4ysz: Difference between revisions

Latest revision as of 08:38, 23 October 2024

Crystal structure of Mitochondrial rhodoquinol-fumarate reductase from Ascaris suum with 2-iodo-N-[3-(1-methylethoxy)phenyl]benzamide

Structural highlights

4ysz 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 3.3Å
Ligands:	12J, EPH, FAD, FES, HEM, MLI
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SDHB_ASCSU Iron-sulfur protein (Ip) subunit of the mitochondrial electron transport chain complex II which, together with the flavoprotein (Fp) subunit forms the catalytic core of the complex (PubMed:10743611, PubMed:12742584, PubMed:17933581, PubMed:2843227, PubMed:7822332, PubMed:8435436). During the free-living egg-larvae stages, which occur in an aerobic environment, complex II acts as a succinate dehydrogenase by transferring electrons from succinate to ubiquinone (PubMed:10743611, PubMed:12742584, PubMed:17933581, PubMed:2843227, PubMed:7822332, PubMed:8435436). During the parasitic larvae and adult stages, which occur in an anaerobic environment, complex II acts as a fumarate reductase by transferring electrons from rhodoquinol to fumarate (PubMed:10743611, PubMed:12742584, PubMed:17933581, PubMed:2843227, PubMed:7822332, PubMed:8435436).^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

Publication Abstract from PubMed

Recent studies on the respiratory chain of Ascaris suum showed that the mitochondrial NADH-fumarate reductase system composed of complex I, rhodoquinone and complex II plays an important role in the anaerobic energy metabolism of adult A. suum. The system is the major pathway of energy metabolism for adaptation to a hypoxic environment not only in parasitic organisms, but also in some types of human cancer cells. Thus, enzymes of the pathway are potential targets for chemotherapy. We found that flutolanil is an excellent inhibitor for A. suum complex II (IC50 = 0.058 muM) but less effectively inhibits homologous porcine complex II (IC50 = 45.9 muM). In order to account for the specificity of flutolanil to A. suum complex II from the standpoint of structural biology, we determined the crystal structures of A. suum and porcine complex IIs binding flutolanil and its derivative compounds. The structures clearly demonstrated key interactions responsible for its high specificity to A. suum complex II and enabled us to find analogue compounds, which surpass flutolanil in both potency and specificity to A. suum complex II. Structures of complex IIs binding these compounds will be helpful to accelerate structure-based drug design targeted for complex IIs.

Structural Insights into the Molecular Design of Flutolanil Derivatives Targeted for Fumarate Respiration of Parasite Mitochondria.,Inaoka DK, Shiba T, Sato D, Balogun EO, Sasaki T, Nagahama M, Oda M, Matsuoka S, Ohmori J, Honma T, Inoue M, Kita K, Harada S Int J Mol Sci. 2015 Jul 7;16(7):15287-308. doi: 10.3390/ijms160715287. PMID:26198225^[7]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Amino H, Wang H, Hirawake H, Saruta F, Mizuchi D, Mineki R, Shindo N, Murayama K, Takamiya S, Aoki T, Kojima S, Kita K. Stage-specific isoforms of Ascaris suum complex. II: The fumarate reductase of the parasitic adult and the succinate dehydrogenase of free-living larvae share a common iron-sulfur subunit. Mol Biochem Parasitol. 2000 Feb 25;106(1):63-76. PMID:10743611 doi:10.1016/s0166-6851(99)00200-5
↑ 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
↑ 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
↑ Inaoka DK, Shiba T, Sato D, Balogun EO, Sasaki T, Nagahama M, Oda M, Matsuoka S, Ohmori J, Honma T, Inoue M, Kita K, Harada S. Structural Insights into the Molecular Design of Flutolanil Derivatives Targeted for Fumarate Respiration of Parasite Mitochondria. Int J Mol Sci. 2015 Jul 7;16(7):15287-308. doi: 10.3390/ijms160715287. PMID:26198225 doi:https://dx.doi.org/10.3390/ijms160715287

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OCA

[1] Amino H, Wang H, Hirawake H, Saruta F, Mizuchi D, Mineki R, Shindo N, Murayama K, Takamiya S, Aoki T, Kojima S, Kita K. Stage-specific isoforms of Ascaris suum complex. II: The fumarate reductase of the parasitic adult and the succinate dehydrogenase of free-living larvae share a common iron-sulfur subunit. Mol Biochem Parasitol. 2000 Feb 25;106(1):63-76. PMID:10743611 doi:10.1016/s0166-6851(99)00200-5

