6myp - Revision history

OCA at 06:41, 11 October 2023

OCA — Wed, 11 Oct 2023 06:41:56 GMT

←Older revision		Revision as of 06:41, 11 October 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6myp]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MYP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MYP FirstGlance]. <br>		<table><tr><td colspan='2'>[[6myp]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MYP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MYP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PE:1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>3PE</scene>, <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OAA:OXALOACETATE+ION'>OAA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TTF:4,4,4-TRIFLUORO-1-THIEN-2-YLBUTANE-1,3-DIONE'>TTF</scene>, <scene name='pdbligand=UMQ:UNDECYL-MALTOSIDE'>UMQ</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</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]] 2.1Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</scene></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PE:1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>3PE</scene>, <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</scene>, <scene name='pdbligand=OAA:OXALOACETATE+ION'>OAA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TTF:4,4,4-TRIFLUORO-1-THIEN-2-YLBUTANE-1,3-DIONE'>TTF</scene>, <scene name='pdbligand=UMQ:UNDECYL-MALTOSIDE'>UMQ</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Succinate_dehydrogenase_(quinone) Succinate dehydrogenase (quinone)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.5.1 1.3.5.1] </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=6myp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6myp OCA], [https://pdbe.org/6myp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6myp RCSB], [https://www.ebi.ac.uk/pdbsum/6myp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6myp 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=6myp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6myp OCA], [https://pdbe.org/6myp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6myp RCSB], [https://www.ebi.ac.uk/pdbsum/6myp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6myp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DHSD_CHICK DHSD_CHICK]] Membrane-anchoring subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q). [[https://www.uniprot.org/uniprot/F1NPJ4_CHICK F1NPJ4_CHICK]] Flavoprotein (FP) subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q).[RuleBase:RU362051] [[https://www.uniprot.org/uniprot/SDHB_CHICK SDHB_CHICK]] Iron-sulfur protein (IP) subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q).	+	[https://www.uniprot.org/uniprot/SDHA_CHICK SDHA_CHICK] Flavoprotein (FP) subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 29:		Line 28:
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Berry~~, E A~~]]	+	[[Category: Berry EA]]
-	[[Category: Huang, L S]]	+	[[Category: Huang L-S]]
-	~~[[Category: Complex ii]]~~	+
-	~~[[Category: Heme protein]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Oxidoreductase-oxidoreductase inhibitor complex~~]]	+

