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	<StructureSection load='6ktk' size='340' side='right'caption='[[6ktk]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='6ktk' size='340' side='right'caption='[[6ktk]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ktk]] 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=6KTK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6KTK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ktk]] 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=6KTK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KTK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8S0:~~(3~{S},4~{R},5~{R},6~{S})~~-6-~~(hydroxymethyl)-3,4~~,5-~~tris(oxidanyl)oxan-2-one~~'>8S0</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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]] 1.65Å</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=8S0:L-glucono-1,5-lactone'>8S0</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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=6ktk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ktk OCA], [~~http~~://pdbe.org/6ktk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ktk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ktk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ktk 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=6ktk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ktk OCA], [https://pdbe.org/6ktk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ktk RCSB], [https://www.ebi.ac.uk/pdbsum/6ktk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ktk 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: Large Structures]]
-	[[Category: Fukano, K]]	+	[[Category: Paracoccus laeviglucosivorans]]
-	[[Category: Ito, S]]	+	[[Category: Fukano K]]
-	[[Category: Koubara, K]]	+	[[Category: Ito S]]
-	[[Category: Nakamura, A]]	+	[[Category: Koubara K]]
-	[[Category: Sasaki, Y]]	+	[[Category: Nakamura A]]
-	[[Category: Suzuki, M]]	+	[[Category: Sasaki Y]]
-	[[Category: Takenoya, M]]	+	[[Category: Suzuki M]]
-	[[Category: Yajima, S]]	+	[[Category: Takenoya M]]
-	~~[[Category: Oxidoreductase~~]]	+	[[Category: Yajima S]]

OCA at 11:19, 1 January 2020

OCA — Wed, 01 Jan 2020 11:19:04 GMT

←Older revision		Revision as of 11:19, 1 January 2020
Line 3:		Line 3:
	<StructureSection load='6ktk' size='340' side='right'caption='[[6ktk]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='6ktk' size='340' side='right'caption='[[6ktk]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ktk]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KTK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KTK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ktk]] 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=6KTK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KTK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8S0:(3~{S},4~{R},5~{R},6~{S})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-one'>8S0</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8S0:(3~{S},4~{R},5~{R},6~{S})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-one'>8S0</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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=6ktk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ktk OCA], [http://pdbe.org/6ktk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ktk RCSB], [http://www.ebi.ac.uk/pdbsum/6ktk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ktk 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=6ktk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ktk OCA], [http://pdbe.org/6ktk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ktk RCSB], [http://www.ebi.ac.uk/pdbsum/6ktk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ktk ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	scyllo-inositol dehydrogenase, isolated from Paracoccus laeviglucosivorans (Pl-sIDH), exhibits a broad substrate specificity: it oxidizes scyllo- and myo-inositols as well as L-glucose, converting L-glucose to L-glucono-1,5-lactone. Based on the crystal structures previously reported, Arg178 residue, located at the entry port of the catalytic site, seemed to be important for accepting substrates. Here, we report the role of Arg178 by using an alanine-substituted mutant for kinetic analysis as well as to determine the crystal structures. The wild-type Pl-sIDH exhibits the activity for scyllo-inositol most preferably followed by myo-inositol and L-glucose. On the contrary, the R178A mutant abolished the activities for both inositols, but remained active for L-glucose to the same extent as its wild-type. Based on the crystal structures of the mutant, the side chain of Asp191 flipped out of the substrate binding site. Therefore, Arg178 is important in positioning Asp191 correctly to exert its catalytic activities.Abbreviations: IDH: inositol dehydrogenase; LB: Luria-Bertani; kcat: catalyst rate constant; Km: Michaelis constant; NAD: nicotinamide dinucleotide; NADH: nicotinamide dinucleotide reduced form; PDB; Protein Data Bank; PDB entry: 6KTJ, 6KTK, 6KTL.
		+
		+	Single amino acid mutation altered substrate specificity for L-glucose and inositol in scyllo-inositol dehydrogenase isolated from Paracoccus laeviglucosivorans.,Suzuki M, Koubara K, Takenoya M, Fukano K, Ito S, Sasaki Y, Nakamura A, Yajima S Biosci Biotechnol Biochem. 2019 Dec 16:1-9. doi: 10.1080/09168451.2019.1702870. PMID:31842701<ref>PMID:31842701</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ktk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Dsm 100094]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Fukano, K]]		[[Category: Fukano, K]]

