5k3i - Revision history

OCA at 09:51, 27 September 2023

OCA — Wed, 27 Sep 2023 09:51:18 GMT

←Older revision		Revision as of 09:51, 27 September 2023
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	<StructureSection load='5k3i' size='340' side='right'caption='[[5k3i]], [[Resolution\|resolution]] 2.68Å' scene=''>		<StructureSection load='5k3i' size='340' side='right'caption='[[5k3i]], [[Resolution\|resolution]] 2.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k3i]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Caeel Caeel~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5K3I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k3i]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K3I FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'~~>~~ATP</scene>, <scene name='pdbligand=FAD:FLAVIN~~-~~ADENINE+DINUCLEOTIDE'>FAD</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.683Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5k3g\|5k3g]], [[5k3h\|5k3h]], [[5k3j\|5k3j]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<~~tr id~~='~~gene~~'><~~td class="sblockLbl"~~><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">acox-1, CELE_F08A8.1, F08A8.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6239 CAEEL])~~</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=5k3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3i OCA], [https://pdbe.org/5k3i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k3i RCSB], [https://www.ebi.ac.uk/pdbsum/5k3i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3i 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=5k3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3i OCA], [~~http~~://pdbe.org/5k3i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5k3i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5k3i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3i ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ACX11_CAEEL ACX11_CAEEL] Involved in the first step of peroxisomal beta-oxidation by catalyzing the desaturation of fatty acid-derived side chains (PubMed:25775534, PubMed:29537254, PubMed:27551084). Specifically, catalyzes the desaturation of fatty acids heptanoyl-CoA (C7), nonanoyl-CoA (C9), dodecanoyl-CoA (C12) and to a lesser extent pentanoyl-CoA (C5) and hexadecanoyl-CoA (C16), and hydroxylated fatty acid hydroxynonanoyl-CoA (PubMed:25775534, PubMed:29537254, PubMed:27551084). Also, catalyzes the desaturation fatty acid-derived side chains of ascaroside pheromones, which regulates development and behavior (PubMed:20610393, PubMed:25775534, PubMed:29537254, PubMed:29863473, PubMed:27551084). Specifically, shortens ascaroside with 5-carbon omega side chain (asc-omega-C5), 7-carbon side chain (asc-C7), 9-carbon side chain (asc-C9), 11-carbon side chain (asc-C11), 13-carbon side chain (asc-C13), 15-carbon side chain (asc-C15) and to a lesser extent ascarosides with 7-omega-carbon side chain (asc-omega-C7) (PubMed:25775534, PubMed:29537254, PubMed:27551084). Also shortens indol-3-carbonyl(IC)-ascarosides with 7-carbon side chain (IC-asc-C7) and to a lesser extent (IC)-ascarosides with 9-carbon side chain (IC-asc-C9) (PubMed:29863473). May associate and regulate the folding and/or the catalytic activity of other acyl-coenzyme A oxidases including acox-1.2, acox-1.3, acox-1.4 and acox-3 modulating the type of ascarosides produced (PubMed:25775534, PubMed:29537254, PubMed:29863473). In association with acox-1.3, catalyzes the desaturation of asc-C7-CoA but not of fatty acids or hydroxylated fatty acids (PubMed:25775534). Involved in the biosynthesis of asc-C6-MK (daumone 2) and asc-delta-C9 (daumone 3) but not asc-C7 (daumone 1); daumones are pheromones produced during unfavourable growth conditions which promote entry into the dauer stage (PubMed:20610393).<ref>PMID:20610393</ref> <ref>PMID:25775534</ref> <ref>PMID:27551084</ref> <ref>PMID:29537254</ref> <ref>PMID:29863473</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Caeel~~]]	+	[[Category: Caenorhabditis elegans]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bruner~~, S D~~]]	+	[[Category: Bruner SD]]
-	[[Category: Butcher~~, R A~~]]	+	[[Category: Butcher RA]]
-	[[Category: Jones~~, R A~~]]	+	[[Category: Jones RA]]
-	[[Category: Li, K]]	+	[[Category: Li K]]
-	[[Category: Zhang, X]]	+	[[Category: Zhang X]]
-	~~[[Category: Ascaroside]]~~	+
-	~~[[Category: Atp]]~~	+
-	~~[[Category: B-oxidation]]~~	+
-	~~[[Category: Dauer pheromone]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:42, 27 November 2019

