4ytn: Difference between revisions

Latest revision as of 12:00, 13 August 2026

Crystal structure of Mitochondrial rhodoquinol-fumarate reductase from Ascaris suum with N-[3-(pentafluorophenoxy)phenyl]-2-(trifluoromethyl)benzamide

Structural highlights

4ytn is a 8 chain structure with sequence from Ascaris suum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3Å
Ligands:	FAD, FD8, FES, HEM, MLI
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SDHA1_ASCSU Flavoprotein (Fp) subunit of the mitochondrial electron transport chain complex II which, together with the iron-sulfur protein (Ip) subunit forms the catalytic core of the complex (PubMed:12742584, PubMed:17933581, PubMed:2843227, PubMed:7739664, PubMed:7822332, PubMed:8435436). During the parasitic larvae and adult stages, which occur in an anaerobic environment, acts as a fumarate reductase by transferring electrons from rhodoquinol to fumarate (PubMed:12742584, PubMed:17933581, PubMed:2843227, PubMed:7739664, PubMed:7822332, PubMed:8435436).^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

References

↑ Amino H, Osanai A, Miyadera H, Shinjyo N, Tomitsuka E, Taka H, Mineki R, Murayama K, Takamiya S, Aoki T, Miyoshi H, Sakamoto K, Kojima S, Kita K. Isolation and characterization of the stage-specific cytochrome b small subunit (CybS) of Ascaris suum complex II from the aerobic respiratory chain of larval mitochondria. Mol Biochem Parasitol. 2003 May;128(2):175-86. PMID:12742584 doi:10.1016/s0166-6851(03)00074-4
↑ Iwata F, Shinjyo N, Amino H, Sakamoto K, Islam MK, Tsuji N, Kita K. Change of subunit composition of mitochondrial complex II (succinate-ubiquinone reductase/quinol-fumarate reductase) in Ascaris suum during the migration in the experimental host. Parasitol Int. 2008 Mar;57(1):54-61. PMID:17933581 doi:10.1016/j.parint.2007.08.002
↑ Kita K, Takamiya S, Furushima R, Ma YC, Suzuki H, Ozawa T, Oya H. Electron-transfer complexes of Ascaris suum muscle mitochondria. III. Composition and fumarate reductase activity of complex II. Biochim Biophys Acta. 1988 Sep 14;935(2):130-40. PMID:2843227 doi:10.1016/0005-2728(88)90210-1
↑ Kuramochi T, Hirawake H, Kojima S, Takamiya S, Furushima R, Aoki T, Komuniecki R, Kita K. Sequence comparison between the flavoprotein subunit of the fumarate reductase (complex II) of the anaerobic parasitic nematode, Ascaris suum and the succinate dehydrogenase of the aerobic, free-living nematode, Caenorhabditis elegans. Mol Biochem Parasitol. 1994 Dec;68(2):177-87. PMID:7739664 doi:10.1016/0166-6851(94)90163-5
↑ Saruta F, Kuramochi T, Nakamura K, Takamiya S, Yu Y, Aoki T, Sekimizu K, Kojima S, Kita K. Stage-specific isoforms of complex II (succinate-ubiquinone oxidoreductase) in mitochondria from the parasitic nematode, Ascaris suum. J Biol Chem. 1995 Jan 13;270(2):928-32. PMID:7822332 doi:10.1074/jbc.270.2.928
↑ Takamiya S, Kita K, Wang H, Weinstein PP, Hiraishi A, Oya H, Aoki T. Developmental changes in the respiratory chain of Ascaris mitochondria. Biochim Biophys Acta. 1993 Feb 8;1141(1):65-74. PMID:8435436 doi:10.1016/0005-2728(93)90190-q

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Amino H, Osanai A, Miyadera H, Shinjyo N, Tomitsuka E, Taka H, Mineki R, Murayama K, Takamiya S, Aoki T, Miyoshi H, Sakamoto K, Kojima S, Kita K. Isolation and characterization of the stage-specific cytochrome b small subunit (CybS) of Ascaris suum complex II from the aerobic respiratory chain of larval mitochondria. Mol Biochem Parasitol. 2003 May;128(2):175-86. PMID:12742584 doi:10.1016/s0166-6851(03)00074-4

[2] Iwata F, Shinjyo N, Amino H, Sakamoto K, Islam MK, Tsuji N, Kita K. Change of subunit composition of mitochondrial complex II (succinate-ubiquinone reductase/quinol-fumarate reductase) in Ascaris suum during the migration in the experimental host. Parasitol Int. 2008 Mar;57(1):54-61. PMID:17933581 doi:10.1016/j.parint.2007.08.002

[3] Kita K, Takamiya S, Furushima R, Ma YC, Suzuki H, Ozawa T, Oya H. Electron-transfer complexes of Ascaris suum muscle mitochondria. III. Composition and fumarate reductase activity of complex II. Biochim Biophys Acta. 1988 Sep 14;935(2):130-40. PMID:2843227 doi:10.1016/0005-2728(88)90210-1