OCA at 09:05, 25 December 2019

OCA — Wed, 25 Dec 2019 09:05:26 GMT

←Older revision		Revision as of 09:05, 25 December 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6ktk is ON HOLD until Paper Publication~~	+	==Crystal structure of scyllo-inositol dehydrogenase R178A mutant, complexed with NADH and L-glucono-1,5-lactone, from Paracoccus laeviglucosivorans==
-		+	<StructureSection load='6ktk' size='340' side='right'caption='[[6ktk]], [[Resolution\|resolution]] 1.65Å' scene=''>
-	~~Authors: Suzuki, M., Koubara, K., Takenoya, M., Fukano, K., Ito, S., Sasaki, Y., Nakamura, A., Yajima, S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6ktk]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KTK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KTK FirstGlance]. <br>
-	~~Description:~~ Crystal structure of scyllo-inositol dehydrogenase R178A mutant, complexed with NADH and L-glucono-1,5-lactone, from Paracoccus laeviglucosivorans	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8S0:(3~{S},4~{R},5~{R},6~{S})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-one'>8S0</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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=6ktk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ktk OCA], [http://pdbe.org/6ktk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ktk RCSB], [http://www.ebi.ac.uk/pdbsum/6ktk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ktk ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Fukano, K]]
		+	[[Category: Ito, S]]
	[[Category: Koubara, K]]		[[Category: Koubara, K]]
		+	[[Category: Nakamura, A]]
		+	[[Category: Sasaki, Y]]
	[[Category: Suzuki, M]]		[[Category: Suzuki, M]]
-	[[Category: Sasaki, Y]]
-	[[Category: Fukano, K]]
-	[[Category: Ito, S]]
	[[Category: Takenoya, M]]		[[Category: Takenoya, M]]
-	[[Category: Nakamura, A]]
	[[Category: Yajima, S]]		[[Category: Yajima, S]]
		+	[[Category: Oxidoreductase]]

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

OCA — Wed, 02 Oct 2019 06:45:41 GMT

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

←Older revision

Revision as of 06:45, 2 October 2019

OCA: New page: '''Unreleased structure''' The entry 6ktk is ON HOLD until Paper Publication Authors: Suzuki, M., Koubara, K., Takenoya, M., Fukano, K., Ito, S., Sasaki, Y., Nakamura, A., Yajima, S. D...

OCA — Wed, 02 Oct 2019 06:45:39 GMT

New page: '''Unreleased structure''' The entry 6ktk is ON HOLD until Paper Publication Authors: Suzuki, M., Koubara, K., Takenoya, M., Fukano, K., Ito, S., Sasaki, Y., Nakamura, A., Yajima, S. D...

New page

'''Unreleased structure'''

The entry 6ktk is ON HOLD until Paper Publication

Authors: Suzuki, M., Koubara, K., Takenoya, M., Fukano, K., Ito, S., Sasaki, Y., Nakamura, A., Yajima, S.

Description: Crystal structure of scyllo-inositol dehydrogenase R178A mutant, complexed with NADH and L-glucono-1,5-lactone, from Paracoccus laeviglucosivorans
[[Category: Unreleased Structures]]
[[Category: Koubara, K]]
[[Category: Suzuki, M]]
[[Category: Sasaki, Y]]
[[Category: Fukano, K]]
[[Category: Ito, S]]
[[Category: Takenoya, M]]
[[Category: Nakamura, A]]
[[Category: Yajima, S]]