1nen

From Proteopedia

(Difference between revisions)

Current revision

Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 inhibitor co-crystallized at the ubiquinone binding site

Structural highlights

1nen is a 4 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.9Å
Ligands:	, , , , , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SDHA_ECOLI Two distinct, membrane-bound, FAD-containing enzymes are responsible for the catalysis of fumarate and succinate interconversion; the fumarate reductase is used in anaerobic growth, and the succinate dehydrogenase is used in aerobic growth.^[1] ^[2] ^[3] ^[4]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

↑ McNeil MB, Hampton HG, Hards KJ, Watson BN, Cook GM, Fineran PC. The succinate dehydrogenase assembly factor, SdhE, is required for the flavinylation and activation of fumarate reductase in bacteria. FEBS Lett. 2014 Jan 31;588(3):414-21. doi: 10.1016/j.febslet.2013.12.019. Epub, 2013 Dec 25. PMID:24374335 doi:http://dx.doi.org/10.1016/j.febslet.2013.12.019
↑ Yankovskaya V, Horsefield R, Tornroth S, Luna-Chavez C, Miyoshi H, Leger C, Byrne B, Cecchini G, Iwata S. Architecture of succinate dehydrogenase and reactive oxygen species generation. Science. 2003 Jan 31;299(5607):700-4. PMID:12560550 doi:10.1126/science.1079605
↑ Horsefield R, Yankovskaya V, Sexton G, Whittingham W, Shiomi K, Omura S, Byrne B, Cecchini G, Iwata S. Structural and computational analysis of the quinone-binding site of complex II (succinate-ubiquinone oxidoreductase): a mechanism of electron transfer and proton conduction during ubiquinone reduction. J Biol Chem. 2006 Mar 17;281(11):7309-16. Epub 2005 Dec 27. PMID:16407191 doi:http://dx.doi.org/10.1074/jbc.M508173200
↑ Ruprecht J, Yankovskaya V, Maklashina E, Iwata S, Cecchini G. Structure of Escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-binding site. J Biol Chem. 2009 Oct 23;284(43):29836-46. Epub 2009 Aug 25. PMID:19710024 doi:10.1074/jbc.M109.010058

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1nen"

@@ Line 1: / Line 1: @@
 ==Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 inhibitor co-crystallized at the ubiquinone binding site==
-<StructureSection load='1nen' size='340' side='right' caption='[[1nen]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+<StructureSection load='1nen' size='340' side='right'caption='[[1nen]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1nen]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NEN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NEN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1nen]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NEN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NEN FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CDN:CARDIOLIPIN'>CDN</scene>, <scene name='pdbligand=DNT:2-[1-METHYLHEXYL]-4,6-DINITROPHENOL'>DNT</scene>, <scene name='pdbligand=EPH:L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE'>EPH</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=OAA:OXALOACETATE+ION'>OAA</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">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SDHA OR B0723 OR Z0877 OR ECS0748 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), SDHB OR B0724 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), SDHC OR CYBA OR B0721 OR Z0875 OR ECS0746 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), SDHD OR B0722 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CDN:CARDIOLIPIN'>CDN</scene>, <scene name='pdbligand=DNT:2-[1-METHYLHEXYL]-4,6-DINITROPHENOL'>DNT</scene>, <scene name='pdbligand=EPH:L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE'>EPH</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=OAA:OXALOACETATE+ION'>OAA</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nen FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nen OCA], [http://pdbe.org/1nen PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nen RCSB], [http://www.ebi.ac.uk/pdbsum/1nen PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nen 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=1nen FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nen OCA], [https://pdbe.org/1nen PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nen RCSB], [https://www.ebi.ac.uk/pdbsum/1nen PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nen ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DHSD_ECOLI DHSD_ECOLI]] Membrane-anchoring subunit of succinate dehydrogenase (SDH). [[http://www.uniprot.org/uniprot/DHSA_ECOLI DHSA_ECOLI]] Two distinct, membrane-bound, FAD-containing enzymes are responsible for the catalysis of fumarate and succinate interconversion; the fumarate reductase is used in anaerobic growth, and the succinate dehydrogenase is used in aerobic growth. [[http://www.uniprot.org/uniprot/DHSC_ECOLI DHSC_ECOLI]] Membrane-anchoring subunit of succinate dehydrogenase (SDH). [[http://www.uniprot.org/uniprot/DHSB_ECOLI DHSB_ECOLI]] Two distinct, membrane-bound, FAD-containing enzymes are responsible for the catalysis of fumarate and succinate interconversion; the fumarate reductase is used in anaerobic growth, and the succinate dehydrogenase is used in aerobic growth.
+[https://www.uniprot.org/uniprot/SDHA_ECOLI SDHA_ECOLI] Two distinct, membrane-bound, FAD-containing enzymes are responsible for the catalysis of fumarate and succinate interconversion; the fumarate reductase is used in anaerobic growth, and the succinate dehydrogenase is used in aerobic growth.<ref>PMID:24374335</ref> <ref>PMID:12560550</ref> <ref>PMID:16407191</ref> <ref>PMID:19710024</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ne/1nen_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ne/1nen_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 20: / Line 20: @@
 </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1nen ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The structure of Escherichia coli succinate dehydrogenase (SQR), analogous to the mitochondrial respiratory complex II, has been determined, revealing the electron transport pathway from the electron donor, succinate, to the terminal electron acceptor, ubiquinone. It was found that the SQR redox centers are arranged in a manner that aids the prevention of reactive oxygen species (ROS) formation at the flavin adenine dinucleotide. This is likely to be the main reason SQR is expressed during aerobic respiration rather than the related enzyme fumarate reductase, which produces high levels of ROS. Furthermore, symptoms of genetic disorders associated with mitochondrial SQR mutations may be a result of ROS formation resulting from impaired electron transport in the enzyme.
-Architecture of succinate dehydrogenase and reactive oxygen species generation.,Yankovskaya V, Horsefield R, Tornroth S, Luna-Chavez C, Miyoshi H, Leger C, Byrne B, Cecchini G, Iwata S Science. 2003 Jan 31;299(5607):700-4. PMID:12560550<ref>PMID:12560550</ref>
+==See Also==
+*[[Succinate dehydrogenase 3D structures|Succinate dehydrogenase 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1nen" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Byrne, B]]
+[[Category: Large Structures]]
-[[Category: Cecchini, G]]
+[[Category: Byrne B]]
-[[Category: Horsefield, R]]
+[[Category: Cecchini G]]
-[[Category: Iwata, S]]
+[[Category: Horsefield R]]
-[[Category: Leger, C]]
+[[Category: Iwata S]]
-[[Category: Luna-Chavez, C]]
+[[Category: Leger C]]
-[[Category: Miyoshi, H]]
+[[Category: Luna-Chavez C]]
-[[Category: Tornroth, S]]
+[[Category: Miyoshi H]]
-[[Category: Yankovskaya, V]]
+[[Category: Tornroth S]]
-[[Category: Membrane protein]]
+[[Category: Yankovskaya V]]
-[[Category: Oxidoreductase-electron transport complex]]
-[[Category: Respiratory complex]]

1nen

From Proteopedia

Current revision

Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 inhibitor co-crystallized at the ubiquinone binding site

Structural highlights

Function

Evolutionary Conservation

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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