6ytz
From Proteopedia
(Difference between revisions)
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==Crystal structure of Malus domestica Double Bond Reductase (MdDBR) in complex with NADPH== | ==Crystal structure of Malus domestica Double Bond Reductase (MdDBR) in complex with NADPH== | ||
| - | <StructureSection load='6ytz' size='340' side='right'caption='[[6ytz]]' scene=''> | + | <StructureSection load='6ytz' size='340' side='right'caption='[[6ytz]], [[Resolution|resolution]] 1.40Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YTZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YTZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6ytz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Malus_domestica Malus domestica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YTZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YTZ FirstGlance]. <br> |
| - | </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=6ytz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ytz OCA], [https://pdbe.org/6ytz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ytz RCSB], [https://www.ebi.ac.uk/pdbsum/6ytz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ytz ProSAT]</span></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]] 1.4Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=PGR:R-1,2-PROPANEDIOL'>PGR</scene></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=6ytz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ytz OCA], [https://pdbe.org/6ytz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ytz RCSB], [https://www.ebi.ac.uk/pdbsum/6ytz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ytz ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | In this study we describe the crystal structures of the apoform, the binary and the ternary complexes of a double bond reductase from Malus domestica L. (MdDBR) and explore a range of potential substrates. The overall fold of MdDBR is similar to that of the medium chain reductase/dehydrogenase/zinc-dependent alcohol dehydrogenase-like family. Structural comparison of MdDBR with Arabidopsis thaliana DBR (AtDBR), Nicotiana tabacum DBR (NtDBR) and Rubus idaeus DBR (RiDBR) allowed the identification of key amino acids involved in cofactor and ligands binding and shed light on how these residues may guide the orientation of the substrates. The enzyme kinetic for the substrate trans-4-phenylbuten-2-one has been analyzed, and MdDBR activity towards a variety of substrates was tested. This enzyme has been reported to be involved in the phenylpropanoid pathway where it would catalyze the NADPH-dependent reduction of the alpha, beta-unsaturated double bond of carbonyl metabolites. Our study provides new data towards the identification of MdDBR natural substrate and the biosynthetic pathway where it belongs. Furthermore, the originally proposed involvement in dihydrochalcone biosynthesis in apple must be questioned. | ||
| + | |||
| + | The structural and functional characterization of Malus domestica double bond reductase MdDBR provides insights towards the identification of its substrates.,Caliandro R, Polsinelli I, Demitri N, Musiani F, Martens S, Benini S Int J Biol Macromol. 2021 Jan 4;171:89-99. doi: 10.1016/j.ijbiomac.2020.12.190. PMID:33412202<ref>PMID:33412202</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6ytz" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| + | [[Category: Malus domestica]] | ||
[[Category: Benini S]] | [[Category: Benini S]] | ||
[[Category: Caliandro R]] | [[Category: Caliandro R]] | ||
[[Category: Demitri N]] | [[Category: Demitri N]] | ||
[[Category: Polsinelli I]] | [[Category: Polsinelli I]] | ||
Current revision
Crystal structure of Malus domestica Double Bond Reductase (MdDBR) in complex with NADPH
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