5zdp: Difference between revisions

Latest revision as of 08:52, 22 November 2023

Crystal structure of cyanide-insensitive alternative oxidase from Trypanosoma brucei with ferulenol

Structural highlights

5zdp is a 4 chain structure with sequence from Trypanosoma brucei brucei. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.71Å
Ligands:	9AU, FE, OH, OXY
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AOX_TRYBB Catalyzes cyanide-resistant oxygen consumption. May increase respiration when the cytochrome respiratory pathway is restricted, or in response to low temperatures.

Publication Abstract from PubMed

The alternative oxidase (AOX) is a monotopic diiron carboxylate protein which catalyzes the four-electron reduction of dioxygen to water by ubiquinol. Although we have recently determined the crystal structure of Trypanosoma brucei AOX (TAO) in the presence and absence of ascofuranone (AF) derivatives (which are potent mixed type inhibitors) the mechanism by which ubiquinol and dioxygen binds to TAO remain inconclusive. In this article, ferulenol was identified as the first competitive inhibitor of AOX which has been used to probe the binding of ubiquinol. Surface plasmon resonance reveals that AF is a quasi-irreversible inhibitor of TAO whilst ferulenol binding is completely reversible. The structure of the TAO-ferulenol complex, determined at 2.7A, provided insights into ubiquinol binding and has also identified a potential dioxygen molecule bound in a side-on conformation to the diiron center for the first time.

Insights into the ubiquinol/dioxygen binding and proton relay pathways of the alternative oxidase.,Shiba T, Inaoka DK, Takahashi G, Tsuge C, Kido Y, Young L, Ueda S, Balogun EO, Nara T, Honma T, Tanaka A, Inoue M, Saimoto H, Harada S, Moore AL, Kita K Biochim Biophys Acta Bioenerg. 2019 Mar 22;1860(5):375-382. doi:, 10.1016/j.bbabio.2019.03.008. PMID:30910528^[1]

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

References

↑ Shiba T, Inaoka DK, Takahashi G, Tsuge C, Kido Y, Young L, Ueda S, Balogun EO, Nara T, Honma T, Tanaka A, Inoue M, Saimoto H, Harada S, Moore AL, Kita K. Insights into the ubiquinol/dioxygen binding and proton relay pathways of the alternative oxidase. Biochim Biophys Acta Bioenerg. 2019 Mar 22;1860(5):375-382. doi:, 10.1016/j.bbabio.2019.03.008. PMID:30910528 doi:https://dx.doi.org/10.1016/j.bbabio.2019.03.008

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OCA

[1] Shiba T, Inaoka DK, Takahashi G, Tsuge C, Kido Y, Young L, Ueda S, Balogun EO, Nara T, Honma T, Tanaka A, Inoue M, Saimoto H, Harada S, Moore AL, Kita K. Insights into the ubiquinol/dioxygen binding and proton relay pathways of the alternative oxidase. Biochim Biophys Acta Bioenerg. 2019 Mar 22;1860(5):375-382. doi:, 10.1016/j.bbabio.2019.03.008. PMID:30910528 doi:https://dx.doi.org/10.1016/j.bbabio.2019.03.008

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='5zdp' size='340' side='right'caption='[[5zdp]], [[Resolution|resolution]] 2.71&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5zdp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Trybb Trybb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZDP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZDP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5zdp]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZDP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZDP FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9AU:4-oxidanyl-3-[(2~{E},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienyl]chromen-2-one'>9AU</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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]] 2.71&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AOX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5702 TRYBB])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9AU:4-oxidanyl-3-[(2~{E},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienyl]chromen-2-one'>9AU</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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=5zdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zdp OCA], [http://pdbe.org/5zdp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zdp RCSB], [http://www.ebi.ac.uk/pdbsum/5zdp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zdp 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=5zdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zdp OCA], [https://pdbe.org/5zdp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zdp RCSB], [https://www.ebi.ac.uk/pdbsum/5zdp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zdp ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/AOX_TRYBB AOX_TRYBB]] Catalyzes cyanide-resistant oxygen consumption. May increase respiration when the cytochrome respiratory pathway is restricted, or in response to low temperatures.
+[https://www.uniprot.org/uniprot/AOX_TRYBB AOX_TRYBB] Catalyzes cyanide-resistant oxygen consumption. May increase respiration when the cytochrome respiratory pathway is restricted, or in response to low temperatures.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Trybb]]
+[[Category: Trypanosoma brucei brucei]]
-[[Category: Balogun, E O]]
+[[Category: Balogun EO]]
-[[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: Kido, Y]]
+[[Category: Kido Y]]
-[[Category: Kita, K]]
+[[Category: Kita K]]
-[[Category: Moore, A L]]
+[[Category: Moore AL]]
-[[Category: Nara, T]]
+[[Category: Nara T]]
-[[Category: Saimoto, H]]
+[[Category: Saimoto H]]
-[[Category: Shiba, T]]
+[[Category: Shiba T]]
-[[Category: Takahashi, G]]
+[[Category: Takahashi G]]
-[[Category: Tanaka, A]]
+[[Category: Tanaka A]]
-[[Category: Tsuge, C]]
+[[Category: Tsuge C]]
-[[Category: Ueda, S]]
+[[Category: Ueda S]]
-[[Category: Young, L]]
+[[Category: Young L]]
-[[Category: Membrane bound diiron protein]]
-[[Category: Membrane protein]]

5zdp: Difference between revisions

Latest revision as of 08:52, 22 November 2023

Crystal structure of cyanide-insensitive alternative oxidase from Trypanosoma brucei with ferulenol

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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