OCA at 10:06, 7 July 2021

OCA — Wed, 07 Jul 2021 10:06:44 GMT

←Older revision		Revision as of 10:06, 7 July 2021
Line 3:		Line 3:
	<StructureSection load='6myp' size='340' side='right'caption='[[6myp]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6myp' size='340' side='right'caption='[[6myp]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6myp]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MYP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6MYP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6myp]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MYP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MYP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3PE:1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>3PE</scene>, <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OAA:OXALOACETATE+ION'>OAA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TTF:4,4,4-TRIFLUORO-1-THIEN-2-YLBUTANE-1,3-DIONE'>TTF</scene>, <scene name='pdbligand=UMQ:UNDECYL-MALTOSIDE'>UMQ</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PE:1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>3PE</scene>, <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OAA:OXALOACETATE+ION'>OAA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TTF:4,4,4-TRIFLUORO-1-THIEN-2-YLBUTANE-1,3-DIONE'>TTF</scene>, <scene name='pdbligand=UMQ:UNDECYL-MALTOSIDE'>UMQ</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Succinate_dehydrogenase_(quinone) Succinate dehydrogenase (quinone)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.5.1 1.3.5.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Succinate_dehydrogenase_(quinone) Succinate dehydrogenase (quinone)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.5.1 1.3.5.1] </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=6myp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6myp OCA], [~~http~~://pdbe.org/6myp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6myp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6myp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6myp 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=6myp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6myp OCA], [https://pdbe.org/6myp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6myp RCSB], [https://www.ebi.ac.uk/pdbsum/6myp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6myp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DHSD_CHICK DHSD_CHICK]] Membrane-anchoring subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q). [[~~http~~://www.uniprot.org/uniprot/F1NPJ4_CHICK F1NPJ4_CHICK]] Flavoprotein (FP) subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q).[RuleBase:RU362051] [[~~http~~://www.uniprot.org/uniprot/SDHB_CHICK SDHB_CHICK]] Iron-sulfur protein (IP) subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q).	+	[[https://www.uniprot.org/uniprot/DHSD_CHICK DHSD_CHICK]] Membrane-anchoring subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q). [[https://www.uniprot.org/uniprot/F1NPJ4_CHICK F1NPJ4_CHICK]] Flavoprotein (FP) subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q).[RuleBase:RU362051] [[https://www.uniprot.org/uniprot/SDHB_CHICK SDHB_CHICK]] Iron-sulfur protein (IP) subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~We report three new structures~~ of ~~mitochondrial respiratory~~ Complex II (succinate ubiquinone oxidoreductase~~, E~~.C. ~~1.3.5.1)~~ at ~~up to~~ 2.1 A ~~resolution, with various inhibitors~~. ~~The~~ structures ~~define~~ the ~~conformation of~~ the ~~bound~~ inhibitors and ~~suggest the residues involved in substrate~~ binding ~~and catalysis at the dicarboxylate~~ site. In ~~particular they support the role of Arg(297) as~~ a ~~general base catalyst accepting a proton in the dehydrogenation~~ of ~~succinate. The dicarboxylate ligand in oxaloacetate~~-~~containing crystals appears~~ to ~~be the same as that reported for Shewanella flavocytochrome c treated with fumarate. The plant~~ and ~~fungal toxin 3~~-~~nitropropionic acid~~, ~~an irreversible inactivator of succinate dehydrogenase, forms~~ a ~~covalent adduct with~~ the side chain of ~~Arg(297)~~. ~~The modification eliminates a trypsin cleavage site in~~ the ~~flavoprotein~~, and ~~tandem mass spectroscopic analysis~~ of the ~~new fragment shows~~ the ~~mass~~ of ~~Arg(297) to be increased by 83 Da~~ and to ~~have~~ the ~~potential~~ of ~~losing 44 Da~~, ~~consistent with decarboxylation~~, ~~during fragmentation~~.	+	The quinone binding site (Q-site) of Mitochondrial Complex II (succinate-ubiquinone oxidoreductase) is the target for a number of inhibitors useful for elucidating the mechanism of the enzyme. Some of these have been developed as fungicides or pesticides, and species-specific Q-site inhibitors may be useful against human pathogens. We report structures of chicken Complex II with six different Q-site inhibitors bound, at resolutions 2.0-2.4 A. These structures show the common interactions between the inhibitors and their binding site. In every case a carbonyl or hydroxyl oxygen of the inhibitor is H-bonded to Tyr58 in subunit SdhD and Trp173 in subunit SdhB. Two of the inhibitors H-bond Ser39 in subunit SdhC directly, while two others do so via a water molecule. There is a distinct cavity that accepts the 2-substituent of the carboxylate ring in flutolanil and related inhibitors. A hydrophobic "tail pocket" opens to receive a side-chain of intermediate-length inhibitors. Shorter inhibitors fit entirely within the main binding cleft, while the long hydrophobic side chains of ferulenol and atpenin A5 protrude out of the cleft into the bulk lipid region, as presumably does that of ubiquinone. Comparison of mitochondrial and Escherichia coli Complex II shows a rotation of the membrane-anchor subunits by 7 degrees relative to the ironsulfur protein. This rotation alters the geometry of the Q-site and the H-bonding pattern of SdhB:His216 and SdhD:Asp57. This conformational difference, rather than any active-site mutation, may be responsible for the different inhibitor sensitivity of the bacterial enzyme.

-	~~3-nitropropionic acid is a suicide inhibitor~~ of ~~mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in~~ the ~~active~~ site of ~~the enzyme~~.,Huang LS, ~~Sun G, Cobessi D, Wang AC, Shen JT, Tung EY, Anderson VE~~, Berry EA ~~J Biol Chem~~. ~~2006 Mar 3~~;~~281~~(9):~~5965-72~~. Epub ~~2005 Dec 21~~. PMID:~~16371358~~<ref>PMID:~~16371358~~</ref>	+	Crystallographic investigation of the ubiquinone binding site of respiratory Complex II and its inhibitors.,Huang LS, Lummen P, Berry EA Biochim Biophys Acta Proteins Proteom. 2021 Sep;1869(9):140679. doi:, 10.1016/j.bbapap.2021.140679. Epub 2021 Jun 3. PMID:34089891<ref>PMID:34089891</ref>

	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 6myp" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6myp" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Succinate dehydrogenase 3D structures\|Succinate dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:42, 6 November 2019

