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| | <StructureSection load='5bkd' size='340' side='right'caption='[[5bkd]], [[Resolution|resolution]] 1.90Å' scene=''> | | <StructureSection load='5bkd' size='340' side='right'caption='[[5bkd]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5bkd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"pseudomonas_desmolytica"_gray_and_thornton_1928 "pseudomonas desmolytica" gray and thornton 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BKD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5bkd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Delftia_acidovorans Delftia acidovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BKD FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=RCF:(2R)-2-[4-(4-cyano-2-fluorophenoxy)phenoxy]propanoic+acid'>RCF</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.9Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5bkb|5bkb]], [[5bk9|5bk9]], [[5bke|5bke]], [[5bkc|5bkc]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=RCF:(2R)-2-[4-(4-cyano-2-fluorophenoxy)phenoxy]propanoic+acid'>RCF</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rdpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=80866 "Pseudomonas desmolytica" Gray and Thornton 1928])</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=5bkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bkd OCA], [https://pdbe.org/5bkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bkd RCSB], [https://www.ebi.ac.uk/pdbsum/5bkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bkd 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/(R)-dichlorprop_dioxygenase_(2-oxoglutarate) (R)-dichlorprop dioxygenase (2-oxoglutarate)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.44 1.14.11.44] </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=5bkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bkd OCA], [http://pdbe.org/5bkd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bkd RCSB], [http://www.ebi.ac.uk/pdbsum/5bkd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bkd ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RDPA_DELAC RDPA_DELAC]] Involved in the degradation of the phenoxypropionate herbicides. Catalyzes the enantiospecific cleavage of the ether bond in the herbicid R-dichlorprop ((R)-2-(2,4-dichlorophenoxy)propionate)(R-2,4-DP) and R-mecoprop ((R)-2-(4-chloro-2-methylphenoxy)propionate)(R-2,4-MCPP). It can also accept (RS)-2-(2,4,5-trichlorophenoxy)propionate, (RS)-2-(4-chlorophenoxy)propionate, (RS)-2-(m-chlorophenoxy)propionate, however it can only accept 2-oxoglutarate as oxygen acceptor.<ref>PMID:12501996</ref> <ref>PMID:12501996</ref> | + | [https://www.uniprot.org/uniprot/RDPA_DELAC RDPA_DELAC] Involved in the degradation of the phenoxypropionate herbicides. Catalyzes the enantiospecific cleavage of the ether bond in the herbicid R-dichlorprop ((R)-2-(2,4-dichlorophenoxy)propionate)(R-2,4-DP) and R-mecoprop ((R)-2-(4-chloro-2-methylphenoxy)propionate)(R-2,4-MCPP). It can also accept (RS)-2-(2,4,5-trichlorophenoxy)propionate, (RS)-2-(4-chlorophenoxy)propionate, (RS)-2-(m-chlorophenoxy)propionate, however it can only accept 2-oxoglutarate as oxygen acceptor.<ref>PMID:12501996</ref> <ref>PMID:12501996</ref> |
| | <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: Pseudomonas desmolytica gray and thornton 1928]] | + | [[Category: Delftia acidovorans]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Chekan, J R]] | + | [[Category: Chekan JR]] |
| - | [[Category: Nair, S K]] | + | [[Category: Nair SK]] |
| - | [[Category: Dioxygenase]]
| + | |
| - | [[Category: Herbicide degradation]]
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| - | [[Category: Oxidoreductase]]
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| Structural highlights
Function
RDPA_DELAC Involved in the degradation of the phenoxypropionate herbicides. Catalyzes the enantiospecific cleavage of the ether bond in the herbicid R-dichlorprop ((R)-2-(2,4-dichlorophenoxy)propionate)(R-2,4-DP) and R-mecoprop ((R)-2-(4-chloro-2-methylphenoxy)propionate)(R-2,4-MCPP). It can also accept (RS)-2-(2,4,5-trichlorophenoxy)propionate, (RS)-2-(4-chlorophenoxy)propionate, (RS)-2-(m-chlorophenoxy)propionate, however it can only accept 2-oxoglutarate as oxygen acceptor.[1] [2]
Publication Abstract from PubMed
The synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D) is an active ingredient of thousands of commercial herbicides. Multiple species of bacteria degrade 2,4-D via a pathway initiated by the Fe(II) and alpha-ketoglutarate (Fe/alphaKG)-dependent aryloxyalkanoate dioxygenases (AADs). Recently, genes encoding 2 AADs have been deployed commercially in herbicide-tolerant crops. Some AADs can also inactivate chiral phenoxypropionate and aryloxyphenoxypropionate (AOPP) herbicides, albeit with varying substrate enantioselectivities. Certain AAD enzymes, such as AAD-1, have expanded utility in weed control systems by enabling the use of diverse modes of action with a single trait. Here, we report 1) the use of a genomic context-based approach to identify 59 additional members of the AAD class, 2) the biochemical characterization of AAD-2 from Bradyrhizobium diazoefficiens USDA 110 as a catalyst to degrade (S)-stereoisomers of chiral synthetic auxins and AOPP herbicides, 3) spectroscopic data that demonstrate the canonical ferryl complex in the AAD-1 reaction, and 4) crystal structures of representatives of the AAD class. Structures of AAD-1, an (R)-enantiomer substrate-specific enzyme, in complexes with a phenoxypropionate synthetic auxin or with AOPP herbicides and of AAD-2, which has the opposite (S)-enantiomeric substrate specificity, reveal the structural basis for stereoselectivity and provide insights into a common catalytic mechanism.
Molecular basis for enantioselective herbicide degradation imparted by aryloxyalkanoate dioxygenases in transgenic plants.,Chekan JR, Ongpipattanakul C, Wright TR, Zhang B, Bollinger JM Jr, Rajakovich LJ, Krebs C, Cicchillo RM, Nair SK Proc Natl Acad Sci U S A. 2019 Jun 17. pii: 1900711116. doi:, 10.1073/pnas.1900711116. PMID:31209034[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Westendorf A, Benndorf D, Muller RH, Babel W. The two enantiospecific dichlorprop/alpha-ketoglutarate-dioxygenases from Delftia acidovorans MC1--protein and sequence data of RdpA and SdpA. Microbiol Res. 2002;157(4):317-22. PMID:12501996
- ↑ Westendorf A, Benndorf D, Muller RH, Babel W. The two enantiospecific dichlorprop/alpha-ketoglutarate-dioxygenases from Delftia acidovorans MC1--protein and sequence data of RdpA and SdpA. Microbiol Res. 2002;157(4):317-22. PMID:12501996
- ↑ Chekan JR, Ongpipattanakul C, Wright TR, Zhang B, Bollinger JM Jr, Rajakovich LJ, Krebs C, Cicchillo RM, Nair SK. Molecular basis for enantioselective herbicide degradation imparted by aryloxyalkanoate dioxygenases in transgenic plants. Proc Natl Acad Sci U S A. 2019 Jun 17. pii: 1900711116. doi:, 10.1073/pnas.1900711116. PMID:31209034 doi:http://dx.doi.org/10.1073/pnas.1900711116
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