[4] Kuramochi T, Hirawake H, Kojima S, Takamiya S, Furushima R, Aoki T, Komuniecki R, Kita K. Sequence comparison between the flavoprotein subunit of the fumarate reductase (complex II) of the anaerobic parasitic nematode, Ascaris suum and the succinate dehydrogenase of the aerobic, free-living nematode, Caenorhabditis elegans. Mol Biochem Parasitol. 1994 Dec;68(2):177-87. PMID:7739664 doi:10.1016/0166-6851(94)90163-5

[5] Saruta F, Kuramochi T, Nakamura K, Takamiya S, Yu Y, Aoki T, Sekimizu K, Kojima S, Kita K. Stage-specific isoforms of complex II (succinate-ubiquinone oxidoreductase) in mitochondria from the parasitic nematode, Ascaris suum. J Biol Chem. 1995 Jan 13;270(2):928-32. PMID:7822332 doi:10.1074/jbc.270.2.928

[6] Takamiya S, Kita K, Wang H, Weinstein PP, Hiraishi A, Oya H, Aoki T. Developmental changes in the respiratory chain of Ascaris mitochondria. Biochim Biophys Acta. 1993 Feb 8;1141(1):65-74. PMID:8435436 doi:10.1016/0005-2728(93)90190-q

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[2]

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@@ Line 1: / Line 1: @@
 ==Crystal structure of Mitochondrial rhodoquinol-fumarate reductase from Ascaris suum with N-[3-(pentafluorophenoxy)phenyl]-2-(trifluoromethyl)benzamide==
-<StructureSection load='4ytn' size='340' side='right' caption='[[4ytn]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+<StructureSection load='4ytn' size='340' side='right'caption='[[4ytn]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ytn]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Ascaris_suum Ascaris suum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YTN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YTN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4ytn]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Ascaris_suum Ascaris suum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YTN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YTN FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FD8:N-[3-(PENTAFLUOROPHENOXY)PHENYL]-2-(TRIFLUOROMETHYL)BENZAMIDE'>FD8</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</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]] 3&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ysx|4ysx]], [[4ysy|4ysy]], [[4ysz|4ysz]], [[4yt0|4yt0]], [[4ytm|4ytm]], [[4ytp|4ytp]], [[4yxd|4yxd]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FD8:N-[3-(PENTAFLUOROPHENOXY)PHENYL]-2-(TRIFLUOROMETHYL)BENZAMIDE'>FD8</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</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'>[https://proteopedia.org/fgij/fg.htm?mol=4ytn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ytn OCA], [https://pdbe.org/4ytn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ytn RCSB], [https://www.ebi.ac.uk/pdbsum/4ytn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ytn ProSAT]</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=4ytn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ytn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ytn RCSB], [http://www.ebi.ac.uk/pdbsum/4ytn PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DHSD_ASCSU DHSD_ASCSU]] 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) (By similarity). [[http://www.uniprot.org/uniprot/U1LRQ3_ASCSU U1LRQ3_ASCSU]] 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/SDHA1_ASCSU SDHA1_ASCSU] Flavoprotein (Fp) subunit of the mitochondrial electron transport chain complex II which, together with the iron-sulfur protein (Ip) subunit forms the catalytic core of the complex (PubMed:12742584, PubMed:17933581, PubMed:2843227, PubMed:7739664, PubMed:7822332, PubMed:8435436). During the parasitic larvae and adult stages, which occur in an anaerobic environment, acts as a fumarate reductase by transferring electrons from rhodoquinol to fumarate (PubMed:12742584, PubMed:17933581, PubMed:2843227, PubMed:7739664, PubMed:7822332, PubMed:8435436).<ref>PMID:12742584</ref> <ref>PMID:17933581</ref> <ref>PMID:2843227</ref> <ref>PMID:7739664</ref> <ref>PMID:7822332</ref> <ref>PMID:8435436</ref>
+==See Also==
+*[[Succinate dehydrogenase 3D structures|Succinate dehydrogenase 3D structures]]
+== References ==
+<references/>
 __TOC__
 </StructureSection>
 [[Category: Ascaris suum]]
-[[Category: Harada, S]]
+[[Category: Large Structures]]
-[[Category: Honma, T]]
+[[Category: Harada S]]
-[[Category: Inaoka, D K]]
+[[Category: Honma T]]
-[[Category: Inoue, M]]
+[[Category: Inaoka DK]]
-[[Category: Kita, K]]
+[[Category: Inoue M]]
-[[Category: Nagahama, M]]
+[[Category: Kita K]]
-[[Category: Sakamoto, K]]
+[[Category: Nagahama M]]
-[[Category: Sato, D]]
+[[Category: Sakamoto K]]
-[[Category: Shiba, T]]
+[[Category: Sato D]]
-[[Category: Yamamoto, A]]
+[[Category: Shiba T]]
-[[Category: Yone, A]]
+[[Category: Yamamoto A]]
-[[Category: Complex ii]]
+[[Category: Yone A]]
-[[Category: Inhibitor]]
-[[Category: Oxidoreductase]]
-[[Category: Oxidoreductase-oxidoreductase inhibitor complex]]
-[[Category: Rhodoquinol-fumarate reductase]]

4ytn: Difference between revisions

Latest revision as of 12:00, 13 August 2026

Crystal structure of Mitochondrial rhodoquinol-fumarate reductase from Ascaris suum with N-[3-(pentafluorophenoxy)phenyl]-2-(trifluoromethyl)benzamide

Structural highlights

Function

See Also

References

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