Extended Data Fig. 5: X-ray structure of holo-AthDHAD and homology model of AstD.
From: Resistance-gene-directed discovery of a natural-product herbicide with a new mode of action
a, Superimpositions of the monomer of holo-AthDHAD (PDB: 5ZE4, 2.11 Å) and RlArDHT (PDB: 5J84). The holo structure containing the 2Fe–2S cofactor and Mg2+ ion in the active site. The structure of holo-AthDHAD is in white; the crystal structure of RlArDHT is in cyan. b, Superimpositions of holo-AthDHAD and homology-modelled AstD. The structure of AstD was constructed by homology modelling on the basis of the structure of holo-AthDHAD. The structure of holo-AthDHAD is in white; the crystal structure of AstD is in green. c, The electron density map of cofactors in the holo structure of AthDHAD. White mesh indicates the 2Fo − Fc map at the 1.2σ level; green mesh indicates the Fo − Fc positive map at the 3.2σ level; cyan sticks represent the acetic acid molecule. d, Comparison of the active sites in the crystal structure of AthDHAD and the modelled structure of AstD. The cartoon represents superimposed binding sites of AthDHAD (white) and AstD (green). The shift of a loop in AstD, where L518 (corresponding to V496 in AthDHAD) is located, coupled with a larger L198 residue (corresponding to I177 in AthDHAD) leads to a smaller hydrophobic pocket in AstD than in AthDHAD. e, The surface of binding sites of AstD (left) and AthDHAD (right). The smaller hydrophobic channel in the modelled AstD cannot accommodate the aspterric acid molecule (yellow ball and stick model).
