3uha - Revision history

OCA at 13:58, 14 March 2024

OCA — Thu, 14 Mar 2024 13:58:12 GMT

←Older revision		Revision as of 13:58, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3uha' size='340' side='right'caption='[[3uha]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3uha' size='340' side='right'caption='[[3uha]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3uha]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UHA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UHA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3uha]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UHA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UHA FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</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"~~>LYS1, YIR034C ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~559292 Baker's yeast])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Saccharopine_dehydrogenase_(NAD(+),_L~~-~~lysine~~-~~forming) Saccharopine dehydrogenase (~~NAD~~(+), L-lysine-forming)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.7 1.5.1.7]~~ </~~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=3uha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uha OCA], [https://pdbe.org/3uha PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3uha RCSB], [https://www.ebi.ac.uk/pdbsum/3uha PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3uha 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=3uha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uha OCA], [https://pdbe.org/3uha PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3uha RCSB], [https://www.ebi.ac.uk/pdbsum/3uha PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3uha ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/LYS1_YEAST LYS1_YEAST]] Catalyzes the NAD(+)-dependent cleavage of saccharopine to L-lysine and 2-oxoglutarate.	+	[https://www.uniprot.org/uniprot/LYS1_YEAST LYS1_YEAST] Catalyzes the NAD(+)-dependent cleavage of saccharopine to L-lysine and 2-oxoglutarate.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Saccharopine dehydrogenase (SDH) catalyzes the final reaction in the alpha-aminoadipate pathway, the conversion of L-saccharopine to L-lysine (Lys) and alpha-ketoglutarate (alpha-Kg) using NAD+ as an oxidant. The enzyme utilizes a general acid-base mechanism to carry out its reaction with a base proposed to accept a proton from the secondary amine of saccharopine in the oxidation step and group proposed to activate water to hydrolyze the resulting imine. Crystal structures of an open apo-form and a closed form of the enzyme with saccharopine and NADH bound have been solved at 2.0 A and 2.2 A resolution, respectively. In the ternary complex, a significant movement of domain I relative to domain II is observed that closes the active site cleft between the two domains and brings H96 and K77 in close proximity to the substrate binding site. The hydride transfer distance is 3.6 A, and the side chains of H96 and K77 are properly positioned to act as acid-base catalysts. Preparation of the K77 to M, H96 to Q single and the K77M/H96Q double mutant enzymes provide data consistent with their role as the general acid-base catalysts in the SDH reaction. The side chain of K77 initially accepts a proton from the epsilon-amine of the substrate Lys and eventually donates it to the imino nitrogen as it is reduced to a secondary amine in the hydride transfer step, and H96 protonates the carbonyl oxygen as the carbinolamine is formed. The K77M, H976Q, and K77M/H96Q mutant enzymes give 145-, 28-, and 700-fold decreases in V/Et and >103 increases in V2/KLysEt and V2/Kalpha-KgEt (the double mutation gives >105-fold decreases in the second order rate constants). In addition, the K77M mutant enzyme exhibits a primary deuterium kinetic isotope effect of 2.0 and an inverse solvent deuterium isotope effect of 0.77 on V2/KLys. A value of 2.0 was also observed for D(V2/KLys)D2O when the primary deuterium kinetic isotope effect was repeated in D2O, consistent with a rate-limiting hydride transfer step. A viscosity effect of 0.8 was observed on V2/KLys indicating the solvent deuterium isotope effect resulted from stabilization of an enzyme form prior to hydride transfer. A small normal solvent isotope effect is observed on V, which decreases slightly when repeated with NADD, consistent with a contribution from product release to rate limitation. In addition, V2/KLysEt is pH independent consistent with the loss of an acid-base catalyst and perturbation of the pKa of the second catalytic group to higher pH, likely a result of a change in the overall charge in the active site. The primary deuterium kinetic isotope effect for H96Q, measured in H2O or D2O, is within error equal to 1. A solvent deuterium isotope effect of 2.4 is observed with NADH or NADD as the dinucleotide substrate. Data suggest rate-limiting imine formation, consistent with the proposed role of H96 in protonating the leaving hydroxyl as the imine is formed. The pH-rate profile for V2/KLysEt exhibits the pKa for K77, perturbed to a value of about 9, which must be unprotonated in order to accept a proton from the epsilon-amine of the substrate Lys so that it can act as a nucleophile. Overall, data are consistent with a role for K77 acting as the base that accepts a proton from the epsilon-amine of the substrate lysine prior to nucleophilic attack on the alpha-oxo group of alpha-ketoglutarate, and finally donating a proton to the imine nitrogen as it is reduced to give saccharopine. In addition, data indicate a role for H96 acting as a general acid-base catalyst in formation of the imine between the epsilon-amine of lysine and the alpha-oxo group of alpha-ketoglutarate.	+
-		+
-	Evidence in Support of Lysine 77 and Histidine 96 as Acid-base Catalytic Residues in Saccharopine Dehydrogenase from Saccharomyces cerevisiae.,Kumar VP, Thomas LM, Bobyk KD, Andi B, Cook PF, West AH Biochemistry. 2012 Jan 13. PMID:22243403<ref>PMID:22243403</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3uha" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Baker's yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Bobyk, K D~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: ~~Cook, P F~~]]	+	[[Category: Bobyk KD]]
-	[[Category: ~~Kumar, V P~~]]	+	[[Category: Cook PF]]
-	[[Category: ~~Thomas, L M~~]]	+	[[Category: Kumar VP]]
-	[[Category: ~~West, A H~~]]	+	[[Category: Thomas LM]]
-	[[Category: ~~Enzyme mechanism]]~~	+	[[Category: West AH]]
-	~~[[Category: Lysine biosynthesis]]~~	+
-	~~[[Category: Nad binding]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Proton shuttle~~]]	+

