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| | ==Studies on DCR shed new light on peroxisomal beta-oxidation: Crystal structure of the ternary complex of pDCR== | | ==Studies on DCR shed new light on peroxisomal beta-oxidation: Crystal structure of the ternary complex of pDCR== |
| - | <StructureSection load='4fc7' size='340' side='right' caption='[[4fc7]], [[Resolution|resolution]] 1.84Å' scene=''> | + | <StructureSection load='4fc7' size='340' side='right'caption='[[4fc7]], [[Resolution|resolution]] 1.84Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4fc7]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FC7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FC7 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4fc7]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FC7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FC7 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4fc6|4fc6]]</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=4fc7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fc7 OCA], [https://pdbe.org/4fc7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fc7 RCSB], [https://www.ebi.ac.uk/pdbsum/4fc7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fc7 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DECR2, PDCR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2,4-dienoyl-CoA_reductase_(NADPH) 2,4-dienoyl-CoA reductase (NADPH)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.34 1.3.1.34] </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=4fc7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fc7 OCA], [http://pdbe.org/4fc7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fc7 RCSB], [http://www.ebi.ac.uk/pdbsum/4fc7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fc7 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DECR2_HUMAN DECR2_HUMAN]] Auxiliary enzyme of beta-oxidation. Participates in the degradation of unsaturated fatty enoyl-CoA esters having double bonds in both even- and odd-numbered positions in peroxisome. Catalyzes the NADP-dependent reduction of 2,4-dienoyl-CoA to yield trans-3-enoyl-CoA. Has activity towards short and medium chain 2,4-dienoyl-CoAs, but also towards 2,4,7,10,13,16,19-docosaheptaenoyl-CoA, suggesting that it does not constitute a rate limiting step in the peroxisomal degradation of docosahexaenoic acid. | + | [https://www.uniprot.org/uniprot/DECR2_HUMAN DECR2_HUMAN] Auxiliary enzyme of beta-oxidation. Participates in the degradation of unsaturated fatty enoyl-CoA esters having double bonds in both even- and odd-numbered positions in peroxisome. Catalyzes the NADP-dependent reduction of 2,4-dienoyl-CoA to yield trans-3-enoyl-CoA. Has activity towards short and medium chain 2,4-dienoyl-CoAs, but also towards 2,4,7,10,13,16,19-docosaheptaenoyl-CoA, suggesting that it does not constitute a rate limiting step in the peroxisomal degradation of docosahexaenoic acid. |
| | <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: Human]] | + | [[Category: Homo sapiens]] |
| - | [[Category: Hua, T]] | + | [[Category: Large Structures]] |
| - | [[Category: Liu, Z J]] | + | [[Category: Hua T]] |
| - | [[Category: Shaw, N]] | + | [[Category: Liu Z-J]] |
| - | [[Category: Wang, J]] | + | [[Category: Shaw N]] |
| - | [[Category: Wu, D]] | + | [[Category: Wang J]] |
| - | [[Category: Oxidoreductase]]
| + | [[Category: Wu D]] |
| - | [[Category: Peroxisomal beta-oxidation]]
| + | |
| - | [[Category: Sdr/rossmann fold]]
| + | |
| Structural highlights
Function
DECR2_HUMAN Auxiliary enzyme of beta-oxidation. Participates in the degradation of unsaturated fatty enoyl-CoA esters having double bonds in both even- and odd-numbered positions in peroxisome. Catalyzes the NADP-dependent reduction of 2,4-dienoyl-CoA to yield trans-3-enoyl-CoA. Has activity towards short and medium chain 2,4-dienoyl-CoAs, but also towards 2,4,7,10,13,16,19-docosaheptaenoyl-CoA, suggesting that it does not constitute a rate limiting step in the peroxisomal degradation of docosahexaenoic acid.
Publication Abstract from PubMed
Peroxisomes play an essential role in maintaining fatty acid homeostasis. Although mitochondria are also known to participate in the catabolism of fatty acids via beta-oxidation, differences exist between the peroxisomal and mitochondrial beta-oxidation. Only peroxisomes, but not mitochondrion, can shorten very long chain fatty acids. Here, we describe the crystal structure of a ternary complex of peroxisomal 2, 4 dienoyl CoA reductases (pDCR) with hexadienoyl CoA and NADP, as a prototype for comparison with the mitochondrial DCR (mDCR) to shed light on the differences between the enzymes from the two organelles at the molecular level. Unexpectedly, the structure of pDCR refined to 1.84 A resolution reveals the absence of the tyrosine-serine pair seen in the active site of mDCR, which together with a lysine and an asparagine, have been deemed a hallmark of the SDR family of enzymes. Instead, aspartate hydrogen bonded to the Calpha hydroxyl via a water molecule, seems to perturb the water molecule for protonation of the substrate. Our studies provide the first structural evidence for participation of water in the DCR catalyzed reactions. Biochemical studies and structural analysis suggest that pDCRs can catalyze the shortening of six carbon long substrates in vitro. However, the Km values of pDCR for short chain acyl CoAs are atleast 6 fold higher than those for substrates with 10 or more aliphatic carbons. Unlike mDCR, hinge movements permit pDCR to process very long chain polyunsaturated fatty acids.
Studies on human 2, 4 dienoyl CoA reductase (DCR) sheds new light on peroxisomal beta-oxidation of unsaturated fatty acids.,Hua T, Wu D, Ding W, Wang J, Shaw N, Liu ZJ J Biol Chem. 2012 Jun 28. PMID:22745130[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Hua T, Wu D, Ding W, Wang J, Shaw N, Liu ZJ. Studies on human 2, 4 dienoyl CoA reductase (DCR) sheds new light on peroxisomal beta-oxidation of unsaturated fatty acids. J Biol Chem. 2012 Jun 28. PMID:22745130 doi:10.1074/jbc.M112.385351
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