5yeq - Revision history

OCA at 08:28, 22 November 2023

2023-11-22T08:28:26Z

←Older revision		Revision as of 08:28, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5yeq' size='340' side='right'caption='[[5yeq]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='5yeq' size='340' side='right'caption='[[5yeq]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yeq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YEQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YEQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yeq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfolobus_acidocaldarius Sulfolobus acidocaldarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YEQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YEQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.75Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Ketol-acid_reductoisomerase Ketol-acid reductoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.86 1.1.1.86]~~ </~~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=5yeq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yeq OCA], [https://pdbe.org/5yeq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yeq RCSB], [https://www.ebi.ac.uk/pdbsum/5yeq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yeq ProSAT]</span></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=5yeq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yeq OCA], [~~http~~://pdbe.org/5yeq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yeq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yeq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yeq ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~A0A0U3H6N8_9CREN A0A0U3H6N8_9CREN]~~] Involved in the biosynthesis of branched-chain amino acids (BCAA). Catalyzes an alkyl-migration followed by a ketol-acid reduction of (S)-2-acetolactate (S2AL) to yield (R)-2,3-dihydroxy-isovalerate. In the isomerase reaction, S2AL is rearranged via a Mg-dependent methyl migration to produce 3-hydroxy-3-methyl-2-ketobutyrate (HMKB). In the reductase reaction, this 2-ketoacid undergoes a metal-dependent reduction by NADPH to yield (R)-2,3-dihydroxy-isovalerate.[HAMAP-Rule:MF_00435]	+	[https://www.uniprot.org/uniprot/ILVC_SULAC ILVC_SULAC] Involved in the biosynthesis of branched-chain amino acids (BCAA). Catalyzes an alkyl-migration followed by a ketol-acid reduction of (S)-2-acetolactate (S2AL) to yield (R)-2,3-dihydroxy-isovalerate. In the isomerase reaction, S2AL is rearranged via a Mg-dependent methyl migration to produce 3-hydroxy-3-methyl-2-ketobutyrate (HMKB). In the reductase reaction, this 2-ketoacid undergoes a metal-dependent reduction by NADPH to yield (R)-2,3-dihydroxy-isovalerate.[HAMAP-Rule:MF_00435]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Ketol-acid reductoisomerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen~~, C Y~~]]	+	[[Category: Sulfolobus acidocaldarius]]
-	[[Category: Chiang~~, C H~~]]	+	[[Category: Chen CY]]
-	[[Category: Horng~~, J C~~]]	+	[[Category: Chiang CH]]
-	[[Category: Huang~~, C H~~]]	+	[[Category: Horng JC]]
-	[[Category: Ko~~, T P~~]]	+	[[Category: Huang CH]]
-	[[Category: Lin~~, B L~~]]	+	[[Category: Ko TP]]
-	[[Category: Lin~~, K F~~]]	+	[[Category: Lin BL]]
-	[[Category: Tsai~~, M D]]~~	+	[[Category: Lin KF]]
-	~~[[Category: Acid tolerant enzyme]]~~	+	[[Category: Tsai MD]]
-	~~[[Category: Ahir]]~~	+
-	~~[[Category: Bcaa]]~~	+
-	~~[[Category: Biofuel]]~~	+
-	~~[[Category: Branched-chain amino acid]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Knot domain]]~~	+
-	~~[[Category: Metal ion cofactor]]~~	+
-	~~[[Category: Nadh]]~~	+
-	~~[[Category: Nadph]]~~	+
-	~~[[Category: Reductase~~]]	+

OCA at 09:17, 21 October 2020

2020-10-21T09:17:17Z

←Older revision		Revision as of 09:17, 21 October 2020
Line 1:		Line 1:

	==The structure of Sac-KARI protein==		==The structure of Sac-KARI protein==
-	<StructureSection load='5yeq' size='340' side='right' caption='[[5yeq]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='5yeq' size='340' side='right'caption='[[5yeq]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yeq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YEQ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YEQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yeq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YEQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YEQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ketol-acid_reductoisomerase Ketol-acid reductoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.86 1.1.1.86] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ketol-acid_reductoisomerase Ketol-acid reductoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.86 1.1.1.86] </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=5yeq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yeq OCA], [http://pdbe.org/5yeq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yeq RCSB], [http://www.ebi.ac.uk/pdbsum/5yeq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yeq ProSAT]</span></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=5yeq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yeq OCA], [http://pdbe.org/5yeq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yeq RCSB], [http://www.ebi.ac.uk/pdbsum/5yeq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yeq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5yeq" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5yeq" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ketol-acid reductoisomerase 3D structures\|Ketol-acid reductoisomerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Ketol-acid reductoisomerase]]		[[Category: Ketol-acid reductoisomerase]]
		+	[[Category: Large Structures]]
	[[Category: Chen, C Y]]		[[Category: Chen, C Y]]
	[[Category: Chiang, C H]]		[[Category: Chiang, C H]]

