9XYW

Crystal structure of the maize chloroplastic non-photosynthetic NADP(+)-dependent malic enzyme

This is a non-PDB format compatible entry.

Summary for 9XYW

• Entry DOI: 10.2210/pdb9xyw/pdb
• Related: 5OU5
• Descriptor: Malic enzyme, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, FORMIC ACID, ... (6 entities in total)
• Functional Keywords: nadp-malic enzyme, oxidative decarboxylase, maize, plant protein
• Biological source: Zea mays
• Total number of polymer chains: 2
• Total formula weight: 131465.38

Authors

Klinke, S.,Schneberger, N.,Boehm, J.M.,Willms, S.,Hagelueken, G.,Geyer, M.,Maurino, V.,Alvarez, C.E. (deposition date: 2025-08-26, release date: 2026-08-12)

Primary citation

Bohm, J.M.,Klinke, S.,Zamarreno, F.,Schneberger, N.,Lunari, R.,Saigo, M.,Drincovich, M.F.,Willms, S.,Costabel, M.,Maurino, V.G.,Alvarez, C.E.
Integrative crystallography and molecular dynamics reveal isoform-specific ligand interaction networks in C4 and nonC4 plant NADP-malic enzyme.
Plant J., 127:e71064-e71064, 2026

PubMed Abstract: NADP-dependent malic enzyme (NADP-ME) has been repeatedly co-opted into distinct metabolic roles across plants, most prominently as the decarboxylase of NADP-ME-type C4 photosynthesis. In maize, the plastidic C4- and nonC4-NADP-ME isoforms are closely related in sequence yet display strikingly different catalytic properties, suggesting that small changes in ligand recognition can re-tune reaction chemistry. However, mechanistic interpretation has been hampered by the scarcity of plant NADP-ME structures captured in catalytically informative, ligand-bound states. Here, we integrate X-ray crystallography with structure-guided docking and atomistic molecular dynamics (MD) to resolve ligand-site interaction networks across reaction states. We determined a 2.55 Å structure of maize plastidic nonC4-NADP-ME bound to NADP, pyruvate, and Mg, revealing a conserved NADP-ME fold with localized active-site flexibility. Comparison with maize C4-NADP-ME uncovers isoform-specific rewiring of NADP and pyruvate contacts, with the nonC4 enzyme forming a denser product-cofactor interaction network. To access substrate-bound states, we reconstructed malate-NADP-Mg complexes by docking followed by MD, identifying distinct malate-Mg coordination geometries and alternative NADP positioning between isoforms. Together, these structures and simulations provide a network-level framework for plastidic NADP-ME functional diversification and generate testable hypotheses for how ligand coordination drives isoform-specific catalysis.

PubMed: 42531153
DOI: 10.1111/tpj.71064

Experimental method

X-RAY DIFFRACTION (2.55 Å)