5k3j - Revision history

OCA at 12:39, 6 March 2024

OCA — Wed, 06 Mar 2024 12:39:04 GMT

←Older revision		Revision as of 12:39, 6 March 2024
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	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/ACX12_CAEEL ACX12_CAEEL] Involved in the first step of peroxisomal beta-oxidation by catalyzing the desaturation of fatty acid-derived side chains of ascaroside pheromones, which regulates development and behavior (PubMed:25775534, PubMed:27551084). Specifically, shortens ascarosides with 5-carbon omega side chain (asc-omega-C5) (PubMed:25775534, PubMed:27551084). Does not shorten indol-3-carbonyl(IC)-ascaroside with 7-carbon or 9-carbon side chains (PubMed:29863473). Does not catalyze the desaturation of fatty acids or hydroxylated fatty acids (PubMed:25775534, PubMed:27551084).<ref>PMID:25775534</ref> <ref>PMID:27551084</ref> <ref>PMID:29863473</ref>		[https://www.uniprot.org/uniprot/ACX12_CAEEL ACX12_CAEEL] Involved in the first step of peroxisomal beta-oxidation by catalyzing the desaturation of fatty acid-derived side chains of ascaroside pheromones, which regulates development and behavior (PubMed:25775534, PubMed:27551084). Specifically, shortens ascarosides with 5-carbon omega side chain (asc-omega-C5) (PubMed:25775534, PubMed:27551084). Does not shorten indol-3-carbonyl(IC)-ascaroside with 7-carbon or 9-carbon side chains (PubMed:29863473). Does not catalyze the desaturation of fatty acids or hydroxylated fatty acids (PubMed:25775534, PubMed:27551084).<ref>PMID:25775534</ref> <ref>PMID:27551084</ref> <ref>PMID:29863473</ref>
-	<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.
-
-	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>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5k3j" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:38, 27 September 2023

OCA — Wed, 27 Sep 2023 10:38:58 GMT

←Older revision		Revision as of 10:38, 27 September 2023
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	<StructureSection load='5k3j' size='340' side='right'caption='[[5k3j]], [[Resolution\|resolution]] 2.68Å' scene=''>		<StructureSection load='5k3j' size='340' side='right'caption='[[5k3j]], [[Resolution\|resolution]] 2.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k3j]] is a 2 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=5K3J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5K3J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k3j]] is a 2 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=5K3J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K3J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6QA:~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL]OXY-3,3-DIMETHYL-2-OXIDANYL-BUTANOYL]AMINO]PROPANOYLAMINO]ETHYL]+5-[(2~{R},3~{R},5~{R},6~{S})-6-METHYL-3,5-BIS(OXIDANYL)OXAN-2-YL]OXYPENTANETHIOATE'>6QA</scene>, <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]] 2.68Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k3g\|5k3g]], [[5k3h\|5k3h]], [[5k3i\|5k3i]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6QA:~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL]OXY-3,3-DIMETHYL-2-OXIDANYL-BUTANOYL]AMINO]PROPANOYLAMINO]ETHYL]+5-[(2~{R},3~{R},5~{R},6~{S})-6-METHYL-3,5-BIS(OXIDANYL)OXAN-2-YL]OXYPENTANETHIOATE'>6QA</scene>, <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-2, CELE_F08A8.2, F08A8.2 ([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=5k3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3j OCA], [https://pdbe.org/5k3j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k3j RCSB], [https://www.ebi.ac.uk/pdbsum/5k3j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3j 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=5k3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3j OCA], [~~http~~://pdbe.org/5k3j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5k3j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5k3j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3j ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ACX12_CAEEL ACX12_CAEEL] Involved in the first step of peroxisomal beta-oxidation by catalyzing the desaturation of fatty acid-derived side chains of ascaroside pheromones, which regulates development and behavior (PubMed:25775534, PubMed:27551084). Specifically, shortens ascarosides with 5-carbon omega side chain (asc-omega-C5) (PubMed:25775534, PubMed:27551084). Does not shorten indol-3-carbonyl(IC)-ascaroside with 7-carbon or 9-carbon side chains (PubMed:29863473). Does not catalyze the desaturation of fatty acids or hydroxylated fatty acids (PubMed:25775534, PubMed:27551084).<ref>PMID:25775534</ref> <ref>PMID:27551084</ref> <ref>PMID:29863473</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__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: Crystal structure]]~~	+
-	~~[[Category: Dauer pheromone]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:42, 27 November 2019

OCA — Wed, 27 Nov 2019 07:42:38 GMT

←Older revision		Revision as of 07:42, 27 November 2019
Line 1:		Line 1:

	==Crystals structure of Acyl-CoA oxidase-2 in Caenorhabditis elegans bound with FAD, ascaroside-CoA, and ATP==		==Crystals structure of Acyl-CoA oxidase-2 in Caenorhabditis elegans bound with FAD, ascaroside-CoA, and ATP==
-	<StructureSection load='5k3j' size='340' side='right' caption='[[5k3j]], [[Resolution\|resolution]] 2.68Å' scene=''>	+	<StructureSection load='5k3j' size='340' side='right'caption='[[5k3j]], [[Resolution\|resolution]] 2.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5k3j]] is a 2 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=5K3J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K3J FirstGlance]. <br>		<table><tr><td colspan='2'>[[5k3j]] is a 2 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=5K3J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K3J FirstGlance]. <br>
Line 23:		Line 23:
	</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 12:57:48 GMT

