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

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

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This is version 1.2 of the entry. See complete history


Molecular adaptations of NADP-malic enzyme for its function in C4photosynthesis in grasses.

Alvarez, C.E.Bovdilova, A.Hoppner, A.Wolff, C.C.Saigo, M.Trajtenberg, F.Zhang, T.Buschiazzo, A.Nagel-Steger, L.Drincovich, M.F.Lercher, M.J.Maurino, V.G.

(2019) Nat Plants 5: 755-765

  • DOI: https://doi.org/10.1038/s41477-019-0451-7
  • Primary Citation of Related Structures:  
    5OU5, 6C7N

  • PubMed Abstract: 

    In C 4 grasses of agronomical interest, malate shuttled into the bundle sheath cells is decarboxylated mainly by nicotinamide adenine dinucleotide phosphate (NADP)-malic enzyme (C 4 -NADP-ME). The activity of C 4 -NADP-ME was optimized by natural selection to efficiently deliver CO 2 to Rubisco. During its evolution from a plastidic non-photosynthetic NADP-ME, C 4 -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 C 4 adaptions based on strict differential conservation of amino acids, combined with solving the crystal structures of maize and sorghum C 4 -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 C 4 metabolism.

  • Organizational Affiliation

    Centro de Estudios Fotosinteticos y Bioquimicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, University of Rosario, Rosario, Argentina.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Malic enzyme
A, B, C, D
576Zea maysMutation(s): 0 
Find proteins for P16243 (Zea mays)
Explore P16243 
Go to UniProtKB:  P16243
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16243
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on K

Download Ideal Coordinates CCD File 
Query on NA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
I [auth B]
J [auth B]
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth C],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
S [auth D],
T [auth D],
U [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.961α = 90
b = 147.155β = 90
c = 261.615γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Refinement description