In C4 grasses of agronomical interest, malate shuttled into the bundle sheath cells is decarboxylated mainly by nicotinamide adenine dinucleotide phosphate (NADP)-malic enzyme (C4-NADP-ME). The activity of C4-NADP-ME was optimized by natural selection to efficiently deliver CO2 to Rubisco. During its evolution from a plastidic non-photosynthetic NADP-ME, C4-NADP-ME acquired increased catalytic efficiency, tetrameric structure and pH-dependent inhibition by its substrate malate. Here, we identified specific amino acids important for these C4 adaptions based on strict differential conservation of amino acids, combined with solving the crystal structures of maize and sorghum C4-NADP-ME. Site-directed mutagenesis and structural analyses show that Q503, L544 and E339 are involved in catalytic efficiency; E339 confers pH-dependent regulation by malate, F140 is critical for the stabilization of the oligomeric structure and the N-terminal region is involved in tetramerization. Together, the identified molecular adaptations form the basis for the efficient catalysis and regulation of one of the central biochemical steps in C4 metabolism.
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This work was funded by grants of the European Union (3to4) to V.G.M. and by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany´s Excellence Strategy (EXC 2048/1, Project ID: 390686111 and EXC 1028, to V.G.M. and M.J.L. We acknowledge the European Synchrotron Radiation Facility (ESRF) for provision of synchrotron radiation facilities and we wish to thank L. Gordon for assistance in using beamline ID23-1. The Center for Structural Biology of Mercosur granted funding to C.E.A. for data collection at Institut Pasteur de Montevideo (IPM). We are grateful to N. Larrieux at the Protein Crystallography Facility IPM for assistance with crystallization and data collection.
The authors declare no competing interests.
Peer review information: Nature Plants thanks Robert Furbank and Liang Tong and other, anonymous, reviewers for their contribution to the peer review of this work.
Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Discussion, Supplementary Figs. 1–8, Supplementary Tables 1–4, Supplementary Video legends.
3D overview of the overall SbC4-NADP-ME structure and the position of the mutated amino acids. The first section (1´´–30´´) shows the overall structure with the active site in each monomer, and the tilted position of each dimer in the dimer–dimer quaternary structure. The second section (30´´–60´´) shows the 3D position of the four mutated amino acids (F140, E339, Q503 and L544).
3D view of the interface connection between monomers in SbC4-NADP-ME. The first section (1´´–30´´) shows the position of F140 in monomers A and B. The second section (30´´-60´´) shows the position of the N-terminal region in the contact interface between each monomer. The N termini were selected such that they range from amino acid 84, the initial residue obtained in the SbC4-NADP-ME crystal structure, to amino acid 102 (corresponding to the chimeric proteins produced in ref. 15). Only selected residues/moieties are shown for clarity.
3D view of putative malate allosteric binding site (0´´–40´´). Shown are different views of the region surrounding E339 with its possible points of connection with active sites in SbC4-NADP-ME and the open/close switch conformation that is essential for catalysis.