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| | ==Crystal structure of acyl-coA oxidase1 from Yarrowia lipolytica== | | ==Crystal structure of acyl-coA oxidase1 from Yarrowia lipolytica== |
| - | <StructureSection load='5y9d' size='340' side='right' caption='[[5y9d]], [[Resolution|resolution]] 2.50Å' scene=''> | + | <StructureSection load='5y9d' size='340' side='right'caption='[[5y9d]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5y9d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Candida_lipolytica Candida lipolytica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y9D FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5y9d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Yarrowia_lipolytica_CLIB122 Yarrowia lipolytica CLIB122]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y9D FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</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]] 2.5Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">POX1, ACO1, YALI0E32835g ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284591 Candida lipolytica])</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></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acyl-CoA_oxidase Acyl-CoA oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.3.6 1.3.3.6] </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=5y9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y9d OCA], [https://pdbe.org/5y9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y9d RCSB], [https://www.ebi.ac.uk/pdbsum/5y9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y9d 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=5y9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y9d OCA], [http://pdbe.org/5y9d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y9d RCSB], [http://www.ebi.ac.uk/pdbsum/5y9d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y9d ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/ACOX1_YARLI ACOX1_YARLI] |
| | <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: Acyl-CoA oxidase]] | + | [[Category: Large Structures]] |
| - | [[Category: Candida lipolytica]] | + | [[Category: Yarrowia lipolytica CLIB122]] |
| - | [[Category: Kim, K J]] | + | [[Category: Kim K-J]] |
| - | [[Category: Kim, S]] | + | [[Category: Kim S]] |
| - | [[Category: Fad-binding protein]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
ACOX1_YARLI
Publication Abstract from PubMed
Acyl-CoA oxidase (ACOX) plays an important role in fatty acid degradation. The enzyme catalyzes the first reaction in peroxisomal fatty acid beta-oxidation by reducing acyl-CoA to 2-trans-enoyl-CoA. The yeast Yarrowia lipolytica is able to utilize fatty acids, fats, and oil as carbon sources to produce valuable bioproducts. We determined the crystal structure of ACOX1 from Y. lipolytica (YlACOX1) at a resolution of 2.5 A. YlACOX1 forms a homodimer, and the monomeric structure is composed of four domains, the Nalpha, Nbeta, Calpha1, and Calpha2. The FAD cofactor is bound at the dimerization interface between the Nbeta- and Calpha1-domains. The substrate-binding tunnel formed by the interface between the Nalpha-, Nbeta-, and Calpha1-domains is located proximal to FAD. Amino acid and structural comparisons of YlACOX1 with other ACOXs show that the substrate-binding pocket of YlACOX1 is much smaller than that of the medium- or long-chain ACOXs but is rather similar to that of the short-chain ACOXs. Moreover, the hydrophilicity of residues constituting the end region of the substrate-binding pocket in YlACOX1 is quite similar to those in the short-chain ACOXs but different from those of the medium- or long-chain ACOXs. These observations provide structural insights how YlACOX1 prefers short-chain dicarboxylyl-CoAs as a substrate.
Structural insight into the substrate specificity of acyl-CoA oxidase1 from Yarrowia lipolytica for short-chain dicarboxylyl-CoAs.,Kim S, Kim KJ Biochem Biophys Res Commun. 2018 Jan 8;495(2):1628-1634. doi:, 10.1016/j.bbrc.2017.11.191. Epub 2017 Dec 2. PMID:29198706[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kim S, Kim KJ. Structural insight into the substrate specificity of acyl-CoA oxidase1 from Yarrowia lipolytica for short-chain dicarboxylyl-CoAs. Biochem Biophys Res Commun. 2018 Jan 8;495(2):1628-1634. doi:, 10.1016/j.bbrc.2017.11.191. Epub 2017 Dec 2. PMID:29198706 doi:http://dx.doi.org/10.1016/j.bbrc.2017.11.191
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