OCA at 06:13, 13 July 2022

OCA — Wed, 13 Jul 2022 06:13:11 GMT

←Older revision		Revision as of 06:13, 13 July 2022
Line 1:		Line 1:

	==Crystal Structure of Saccharopine Dehydrogenase from Saccharomyces cervisiae complexed with NAD.==		==Crystal Structure of Saccharopine Dehydrogenase from Saccharomyces cervisiae complexed with NAD.==
-	<StructureSection load='3uha' size='340' side='right' caption='[[3uha]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='3uha' size='340' side='right'caption='[[3uha]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3uha]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UHA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3UHA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3uha]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UHA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UHA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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">LYS1, YIR034C ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LYS1, YIR034C ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Saccharopine_dehydrogenase_(NAD(+),_L-lysine-forming) Saccharopine dehydrogenase (NAD(+), L-lysine-forming)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.7 1.5.1.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Saccharopine_dehydrogenase_(NAD(+),_L-lysine-forming) Saccharopine dehydrogenase (NAD(+), L-lysine-forming)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.7 1.5.1.7] </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=3uha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uha OCA], [~~http~~://pdbe.org/3uha PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3uha RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3uha PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3uha 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=3uha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uha OCA], [https://pdbe.org/3uha PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3uha RCSB], [https://www.ebi.ac.uk/pdbsum/3uha PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3uha ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/LYS1_YEAST LYS1_YEAST]] Catalyzes the NAD(+)-dependent cleavage of saccharopine to L-lysine and 2-oxoglutarate.	+	[[https://www.uniprot.org/uniprot/LYS1_YEAST LYS1_YEAST]] Catalyzes the NAD(+)-dependent cleavage of saccharopine to L-lysine and 2-oxoglutarate.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Baker's yeast]]		[[Category: Baker's yeast]]
		+	[[Category: Large Structures]]
	[[Category: Bobyk, K D]]		[[Category: Bobyk, K D]]
	[[Category: Cook, P F]]		[[Category: Cook, P F]]

