4i3x

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Structure of phosphonoacetaldehyde dehydrogenase in complex with phosphonoacetate and cofactor NAD+

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Categories: Large Structures | Sinorhizobium meliloti 1021 | Agarwal V | Nair SK

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 ==Structure of phosphonoacetaldehyde dehydrogenase in complex with phosphonoacetate and cofactor NAD+==
-<StructureSection load='4i3x' size='340' side='right' caption='[[4i3x]], [[Resolution|resolution]] 2.07&Aring;' scene=''>
+<StructureSection load='4i3x' size='340' side='right'caption='[[4i3x]], [[Resolution|resolution]] 2.07&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4i3x]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Ensifer_meliloti Ensifer meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I3X FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4i3x]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Sinorhizobium_meliloti_1021 Sinorhizobium meliloti 1021]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4I3X 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>, <scene name='pdbligand=PAE:PHOSPHONOACETIC+ACID'>PAE</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]] 2.07&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4i3t|4i3t]], [[4i3u|4i3u]], [[4i3v|4i3v]], [[4i3w|4i3w]]</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>, <scene name='pdbligand=PAE:PHOSPHONOACETIC+ACID'>PAE</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">phnY, RB0979, SM_b21539 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266834 Ensifer meliloti])</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=4i3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i3x OCA], [https://pdbe.org/4i3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4i3x RCSB], [https://www.ebi.ac.uk/pdbsum/4i3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4i3x ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aldehyde_dehydrogenase_(NAD(+)) Aldehyde dehydrogenase (NAD(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.3 1.2.1.3] </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=4i3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i3x OCA], [http://pdbe.org/4i3x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4i3x RCSB], [http://www.ebi.ac.uk/pdbsum/4i3x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4i3x ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/PHNY_RHIME PHNY_RHIME] Plays an important role in phosphonate degradation by catalyzing the NAD-dependent conversion of phosphonoacetaldehyde (PnAA) to phosphonoacetate (PnA). Has low in vitro activity with the related compounds phosphonopropionaldehyde (3-oxopropyl phosphonate) and glyceraldehyde 3-phosphate.<ref>PMID:24361046</ref>
-Phosphonates (C-PO3(2-)) have applications as antibiotics, herbicides, and detergents. In some environments, these molecules represent the predominant source of phosphorus, and several microbes have evolved dedicated enzymatic machineries for phosphonate degradation. For example, most common naturally occurring phosphonates can be catabolized to either phosphonoacetaldehyde or phosphonoacetate, which can then be hydrolyzed to generate inorganic phosphate and acetaldehyde or acetate, respectively. The phosphonoacetaldehyde oxidase gene (phnY) links these two hydrolytic processes and provides a previously unknown catabolic mechanism for phosphonoacetate production in the microbial metabolome. Here, we present biochemical characterization of PhnY and high-resolution crystal structures of the apo state, as well as complexes with substrate, cofactor, and product. Kinetic analysis of active site mutants demonstrates how a highly conserved aldehyde dehydrogenase active site has been modified in nature to generate activity with a phosphonate substrate.
-Structure and function of phosphonoacetaldehyde dehydrogenase: the missing link in phosphonoacetate formation.,Agarwal V, Peck SC, Chen JH, Borisova SA, Chekan JR, van der Donk WA, Nair SK Chem Biol. 2014 Jan 16;21(1):125-35. doi: 10.1016/j.chembiol.2013.11.006. Epub, 2013 Dec 19. PMID:24361046<ref>PMID:24361046</ref>
+==See Also==
+*[[Aldehyde dehydrogenase 3D structures|Aldehyde dehydrogenase 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4i3x" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Ensifer meliloti]]
+[[Category: Large Structures]]
-[[Category: Agarwal, V]]
+[[Category: Sinorhizobium meliloti 1021]]
-[[Category: Nair, S K]]
+[[Category: Agarwal V]]
-[[Category: Aldehyde dehydrogenase]]
+[[Category: Nair SK]]
-[[Category: Oxidoreductase]]
-[[Category: Phosphonate catabolism]]

4i3x

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Structure of phosphonoacetaldehyde dehydrogenase in complex with phosphonoacetate and cofactor NAD+

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Function

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