9EVV
His579Leu variant of L-arabinonate dehydratase co-crystallized with 2-oxobutyrate
Summary for 9EVV
| Entry DOI | 10.2210/pdb9evv/pdb |
| Descriptor | L-arabinonate dehydratase, MAGNESIUM ION, FE2/S2 (INORGANIC) CLUSTER, ... (5 entities in total) |
| Functional Keywords | arabinonate dehydratase, ilvd/edd superfamily, dihydroxy acid dehydratase, weimberg/dahms pathway, [2fe-2s] cluster, lyase |
| Biological source | Rhizobium leguminosarum bv. trifolii |
| Total number of polymer chains | 4 |
| Total formula weight | 256238.37 |
| Authors | |
| Primary citation | Ren, Y.,Vettenranta, E.,Penttinen, L.,Blomster Andberg, M.,Koivula, A.,Rouvinen, J.,Hakulinen, N. Unveiling the importance of the C-terminus in the sugar acid dehydratase of the IlvD/EDD superfamily. Appl.Microbiol.Biotechnol., 108:436-436, 2024 Cited by PubMed Abstract: Microbial non-phosphorylative oxidative pathways present promising potential in the biosynthesis of platform chemicals from the hemicellulosic fraction of lignocellulose. An L-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii catalyzes the rate-limiting step in the non-phosphorylative oxidative pathways, that is, converts sugar acid to 2-dehydro-3-deoxy sugar acid. We have shown earlier that the enzyme forms a dimer of dimers, in which the C-terminal histidine residue from one monomer participates in the formation of the active site of an adjacent monomer. The histidine appears to be conserved across the sequences of sugar acid dehydratases. To study the role of the C-terminus, five variants (H579A, H579F, H579L, H579Q, and H579W) were produced. All variants showed decreased activity for the tested sugar acid substrates, except the variant H579L on D-fuconate, which showed about 20% increase in activity. The reaction kinetic data showed that the substrate preference was slightly modified in H579L compared to the wild-type enzyme, demonstrating that the alternation of the substrate preference of sugar acid dehydratases is possible. In addition, a crystal structure of H579L was determined at 2.4 Å with a product analog 2-oxobutyrate. This is the first enzyme-ligand complex structure from an IlvD/EDD superfamily enzyme. The binding of 2-oxobutyrate suggests how the substrate would bind into the active site in the orientation, which could lead to the dehydration reaction. KEY POINTS: • Mutation of the last histidine at the C-terminus changed the catalytic activity of L-arabinonate dehydratase from R. leguminosarum bv. trifolii against various C5/C6 sugar acids. • The variant H579L of L-arabinonate dehydratase showed an alteration of substrate preferences compared with the wild type. • The first enzyme-ligand complex crystal structure of an IlvD/EDD superfamily enzyme was solved. PubMed: 39126499DOI: 10.1007/s00253-024-13270-8 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.44 Å) |
Structure validation
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