OCA at 07:09, 4 July 2018

2018-07-04T07:09:07Z

←Older revision		Revision as of 07:09, 4 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5yeq is ~~ON HOLD until Paper~~ Publication	+	==The structure of Sac-KARI protein==
		+	<StructureSection load='5yeq' size='340' side='right' caption='[[5yeq]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yeq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YEQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YEQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ketol-acid_reductoisomerase Ketol-acid reductoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.86 1.1.1.86] </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=5yeq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yeq OCA], [http://pdbe.org/5yeq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yeq RCSB], [http://www.ebi.ac.uk/pdbsum/5yeq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yeq ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0A0U3H6N8_9CREN A0A0U3H6N8_9CREN]] Involved in the biosynthesis of branched-chain amino acids (BCAA). Catalyzes an alkyl-migration followed by a ketol-acid reduction of (S)-2-acetolactate (S2AL) to yield (R)-2,3-dihydroxy-isovalerate. In the isomerase reaction, S2AL is rearranged via a Mg-dependent methyl migration to produce 3-hydroxy-3-methyl-2-ketobutyrate (HMKB). In the reductase reaction, this 2-ketoacid undergoes a metal-dependent reduction by NADPH to yield (R)-2,3-dihydroxy-isovalerate.[HAMAP-Rule:MF_00435]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ketol-acid reductoisomerase (KARI) is a bifunctional enzyme in the second step of branched-chain amino acids biosynthetic pathway. Most KARIs prefer NADPH as a cofactor. However, KARI with a preference for NADH is desirable in industrial applications including anaerobic fermentation for the production of branched-chain amino acids or biofuels. Here, we characterize a thermoacidophilic archaeal Sac-KARI from Sulfolobus acidocaldarius and present its crystal structure at a 1.75-A resolution. By comparison with other holo-KARI structures, one sulphate ion is observed in each binding site for the 2'-phosphate of NADPH, implicating its NADPH preference. Sac-KARI has very high affinity for NADPH and NADH, with K M values of 0.4 muM for NADPH and 6.0 muM for NADH, suggesting that both are good cofactors at low concentrations although NADPH is favoured over NADH. Furthermore, Sac-KARI can catalyze 2(S)-acetolactate (2S-AL) with either cofactor from 25 to 60 degrees C, but the enzyme has higher activity by using NADPH. In addition, the catalytic activity of Sac-KARI increases significantly with elevated temperatures and reaches an optimum at 60 degrees C. Bi-cofactor utilization and the thermoactivity of Sac-KARI make it a potential candidate for use in metabolic engineering or industrial applications under anaerobic or harsh conditions.

-	~~Authors: Ko, T.P~~., Chen, ~~C.Y.~~, Lin~~, K.F.~~, Lin~~, B.L.~~, Huang~~, C.H.~~, Chiang~~, C.H.~~, Horng~~, J~~.C.~~, Tsai, M~~.D.	+	NADH/NADPH bi-cofactor-utilizing and thermoactive ketol-acid reductoisomerase from Sulfolobus acidocaldarius.,Chen CY, Ko TP, Lin KF, Lin BL, Huang CH, Chiang CH, Horng JC Sci Rep. 2018 May 8;8(1):7176. doi: 10.1038/s41598-018-25361-4. PMID:29739976<ref>PMID:29739976</ref>

-	~~Description: The structure~~ of ~~Sac~~-~~KARI protein~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Ko, ~~T.P~~]]	+	<div class="pdbe-citations 5yeq" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Lin~~, ~~B.L~~]]	+	== References ==
-	[[Category: Huang, C.H]]	+	<references/>
-	[[Category: ~~Horng~~, ~~J.C~~]]	+	__TOC__
-	[[Category: Lin, ~~K.F~~]]	+	</StructureSection>
-	[[Category: ~~Chen~~, ~~C.Y~~]]	+	[[Category: Ketol-acid reductoisomerase]]
-	[[Category: Tsai, M.D]]	+	[[Category: Chen, C Y]]
-	[[Category: ~~Chiang, C.H~~]]	+	[[Category: Chiang, C H]]
		+	[[Category: Horng, J C]]
		+	[[Category: Huang, C H]]
		+	[[Category: Ko, T P]]
		+	[[Category: Lin, B L]]
		+	[[Category: Lin, K F]]
		+	[[Category: Tsai, M D]]
		+	[[Category: Acid tolerant enzyme]]
		+	[[Category: Ahir]]
		+	[[Category: Bcaa]]
		+	[[Category: Biofuel]]
		+	[[Category: Branched-chain amino acid]]
		+	[[Category: Isomerase]]
		+	[[Category: Knot domain]]
		+	[[Category: Metal ion cofactor]]
		+	[[Category: Nadh]]
		+	[[Category: Nadph]]
		+	[[Category: Reductase]]

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

2017-09-27T16:28:55Z

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

←Older revision

Revision as of 16:28, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5yeq is ON HOLD until Paper Publication Authors: Ko, T.P., Chen, C.Y., Lin, K.F., Lin, B.L., Huang, C.H., Chiang, C.H., Horng, J.C., Tsai, M.D. Des...

2017-09-27T16:28:54Z

New page: '''Unreleased structure''' The entry 5yeq is ON HOLD until Paper Publication Authors: Ko, T.P., Chen, C.Y., Lin, K.F., Lin, B.L., Huang, C.H., Chiang, C.H., Horng, J.C., Tsai, M.D. Des...

New page

'''Unreleased structure'''

The entry 5yeq is ON HOLD until Paper Publication

Authors: Ko, T.P., Chen, C.Y., Lin, K.F., Lin, B.L., Huang, C.H., Chiang, C.H., Horng, J.C., Tsai, M.D.

Description: The structure of Sac-KARI protein
[[Category: Unreleased Structures]]
[[Category: Ko, T.P]]
[[Category: Lin, B.L]]
[[Category: Huang, C.H]]
[[Category: Horng, J.C]]
[[Category: Lin, K.F]]
[[Category: Chen, C.Y]]
[[Category: Tsai, M.D]]
[[Category: Chiang, C.H]]