OCA — Wed, 06 Nov 2019 06:42:45 GMT

←Older revision		Revision as of 06:42, 6 November 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6myp is ~~ON HOLD until Paper~~ Publication	+	==Avian mitochondrial complex II with TTFA (thenoyltrifluoroacetone) bound==
		+	<StructureSection load='6myp' size='340' side='right'caption='[[6myp]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6myp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MYP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MYP FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3PE:1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>3PE</scene>, <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OAA:OXALOACETATE+ION'>OAA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TTF:4,4,4-TRIFLUORO-1-THIEN-2-YLBUTANE-1,3-DIONE'>TTF</scene>, <scene name='pdbligand=UMQ:UNDECYL-MALTOSIDE'>UMQ</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Succinate_dehydrogenase_(quinone) Succinate dehydrogenase (quinone)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.5.1 1.3.5.1] </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=6myp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6myp OCA], [http://pdbe.org/6myp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6myp RCSB], [http://www.ebi.ac.uk/pdbsum/6myp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6myp ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DHSD_CHICK DHSD_CHICK]] Membrane-anchoring subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q). [[http://www.uniprot.org/uniprot/F1NPJ4_CHICK F1NPJ4_CHICK]] Flavoprotein (FP) subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q).[RuleBase:RU362051] [[http://www.uniprot.org/uniprot/SDHB_CHICK SDHB_CHICK]] Iron-sulfur protein (IP) subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We report three new structures of mitochondrial respiratory Complex II (succinate ubiquinone oxidoreductase, E.C. 1.3.5.1) at up to 2.1 A resolution, with various inhibitors. The structures define the conformation of the bound inhibitors and suggest the residues involved in substrate binding and catalysis at the dicarboxylate site. In particular they support the role of Arg(297) as a general base catalyst accepting a proton in the dehydrogenation of succinate. The dicarboxylate ligand in oxaloacetate-containing crystals appears to be the same as that reported for Shewanella flavocytochrome c treated with fumarate. The plant and fungal toxin 3-nitropropionic acid, an irreversible inactivator of succinate dehydrogenase, forms a covalent adduct with the side chain of Arg(297). The modification eliminates a trypsin cleavage site in the flavoprotein, and tandem mass spectroscopic analysis of the new fragment shows the mass of Arg(297) to be increased by 83 Da and to have the potential of losing 44 Da, consistent with decarboxylation, during fragmentation.

-	~~Authors: Berry~~, ~~E.A~~., Huang, L.-S.	+	3-nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme.,Huang LS, Sun G, Cobessi D, Wang AC, Shen JT, Tung EY, Anderson VE, Berry EA J Biol Chem. 2006 Mar 3;281(9):5965-72. Epub 2005 Dec 21. PMID:16371358<ref>PMID:16371358</ref>

-	~~Description~~: ~~Avian mitochondrial complex II with TTFA (thenoyltrifluoroacetone) bound~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Huang, L.-S]]	+	<div class="pdbe-citations 6myp" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Berry, E.A~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Gallus gallus]]
		+	[[Category: Large Structures]]
		+	[[Category: Berry, E A]]
		+	[[Category: Huang, L S]]
		+	[[Category: Complex ii]]
		+	[[Category: Heme protein]]
		+	[[Category: Membrane protein]]
		+	[[Category: Oxidoreductase-oxidoreductase inhibitor complex]]

OCA at 06:31, 19 December 2018

OCA — Wed, 19 Dec 2018 06:31:34 GMT

←Older revision		Revision as of 06:31, 19 December 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6myp is ON HOLD	+	The entry 6myp is ON HOLD until Paper Publication

	Authors: Berry, E.A., Huang, L.-S.		Authors: Berry, E.A., Huang, L.-S.

OCA at 06:40, 14 November 2018

OCA — Wed, 14 Nov 2018 06:40:11 GMT

←Older revision		Revision as of 06:40, 14 November 2018
Line 5:		Line 5:
	Authors: Berry, E.A., Huang, L.-S.		Authors: Berry, E.A., Huang, L.-S.

-	Description: ~~AVIAN MITOCHONDRIAL COMPLEX~~ II ~~WITH~~ TTFA (thenoyltrifluoroacetone) ~~BOUND~~	+	Description: Avian mitochondrial complex II with TTFA (thenoyltrifluoroacetone) bound
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Huang, L.-S]]		[[Category: Huang, L.-S]]
	[[Category: Berry, E.A]]		[[Category: Berry, E.A]]

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

OCA — Wed, 07 Nov 2018 11:00:04 GMT

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

←Older revision

Revision as of 11:00, 7 November 2018

OCA: New page: '''Unreleased structure''' The entry 6myp is ON HOLD Authors: Berry, E.A., Huang, L.-S. Description: AVIAN MITOCHONDRIAL COMPLEX II WITH TTFA (thenoyltrifluoroacetone) BOUND [[Category...

OCA — Wed, 07 Nov 2018 11:00:03 GMT

New page: '''Unreleased structure''' The entry 6myp is ON HOLD Authors: Berry, E.A., Huang, L.-S. Description: AVIAN MITOCHONDRIAL COMPLEX II WITH TTFA (thenoyltrifluoroacetone) BOUND [[Category...

New page

'''Unreleased structure'''

The entry 6myp is ON HOLD

Authors: Berry, E.A., Huang, L.-S.

Description: AVIAN MITOCHONDRIAL COMPLEX II WITH TTFA (thenoyltrifluoroacetone) BOUND
[[Category: Unreleased Structures]]
[[Category: Huang, L.-S]]
[[Category: Berry, E.A]]