6d3m: Difference between revisions

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<StructureSection load='6d3m' size='340' side='right'caption='[[6d3m]], [[Resolution|resolution]] 2.03&Aring;' scene=''>
<StructureSection load='6d3m' size='340' side='right'caption='[[6d3m]], [[Resolution|resolution]] 2.03&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6d3m]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_700291 Atcc 700291]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D3M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D3M FirstGlance]. <br>
<table><tr><td colspan='2'>[[6d3m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingobium_herbicidovorans Sphingobium herbicidovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D3M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6D3M 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=FTJ:(2R)-2-{4-[(6-chloroquinoxalin-2-yl)oxy]phenoxy}propanoic+acid'>FTJ</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]] 2.03&#8491;</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=76947 ATCC 700291])</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=FTJ:(2R)-2-{4-[(6-chloroquinoxalin-2-yl)oxy]phenoxy}propanoic+acid'>FTJ</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=6d3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d3m OCA], [https://pdbe.org/6d3m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6d3m RCSB], [https://www.ebi.ac.uk/pdbsum/6d3m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6d3m ProSAT]</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=6d3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d3m OCA], [http://pdbe.org/6d3m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d3m RCSB], [http://www.ebi.ac.uk/pdbsum/6d3m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d3m ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/RDPA_SPHHM RDPA_SPHHM] 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)-4-chlorophenoxypropanoate, however it can only accept 2-oxoglutarate as oxygen acceptor.<ref>PMID:16731970</ref> <ref>PMID:16820480</ref> <ref>PMID:11423952</ref>  
BACKGROUND: Effective management of weedy species in agricultural fields is essential for maintaining favorable growing conditions and crop yields. The introduction of genetically modified crops containing herbicide tolerance traits has been a successful additional tool available to farmers to better control weeds. However, weed resistance challenges present a need for additional herbicide tolerance trait options. RESULTS: To help meet this challenge, a new trait that provides tolerance to an aryloxyphenoxypropionate (FOP) herbicide and members of the synthetic auxin herbicide family, such as 2,4-D, was developed. Development of this herbicide tolerance trait employed an enzyme engineered with robust and specific enzymatic activity for these two herbicide families. This engineering effort utilized a microbial-sourced dioxygenase scaffold to generate variants with improved enzymatic parameters. Additional optimization to enhance in-plant stability of the enzyme enabled an efficacious trait that can withstand the higher temperature conditions often found in field environments. CONCLUSION: Optimized herbicide tolerance enzyme variants with enhanced enzymatic and temperature stability parameters enabled robust herbicide tolerance for two herbicide families in transgenic maize and soybeans. This herbicide tolerance trait for FOP and synthetic auxin herbicides such as 2,4-D could be useful in weed management systems, providing additional tools for farmers to control weeds. This article is protected by copyright. All rights reserved.
 
Development of Enzymes for Robust Aryloxyphenoxypropionate and Synthetic Auxin Herbicide Tolerance Traits in Maize and Soybean Crops.,Larue CT, Goley M, Shi L, Evdokimov AG, Sparks OC, Ellis C, Wollacott AM, Rydel TJ, Halls CE, Van Scoyoc B, Fu X, Nageotte JR, Adio AM, Zheng M, Sturman EJ, Garvey GS, Varagona MJ Pest Manag Sci. 2019 Mar 3. doi: 10.1002/ps.5393. PMID:30828945<ref>PMID:30828945</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6d3m" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 700291]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Halls, C E]]
[[Category: Sphingobium herbicidovorans]]
[[Category: Rydel, T J]]
[[Category: Halls CE]]
[[Category: Alpha-ketoglutarate-dependent dioxygenase]]
[[Category: Rydel TJ]]
[[Category: Oxidoreductase]]

Latest revision as of 17:32, 13 March 2024

FT_T dioxygenase with bound quizalofopFT_T dioxygenase with bound quizalofop

Structural highlights

6d3m is a 4 chain structure with sequence from Sphingobium herbicidovorans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.03Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RDPA_SPHHM 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)-4-chlorophenoxypropanoate, however it can only accept 2-oxoglutarate as oxygen acceptor.[1] [2] [3]

See Also

References

  1. ↑ Muller TA, Zavodszky MI, Feig M, Kuhn LA, Hausinger RP. Structural basis for the enantiospecificities of R- and S-specific phenoxypropionate/alpha-ketoglutarate dioxygenases. Protein Sci. 2006 Jun;15(6):1356-68. doi: 10.1110/ps.052059406. PMID:16731970 doi:http://dx.doi.org/10.1110/ps.052059406
  2. ↑ Muller TA, Fleischmann T, van der Meer JR, Kohler HP. Purification and characterization of two enantioselective alpha-ketoglutarate-dependent dioxygenases, RdpA and SdpA, from Sphingomonas herbicidovorans MH. Appl Environ Microbiol. 2006 Jul;72(7):4853-61. doi: 10.1128/AEM.02758-05. PMID:16820480 doi:http://dx.doi.org/10.1128/AEM.02758-05
  3. ↑ Kohler HP. Sphingomonas herbicidovorans MH: a versatile phenoxyalkanoic acid herbicide degrader. J Ind Microbiol Biotechnol. 1999 Oct;23(4-5):336-340. doi:, 10.1038/sj/jim/2900751. PMID:11423952 doi:http://dx.doi.org/10.1038/sj/jim/2900751

6d3m, resolution 2.03Å

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