OCA at 07:15, 5 August 2016

OCA — Fri, 05 Aug 2016 07:15:15 GMT

←Older revision		Revision as of 07:15, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of Saccharopine Dehydrogenase from Saccharomyces cervisiae complexed with NAD.==		==Crystal Structure of Saccharopine Dehydrogenase from Saccharomyces cervisiae complexed with NAD.==
	<StructureSection load='3uha' size='340' side='right' caption='[[3uha]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3uha' size='340' side='right' caption='[[3uha]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3uha]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UHA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UHA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3uha]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UHA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UHA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=CL:CHLORIDE+ION'>CL</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">LYS1, YIR034C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~4932 Saccharomyces cerevisiae~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LYS1, YIR034C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Saccharopine_dehydrogenase_(NAD(+),_L-lysine-forming) Saccharopine dehydrogenase (NAD(+), L-lysine-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.7 1.5.1.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Saccharopine_dehydrogenase_(NAD(+),_L-lysine-forming) Saccharopine dehydrogenase (NAD(+), L-lysine-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.7 1.5.1.7] </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=3uha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uha OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3uha RCSB], [http://www.ebi.ac.uk/pdbsum/3uha PDBsum]</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=3uha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uha OCA], [http://pdbe.org/3uha PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3uha RCSB], [http://www.ebi.ac.uk/pdbsum/3uha PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3uha ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3uha" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Saccharomyces cerevisiae~~]]	+	[[Category: Baker's yeast]]
	[[Category: Bobyk, K D]]		[[Category: Bobyk, K D]]
	[[Category: Cook, P F]]		[[Category: Cook, P F]]

OCA at 16:47, 25 December 2014

OCA — Thu, 25 Dec 2014 16:47:48 GMT

←Older revision		Revision as of 16:47, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3uha]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UHA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UHA FirstGlance]. <br>		<table><tr><td colspan='2'>[[3uha]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UHA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UHA FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LYS1, YIR034C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LYS1, YIR034C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Saccharopine_dehydrogenase_(NAD(+),_L-lysine-forming) Saccharopine dehydrogenase (NAD(+), L-lysine-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.7 1.5.1.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Saccharopine_dehydrogenase_(NAD(+),_L-lysine-forming) Saccharopine dehydrogenase (NAD(+), L-lysine-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.7 1.5.1.7] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3uha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uha OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3uha RCSB], [http://www.ebi.ac.uk/pdbsum/3uha PDBsum]</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=3uha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uha OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3uha RCSB], [http://www.ebi.ac.uk/pdbsum/3uha PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LYS1_YEAST LYS1_YEAST]] Catalyzes the NAD(+)-dependent cleavage of saccharopine to L-lysine and 2-oxoglutarate.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Bobyk, K D.]]	+	[[Category: Bobyk, K D]]
-	[[Category: Cook, P F.]]	+	[[Category: Cook, P F]]
-	[[Category: Kumar, V P.]]	+	[[Category: Kumar, V P]]
-	[[Category: Thomas, L M.]]	+	[[Category: Thomas, L M]]
-	[[Category: West, A H.]]	+	[[Category: West, A H]]
	[[Category: Enzyme mechanism]]		[[Category: Enzyme mechanism]]
	[[Category: Lysine biosynthesis]]		[[Category: Lysine biosynthesis]]

