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| | <StructureSection load='6nor' size='340' side='right'caption='[[6nor]], [[Resolution|resolution]] 2.40Å' scene=''> | | <StructureSection load='6nor' size='340' side='right'caption='[[6nor]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6nor]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_15837 Atcc 15837]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NOR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NOR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6nor]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Micromonospora_echinospora Micromonospora echinospora]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NOR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NOR FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 2.402Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gtmC, genD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1877 ATCC 15837])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></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=6nor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nor OCA], [http://pdbe.org/6nor PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nor RCSB], [http://www.ebi.ac.uk/pdbsum/6nor PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nor ProSAT]</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=6nor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nor OCA], [https://pdbe.org/6nor PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6nor RCSB], [https://www.ebi.ac.uk/pdbsum/6nor PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6nor ProSAT]</span></td></tr> |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/Q70KD1_MICEC Q70KD1_MICEC] |
| - | Gentamicins are clinically relevant aminoglycoside antibiotics produced by several Micromonospora species. Gentamicins are highly methylated and functionalized molecules, and their biosynthesis include glycosyltransferases, dehydratase/oxidoreductases, aminotransferases, and methyltransferases. The biosynthesis of gentamicin A from gentamicin A2 involves three enzymatic steps that modify the hydroxyl group at position 3'' of the unusual garosamine sugar to provide its substitution for an amino group, followed by an N-methylation. The first of these reactions is catalyzed by GenD2, an oxidoreductase from the Gfo/Idh/MocA protein family, which reduces the hydroxyl at the C3'' of gentamicin A to produce 3''-dehydro-3''-oxo-gentamicin A2 (DOA2). In this work, we solved the structure of GenD2 in complex with NAD+. Although the structure of GenD2 has a similar fold to other members of the Gfo/Idh/MocA family, this enzyme has several new features, including a 3D-domain swapping of two beta-strands that are involved in a novel oligomerization interface for this protein family. In addition, the active site of this enzyme also has several specialties which are possibly involved in the substrate specificity, including a number of aromatic residues and a negatively charged region, which is complementary to the polycationic aminoglycoside-substrate. Therefore, docking simulations provided insights into the recognition of gentamicin A2 and into the catalytic mechanism of GenD2. This is the first report describing the structure of an oxidoreductase involved in aminoglycoside biosynthesis and could open perspectives into producing new aminoglycoside derivatives by protein engineering.
| + | |
| - | | + | |
| - | Crystal Structure of GenD2, an NAD-Dependent Oxidoreductase Involved in the Biosynthesis of Gentamicin.,de Araujo NC, Bury PDS, Tavares MT, Huang F, Parise-Filho R, Leadlay P, Dias MVB ACS Chem Biol. 2019 May 17;14(5):925-933. doi: 10.1021/acschembio.9b00115. Epub, 2019 Apr 30. PMID:30995396<ref>PMID:30995396</ref>
| + | |
| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 6nor" style="background-color:#fffaf0;"></div>
| + | |
| - | == References ==
| + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 15837]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Araujo, N C]] | + | [[Category: Micromonospora echinospora]] |
| - | [[Category: Bury, P S]] | + | [[Category: Araujo NC]] |
| - | [[Category: Dias, M V.B]] | + | [[Category: Bury PS]] |
| - | [[Category: Huang, F]] | + | [[Category: Dias MVB]] |
| - | [[Category: Leadlay, P F]] | + | [[Category: Huang F]] |
| - | [[Category: 3d swapping domain]] | + | [[Category: Leadlay PF]] |
| - | [[Category: Nad depedent enzyme]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