OCA — Wed, 27 Nov 2019 07:42:41 GMT

←Older revision		Revision as of 07:42, 27 November 2019
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	==Crystal structure of Acyl-CoA oxidase-1 in Caenorhabditis elegans complexed with FAD and ATP==		==Crystal structure of Acyl-CoA oxidase-1 in Caenorhabditis elegans complexed with FAD and ATP==
-	<StructureSection load='5k3i' size='340' side='right' caption='[[5k3i]], [[Resolution\|resolution]] 2.68Å' scene=''>	+	<StructureSection load='5k3i' size='340' side='right'caption='[[5k3i]], [[Resolution\|resolution]] 2.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5k3i]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Caeel Caeel]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K3I FirstGlance]. <br>		<table><tr><td colspan='2'>[[5k3i]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Caeel Caeel]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K3I FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Caeel]]		[[Category: Caeel]]
		+	[[Category: Large Structures]]
	[[Category: Bruner, S D]]		[[Category: Bruner, S D]]
	[[Category: Butcher, R A]]		[[Category: Butcher, R A]]

OCA at 12:57, 6 November 2017

OCA — Mon, 06 Nov 2017 12:57:47 GMT

←Older revision		Revision as of 12:57, 6 November 2017
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	<StructureSection load='5k3i' size='340' side='right' caption='[[5k3i]], [[Resolution\|resolution]] 2.68Å' scene=''>		<StructureSection load='5k3i' size='340' side='right' caption='[[5k3i]], [[Resolution\|resolution]] 2.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k3i]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K3I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k3i]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Caeel Caeel]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K3I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k3g\|5k3g]], [[5k3h\|5k3h]], [[5k3j\|5k3j]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k3g\|5k3g]], [[5k3h\|5k3h]], [[5k3j\|5k3j]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">acox-1, CELE_F08A8.1, F08A8.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6239 CAEEL])</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=5k3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3i OCA], [http://pdbe.org/5k3i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k3i RCSB], [http://www.ebi.ac.uk/pdbsum/5k3i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3i 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=5k3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3i OCA], [http://pdbe.org/5k3i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k3i RCSB], [http://www.ebi.ac.uk/pdbsum/5k3i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3i ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Caeel]]
	[[Category: Bruner, S D]]		[[Category: Bruner, S D]]
	[[Category: Butcher, R A]]		[[Category: Butcher, R A]]

OCA at 04:57, 9 September 2016

OCA — Fri, 09 Sep 2016 04:57:46 GMT

←Older revision		Revision as of 04:57, 9 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5k3i is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Acyl-CoA oxidase-1 in Caenorhabditis elegans complexed with FAD and ATP==
		+	<StructureSection load='5k3i' size='340' side='right' caption='[[5k3i]], [[Resolution\|resolution]] 2.68Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5k3i]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K3I FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k3g\|5k3g]], [[5k3h\|5k3h]], [[5k3j\|5k3j]]</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=5k3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3i OCA], [http://pdbe.org/5k3i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k3i RCSB], [http://www.ebi.ac.uk/pdbsum/5k3i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3i ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Caenorhabditis elegans secretes ascarosides as pheromones to communicate with other worms and to coordinate the development and behavior of the population. Peroxisomal beta-oxidation cycles shorten the side chains of ascaroside precursors to produce the short-chain ascaroside pheromones. Acyl-CoA oxidases, which catalyze the first step in these beta-oxidation cycles, have different side chain-length specificities and enable C. elegans to regulate the production of specific ascaroside pheromones. Here, we determine the crystal structure of the acyl-CoA oxidase 1 (ACOX-1) homodimer and the ACOX-2 homodimer bound to its substrate. Our results provide a molecular basis for the substrate specificities of the acyl-CoA oxidases and reveal why some of these enzymes have a very broad substrate range, whereas others are quite specific. Our results also enable predictions to be made for the roles of uncharacterized acyl-CoA oxidases in C. elegans and in other nematode species. Remarkably, we show that most of the C. elegans acyl-CoA oxidases that participate in ascaroside biosynthesis contain a conserved ATP-binding pocket that lies at the dimer interface, and we identify key residues in this binding pocket. ATP binding induces a structural change that is associated with tighter binding of the FAD cofactor. Mutations that disrupt ATP binding reduce FAD binding and reduce enzyme activity. Thus, ATP may serve as a regulator of acyl-CoA oxidase activity, thereby directly linking ascaroside biosynthesis to ATP concentration and metabolic state.