[2] 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

[3] 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

[4] 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

[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

[7] Inaoka DK, Shiba T, Sato D, Balogun EO, Sasaki T, Nagahama M, Oda M, Matsuoka S, Ohmori J, Honma T, Inoue M, Kita K, Harada S. Structural Insights into the Molecular Design of Flutolanil Derivatives Targeted for Fumarate Respiration of Parasite Mitochondria. Int J Mol Sci. 2015 Jul 7;16(7):15287-308. doi: 10.3390/ijms160715287. PMID:26198225 doi:https://dx.doi.org/10.3390/ijms160715287

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[2]

[3]

[4]

[5]

[6]

[7]

@@ Line 3: / Line 3: @@
 <StructureSection load='4ysz' size='340' side='right'caption='[[4ysz]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ysz]] 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=4YSZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YSZ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4ysz]] 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=4YSZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YSZ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=12J:2-IODO-N-[3-(1-METHYLETHOXY)PHENYL]BENZAMIDE'>12J</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=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]] 3.3&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ysx|4ysx]], [[4ysy|4ysy]], [[4yt0|4yt0]], [[4ytm|4ytm]], [[4ytn|4ytn]], [[4ytp|4ytp]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=12J:2-IODO-N-[3-(1-METHYLETHOXY)PHENYL]BENZAMIDE'>12J</scene>, <scene name='pdbligand=EPH:L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE'>EPH</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=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=4ysz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ysz OCA], [https://pdbe.org/4ysz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ysz RCSB], [https://www.ebi.ac.uk/pdbsum/4ysz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ysz 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=4ysz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ysz OCA], [http://pdbe.org/4ysz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ysz RCSB], [http://www.ebi.ac.uk/pdbsum/4ysz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ysz ProSAT]</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/SDHB_ASCSU SDHB_ASCSU] Iron-sulfur protein (Ip) subunit of the mitochondrial electron transport chain complex II which, together with the flavoprotein (Fp) subunit forms the catalytic core of the complex (PubMed:10743611, PubMed:12742584, PubMed:17933581, PubMed:2843227, PubMed:7822332, PubMed:8435436). During the free-living egg-larvae stages, which occur in an aerobic environment, complex II acts as a succinate dehydrogenase by transferring electrons from succinate to ubiquinone (PubMed:10743611, PubMed:12742584, PubMed:17933581, PubMed:2843227, PubMed:7822332, PubMed:8435436). During the parasitic larvae and adult stages, which occur in an anaerobic environment, complex II acts as a fumarate reductase by transferring electrons from rhodoquinol to fumarate (PubMed:10743611, PubMed:12742584, PubMed:17933581, PubMed:2843227, PubMed:7822332, PubMed:8435436).<ref>PMID:10743611</ref> <ref>PMID:12742584</ref> <ref>PMID:17933581</ref> <ref>PMID:2843227</ref> <ref>PMID:7822332</ref> <ref>PMID:8435436</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 21: @@
 ==See Also==
-*[[Succinate Dehydrogenase|Succinate Dehydrogenase]]
+*[[Succinate dehydrogenase 3D structures|Succinate dehydrogenase 3D structures]]
 == References ==
 <references/>
@@ Line 29: / Line 28: @@
 [[Category: Ascaris suum]]
 [[Category: Large Structures]]
-[[Category: Harada, S]]
+[[Category: Harada S]]
-[[Category: Honma, T]]
+[[Category: Honma T]]
-[[Category: Inaoka, D K]]
+[[Category: Inaoka DK]]
-[[Category: Inoue, M]]
+[[Category: Inoue M]]
-[[Category: Kita, K]]
+[[Category: Kita K]]
-[[Category: Nagahama, M]]
+[[Category: Nagahama M]]
-[[Category: Sakamoto, K]]
+[[Category: Sakamoto K]]
-[[Category: Sato, D]]
+[[Category: Sato D]]
-[[Category: Shiba, T]]
+[[Category: Shiba T]]
-[[Category: Yamamoto, A]]
+[[Category: Yamamoto A]]
-[[Category: Yone, A]]
+[[Category: Yone A]]
-[[Category: Complex ii]]
-[[Category: Oxidoreductase-oxidoreductase inhibitor complex]]
-[[Category: Rhodoquinol-fumarate reductase]]

4ysz: Difference between revisions

Latest revision as of 08:38, 23 October 2024

Crystal structure of Mitochondrial rhodoquinol-fumarate reductase from Ascaris suum with 2-iodo-N-[3-(1-methylethoxy)phenyl]benzamide

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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