OCA at 09:27, 11 June 2014

OCA — Wed, 11 Jun 2014 09:27:13 GMT

←Older revision		Revision as of 09:27, 11 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3uha.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal Structure of Saccharopine Dehydrogenase from Saccharomyces cervisiae complexed with NAD.==
		+	<StructureSection load='3uha' size='340' side='right' caption='[[3uha]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3uha]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UHA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UHA FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LYS1, YIR034C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Saccharopine_dehydrogenase_(NAD(+),_L-lysine-forming) Saccharopine dehydrogenase (NAD(+), L-lysine-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.7 1.5.1.7] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3uha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uha OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3uha RCSB], [http://www.ebi.ac.uk/pdbsum/3uha PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Saccharopine dehydrogenase (SDH) catalyzes the final reaction in the alpha-aminoadipate pathway, the conversion of L-saccharopine to L-lysine (Lys) and alpha-ketoglutarate (alpha-Kg) using NAD+ as an oxidant. The enzyme utilizes a general acid-base mechanism to carry out its reaction with a base proposed to accept a proton from the secondary amine of saccharopine in the oxidation step and group proposed to activate water to hydrolyze the resulting imine. Crystal structures of an open apo-form and a closed form of the enzyme with saccharopine and NADH bound have been solved at 2.0 A and 2.2 A resolution, respectively. In the ternary complex, a significant movement of domain I relative to domain II is observed that closes the active site cleft between the two domains and brings H96 and K77 in close proximity to the substrate binding site. The hydride transfer distance is 3.6 A, and the side chains of H96 and K77 are properly positioned to act as acid-base catalysts. Preparation of the K77 to M, H96 to Q single and the K77M/H96Q double mutant enzymes provide data consistent with their role as the general acid-base catalysts in the SDH reaction. The side chain of K77 initially accepts a proton from the epsilon-amine of the substrate Lys and eventually donates it to the imino nitrogen as it is reduced to a secondary amine in the hydride transfer step, and H96 protonates the carbonyl oxygen as the carbinolamine is formed. The K77M, H976Q, and K77M/H96Q mutant enzymes give 145-, 28-, and 700-fold decreases in V/Et and >103 increases in V2/KLysEt and V2/Kalpha-KgEt (the double mutation gives >105-fold decreases in the second order rate constants). In addition, the K77M mutant enzyme exhibits a primary deuterium kinetic isotope effect of 2.0 and an inverse solvent deuterium isotope effect of 0.77 on V2/KLys. A value of 2.0 was also observed for D(V2/KLys)D2O when the primary deuterium kinetic isotope effect was repeated in D2O, consistent with a rate-limiting hydride transfer step. A viscosity effect of 0.8 was observed on V2/KLys indicating the solvent deuterium isotope effect resulted from stabilization of an enzyme form prior to hydride transfer. A small normal solvent isotope effect is observed on V, which decreases slightly when repeated with NADD, consistent with a contribution from product release to rate limitation. In addition, V2/KLysEt is pH independent consistent with the loss of an acid-base catalyst and perturbation of the pKa of the second catalytic group to higher pH, likely a result of a change in the overall charge in the active site. The primary deuterium kinetic isotope effect for H96Q, measured in H2O or D2O, is within error equal to 1. A solvent deuterium isotope effect of 2.4 is observed with NADH or NADD as the dinucleotide substrate. Data suggest rate-limiting imine formation, consistent with the proposed role of H96 in protonating the leaving hydroxyl as the imine is formed. The pH-rate profile for V2/KLysEt exhibits the pKa for K77, perturbed to a value of about 9, which must be unprotonated in order to accept a proton from the epsilon-amine of the substrate Lys so that it can act as a nucleophile. Overall, data are consistent with a role for K77 acting as the base that accepts a proton from the epsilon-amine of the substrate lysine prior to nucleophilic attack on the alpha-oxo group of alpha-ketoglutarate, and finally donating a proton to the imine nitrogen as it is reduced to give saccharopine. In addition, data indicate a role for H96 acting as a general acid-base catalyst in formation of the imine between the epsilon-amine of lysine and the alpha-oxo group of alpha-ketoglutarate.

-	~~{{STRUCTURE_3uha\| PDB=3uha \| SCENE= }}~~	+	Evidence in Support of Lysine 77 and Histidine 96 as Acid-base Catalytic Residues in Saccharopine Dehydrogenase from Saccharomyces cerevisiae.,Kumar VP, Thomas LM, Bobyk KD, Andi B, Cook PF, West AH Biochemistry. 2012 Jan 13. PMID:22243403<ref>PMID:22243403</ref>

-	~~===Crystal Structure~~ of ~~Saccharopine Dehydrogenase from Saccharomyces cervisiae complexed with NAD~~.~~===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_22243403}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3uha]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UHA OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022243403<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Bobyk, K D.]]		[[Category: Bobyk, K D.]]

