6ysb: Difference between revisions
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==Crystal structure of Malus domestica Double Bond Reductase (MdDBR) apo form== | ==Crystal structure of Malus domestica Double Bond Reductase (MdDBR) apo form== | ||
<StructureSection load='6ysb' size='340' side='right'caption='[[6ysb]]' scene=''> | <StructureSection load='6ysb' size='340' side='right'caption='[[6ysb]], [[Resolution|resolution]] 1.20Å' 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=6YSB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YSB FirstGlance]. <br> | <table><tr><td colspan='2'>[[6ysb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrus_ussuriensis_x_Pyrus_communis Pyrus ussuriensis x Pyrus communis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YSB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YSB 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=6ysb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ysb OCA], [https://pdbe.org/6ysb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ysb RCSB], [https://www.ebi.ac.uk/pdbsum/6ysb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ysb 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]] 1.2Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6ysb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ysb OCA], [https://pdbe.org/6ysb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ysb RCSB], [https://www.ebi.ac.uk/pdbsum/6ysb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ysb ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A5N5GUE7_9ROSA A0A5N5GUE7_9ROSA] | |||
<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 6ysb" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Pyrus ussuriensis x Pyrus communis]] | |||
[[Category: Benini S]] | [[Category: Benini S]] | ||
[[Category: Caliandro R]] | [[Category: Caliandro R]] | ||
[[Category: Demitri N]] | [[Category: Demitri N]] | ||
[[Category: Polsinelli I]] | [[Category: Polsinelli I]] | ||
Latest revision as of 16:34, 24 January 2024
Crystal structure of Malus domestica Double Bond Reductase (MdDBR) apo formCrystal structure of Malus domestica Double Bond Reductase (MdDBR) apo form
Structural highlights
FunctionPublication Abstract from PubMedIn 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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