6lum: Difference between revisions

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<StructureSection load='6lum' size='340' side='right'caption='[[6lum]], [[Resolution|resolution]] 2.84&Aring;' scene=''>
<StructureSection load='6lum' size='340' side='right'caption='[[6lum]], [[Resolution|resolution]] 2.84&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6lum]] is a 15 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_mc2_51 Mycolicibacterium smegmatis mc2 51]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LUM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LUM FirstGlance]. <br>
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LUM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LUM FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CDL:CARDIOLIPIN'>CDL</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=LPP:2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL+HEXADECANOATE'>LPP</scene>, <scene name='pdbligand=MQ9:MENAQUINONE-9'>MQ9</scene>, <scene name='pdbligand=PEV:(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL+STEARATE'>PEV</scene>, <scene name='pdbligand=PIE:1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL'>PIE</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.84&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CDL:CARDIOLIPIN'>CDL</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=LPP:2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL+HEXADECANOATE'>LPP</scene>, <scene name='pdbligand=MQ9:MENAQUINONE-9'>MQ9</scene>, <scene name='pdbligand=PEV:(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL+STEARATE'>PEV</scene>, <scene name='pdbligand=PIE:1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL'>PIE</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></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=6lum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lum OCA], [https://pdbe.org/6lum PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lum RCSB], [https://www.ebi.ac.uk/pdbsum/6lum PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lum 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=6lum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lum OCA], [https://pdbe.org/6lum PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lum RCSB], [https://www.ebi.ac.uk/pdbsum/6lum PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lum ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are widespread in Gram-positive bacteria but little is known about the catalytic mechanisms they employ for succinate oxidation by menaquinone. Here, we present the 2.8 A cryo-electron microscopy structure of a Mycobacterium smegmatis Sdh, which forms a trimer. We identified the membrane-anchored SdhF as a subunit of the complex. The 3 kDa SdhF forms a single transmembrane helix and this helix plays a role in blocking the canonically proximal quinone-binding site. We also identified two distal quinone-binding sites with bound quinones. One distal binding site is formed by neighboring subunits of the complex. Our structure further reveals the electron/proton transfer pathway for succinate oxidation by menaquinone. Moreover, this study provides further structural insights into the physiological significance of a trimeric respiratory complex II. The structure of the menaquinone binding site could provide a framework for the development of Sdh-selective anti-mycobacterial drugs.
Cryo-EM structure of trimeric Mycobacterium smegmatis succinate dehydrogenase with a membrane-anchor SdhF.,Gong H, Gao Y, Zhou X, Xiao Y, Wang W, Tang Y, Zhou S, Zhang Y, Ji W, Yu L, Tian C, Lam SM, Shui G, Guddat LW, Wong LL, Wang Q, Rao Z Nat Commun. 2020 Aug 25;11(1):4245. doi: 10.1038/s41467-020-18011-9. PMID:32843629<ref>PMID:32843629</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6lum" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Succinate dehydrogenase 3D structures|Succinate dehydrogenase 3D structures]]
*[[Succinate dehydrogenase 3D structures|Succinate dehydrogenase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Mycolicibacterium smegmatis mc2 51]]
[[Category: Gao Y]]
[[Category: Gao, Y]]
[[Category: Gong H]]
[[Category: Gong, H]]
[[Category: Ji W]]
[[Category: Ji, W]]
[[Category: Rao Z]]
[[Category: Rao, Z]]
[[Category: Wang Q]]
[[Category: Wang, Q]]
[[Category: Wang W]]
[[Category: Wang, W]]
[[Category: Xiao Y]]
[[Category: Xiao, Y]]
[[Category: Zhou X]]
[[Category: Zhou, X]]
[[Category: Electron transfer chain]]
[[Category: Oxidoreductase]]
[[Category: Trimer]]

Latest revision as of 19:28, 29 May 2024

Structure of Mycobacterium smegmatis succinate dehydrogenase 2

6lum, resolution 2.84Å

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