←Older revision		Revision as of 12:57, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5k3j' size='340' side='right' caption='[[5k3j]], [[Resolution\|resolution]] 2.68Å' scene=''>		<StructureSection load='5k3j' size='340' side='right' caption='[[5k3j]], [[Resolution\|resolution]] 2.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k3j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K3J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k3j]] is a 2 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=5K3J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K3J FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6QA:~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL]OXY-3,3-DIMETHYL-2-OXIDANYL-BUTANOYL]AMINO]PROPANOYLAMINO]ETHYL]+5-[(2~{R},3~{R},5~{R},6~{S})-6-METHYL-3,5-BIS(OXIDANYL)OXAN-2-YL]OXYPENTANETHIOATE'>6QA</scene>, <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=6QA:~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL]OXY-3,3-DIMETHYL-2-OXIDANYL-BUTANOYL]AMINO]PROPANOYLAMINO]ETHYL]+5-[(2~{R},3~{R},5~{R},6~{S})-6-METHYL-3,5-BIS(OXIDANYL)OXAN-2-YL]OXYPENTANETHIOATE'>6QA</scene>, <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]], [[5k3i\|5k3i]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k3g\|5k3g]], [[5k3h\|5k3h]], [[5k3i\|5k3i]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">acox-2, CELE_F08A8.2, F08A8.2 ([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=5k3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3j OCA], [http://pdbe.org/5k3j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k3j RCSB], [http://www.ebi.ac.uk/pdbsum/5k3j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3j 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=5k3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3j OCA], [http://pdbe.org/5k3j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k3j RCSB], [http://www.ebi.ac.uk/pdbsum/5k3j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3j 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 06:53, 10 September 2016

OCA — Sat, 10 Sep 2016 06:53:32 GMT

←Older revision		Revision as of 06:53, 10 September 2016
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5k3j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K3J FirstGlance]. <br>		<table><tr><td colspan='2'>[[5k3j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K3J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6QA:~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-~~aminopurin~~-9-yl)-4-~~oxidanyl~~-3-~~phosphonooxy~~-~~oxolan~~-2-yl]~~methoxy~~-~~oxidanyl~~-~~phosphoryl~~]~~oxy~~-~~oxidanyl~~-~~phosphoryl~~]~~oxy~~-3,3-~~dimethyl~~-2-~~oxidanyl~~-~~butanoyl~~]~~amino~~]~~propanoylamino~~]~~ethyl~~]+5-[(2~{R},3~{R},5~{R},6~{S})-6-~~methyl~~-3,5-~~bis~~(~~oxidanyl~~)~~oxan~~-2-yl]~~oxypentanethioate~~'>6QA</scene>, <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=6QA:~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL]OXY-3,3-DIMETHYL-2-OXIDANYL-BUTANOYL]AMINO]PROPANOYLAMINO]ETHYL]+5-[(2~{R},3~{R},5~{R},6~{S})-6-METHYL-3,5-BIS(OXIDANYL)OXAN-2-YL]OXYPENTANETHIOATE'>6QA</scene>, <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]], [[5k3i\|5k3i]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k3g\|5k3g]], [[5k3h\|5k3h]], [[5k3i\|5k3i]]</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=5k3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3j OCA], [http://pdbe.org/5k3j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k3j RCSB], [http://www.ebi.ac.uk/pdbsum/5k3j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3j 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=5k3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3j OCA], [http://pdbe.org/5k3j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k3j RCSB], [http://www.ebi.ac.uk/pdbsum/5k3j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3j ProSAT]</span></td></tr>

OCA at 05:39, 9 September 2016

OCA — Fri, 09 Sep 2016 05:39:40 GMT

←Older revision		Revision as of 05:39, 9 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5k3j is ~~ON HOLD until Paper~~ Publication	+	==Crystals structure of Acyl-CoA oxidase-2 in Caenorhabditis elegans bound with FAD, ascaroside-CoA, and ATP==
		+	<StructureSection load='5k3j' size='340' side='right' caption='[[5k3j]], [[Resolution\|resolution]] 2.68Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5k3j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K3J FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6QA:~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl]+5-[(2~{R},3~{R},5~{R},6~{S})-6-methyl-3,5-bis(oxidanyl)oxan-2-yl]oxypentanethioate'>6QA</scene>, <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]], [[5k3i\|5k3i]]</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=5k3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3j OCA], [http://pdbe.org/5k3j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k3j RCSB], [http://www.ebi.ac.uk/pdbsum/5k3j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3j 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~~:	+	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~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5k3j" 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: Zhang, X]]
		+	[[Category: Ascaroside]]
		+	[[Category: Atp]]
		+	[[Category: B-oxidation]]
		+	[[Category: Crystal structure]]
		+	[[Category: Dauer pheromone]]
		+	[[Category: Oxidoreductase]]

OCA: Protected "5k3j" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 14:16:32 GMT

Protected "5k3j" [edit=sysop:move=sysop]

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Revision as of 14:16, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5k3j is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 01 Jun 2016 14:16:31 GMT

New page: '''Unreleased structure''' The entry 5k3j is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5k3j is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]