OCA at 10:28, 8 August 2012

OCA — Wed, 08 Aug 2012 10:28:04 GMT

←Older revision		Revision as of 10:28, 8 August 2012
Line 1:		Line 1:
	[[Image:3uha.png\|left\|200px]]		[[Image:3uha.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3uha", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3uha\| PDB=3uha \| SCENE= }}		{{STRUCTURE_3uha\| PDB=3uha \| SCENE= }}

	===Crystal Structure of Saccharopine Dehydrogenase from Saccharomyces cervisiae complexed with NAD.===		===Crystal Structure of Saccharopine Dehydrogenase from Saccharomyces cervisiae complexed with NAD.===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_22243403}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 22243403 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_22243403}}		{{ABSTRACT_PUBMED_22243403}}

OCA at 07:08, 22 February 2012

OCA — Wed, 22 Feb 2012 07:08:55 GMT

←Older revision		Revision as of 07:08, 22 February 2012
Line 1:		Line 1:
-	[[Image:3uha.~~jpg~~\|left\|200px]]	+	[[Image:3uha.png\|left\|200px]]

	<!--		<!--

OCA at 07:23, 1 February 2012

OCA — Wed, 01 Feb 2012 07:23:33 GMT

←Older revision		Revision as of 07:23, 1 February 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3uha.jpg\|left\|200px]]

-	The ~~entry 3uha~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3uha", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3uha\| PDB=3uha \| SCENE= }}

-	~~Authors: Cook, P.F., Kumar, V.P., Thomas, L.M., West, A.H., Bobyk, K.D~~.	+	===Crystal Structure of Saccharopine Dehydrogenase from Saccharomyces cervisiae complexed with NAD.===

-	~~Description~~: ~~Crystal~~ Structure ~~of Saccharopine Dehydrogenase~~ from Saccharomyces ~~cervisiae complexed with NAD~~.	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22243403}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22243403 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22243403}}
		+
		+	==About this Structure==
		+	[[3uha]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UHA OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022243403</ref><references group="xtra"/>
		+	[[Category: Saccharomyces cerevisiae]]
		+	[[Category: Bobyk, K D.]]
		+	[[Category: Cook, P F.]]
		+	[[Category: Kumar, V P.]]
		+	[[Category: Thomas, L M.]]
		+	[[Category: West, A H.]]
		+	[[Category: Enzyme mechanism]]
		+	[[Category: Lysine biosynthesis]]
		+	[[Category: Nad binding]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Proton shuttle]]

OCA at 10:14, 18 January 2012

OCA — Wed, 18 Jan 2012 10:14:10 GMT

←Older revision		Revision as of 10:14, 18 January 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3uha is ON HOLD	+	The entry 3uha is ON HOLD until Paper Publication

	Authors: Cook, P.F., Kumar, V.P., Thomas, L.M., West, A.H., Bobyk, K.D.		Authors: Cook, P.F., Kumar, V.P., Thomas, L.M., West, A.H., Bobyk, K.D.

	Description: Crystal Structure of Saccharopine Dehydrogenase from Saccharomyces cervisiae complexed with NAD.		Description: Crystal Structure of Saccharopine Dehydrogenase from Saccharomyces cervisiae complexed with NAD.

OCA at 11:53, 16 November 2011

OCA — Wed, 16 Nov 2011 11:53:26 GMT

←Older revision		Revision as of 11:53, 16 November 2011
Line 3:		Line 3:
	The entry 3uha is ON HOLD		The entry 3uha is ON HOLD

-	Authors: Cook, P. F., Kumar, V.P., Thomas, L.M., West, A.H., Bobyk, K.D.	+	Authors: Cook, P.F., Kumar, V.P., Thomas, L.M., West, A.H., Bobyk, K.D.

	Description: Crystal Structure of Saccharopine Dehydrogenase from Saccharomyces cervisiae complexed with NAD.		Description: Crystal Structure of Saccharopine Dehydrogenase from Saccharomyces cervisiae complexed with NAD.