-	~~Authors: Zhang~~, X., Li, K., Jones~~, R.A.~~, Bruner, S.D., ~~Butcher, R~~.A.	+	Structural characterization of acyl-CoA oxidases reveals a direct link between pheromone biosynthesis and metabolic state in Caenorhabditis elegans.,Zhang X, Li K, Jones RA, Bruner SD, Butcher RA Proc Natl Acad Sci U S A. 2016 Sep 6;113(36):10055-60. doi:, 10.1073/pnas.1608262113. Epub 2016 Aug 22. PMID:27551084<ref>PMID:27551084</ref>

-	~~Description: Crystal structure~~ of ~~Acyl~~-~~CoA oxidase~~-~~1 in Caenorhabditis elegans complexed with FAD and ATP~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Jones, R.A]]	+	<div class="pdbe-citations 5k3i" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bruner, S D]]
		+	[[Category: Butcher, R A]]
		+	[[Category: Jones, R A]]
	[[Category: Li, K]]		[[Category: Li, K]]
	[[Category: Zhang, X]]		[[Category: Zhang, X]]
-	[[Category: ~~Bruner, S.D~~]]	+	[[Category: Ascaroside]]
-	[[Category: ~~Butcher, R.A~~]]	+	[[Category: Atp]]
		+	[[Category: B-oxidation]]
		+	[[Category: Dauer pheromone]]
		+	[[Category: Oxidoreductase]]

OCA at 13:24, 20 June 2016

OCA — Mon, 20 Jun 2016 13:24:02 GMT

←Older revision		Revision as of 13:24, 20 June 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5k3i is ON HOLD	+	The entry 5k3i is ON HOLD until Paper Publication

	Authors: Zhang, X., Li, K., Jones, R.A., Bruner, S.D., Butcher, R.A.		Authors: Zhang, X., Li, K., Jones, R.A., Bruner, S.D., Butcher, R.A.

OCA: Protected "5k3i" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 14:16:29 GMT

Protected "5k3i" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:16, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5k3i is ON HOLD Authors: Zhang, X., Li, K., Jones, R.A., Bruner, S.D., Butcher, R.A. Description: Crystal structure of Acyl-CoA oxidase-1 in Caenor...

OCA — Wed, 01 Jun 2016 14:16:28 GMT

New page: '''Unreleased structure''' The entry 5k3i is ON HOLD Authors: Zhang, X., Li, K., Jones, R.A., Bruner, S.D., Butcher, R.A. Description: Crystal structure of Acyl-CoA oxidase-1 in Caenor...

New page

'''Unreleased structure'''

The entry 5k3i is ON HOLD

Authors: Zhang, X., Li, K., Jones, R.A., Bruner, S.D., Butcher, R.A.

Description: Crystal structure of Acyl-CoA oxidase-1 in Caenorhabditis elegans complexed with FAD and ATP
[[Category: Unreleased Structures]]
[[Category: Jones, R.A]]
[[Category: Li, K]]
[[Category: Zhang, X]]
[[Category: Bruner, S.D]]
[[Category: Butcher, R.A]]