5BKE

Crystal structure of AAD-2 in complex with Mn(II) and N-oxalylglycine

Summary for 5BKE

• Entry DOI: 10.2210/pdb5bke/pdb
• Related: 5BK9 5BKB 5BKC 5BKD
• Descriptor: Alpha-ketoglutarate-dependent 2,4-dichlorophenoxyacetate dioxygenase, MANGANESE (II) ION, N-OXALYLGLYCINE, ... (5 entities in total)
• Functional Keywords: dioxygenase, herbicide degradation, oxidoreductase
• Biological source: Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
• Total number of polymer chains: 7
• Total formula weight: 237506.73

Authors

Chekan, J.R.,Nair, S.K. (deposition date: 2019-06-02, release date: 2019-06-12, Last modification date: 2023-09-27)

Primary citation

Chekan, J.R.,Ongpipattanakul, C.,Wright, T.R.,Zhang, B.,Bollinger Jr., J.M.,Rajakovich, L.J.,Krebs, C.,Cicchillo, R.M.,Nair, S.K.
Molecular basis for enantioselective herbicide degradation imparted by aryloxyalkanoate dioxygenases in transgenic plants.
Proc.Natl.Acad.Sci.USA, 116:13299-13304, 2019

PubMed Abstract: 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 α-ketoglutarate (Fe/αKG)-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 USDA 110 as a catalyst to degrade ()-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 ()-enantiomer substrate-specific enzyme, in complexes with a phenoxypropionate synthetic auxin or with AOPP herbicides and of AAD-2, which has the opposite ()-enantiomeric substrate specificity, reveal the structural basis for stereoselectivity and provide insights into a common catalytic mechanism.

PubMed: 31209034
DOI: 10.1073/pnas.1900711116

Experimental method

X-RAY DIFFRACTION (2.15 Å)