5OU5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1038/s41477-019-0451-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In C <sub>4 </sub> grasses of agronomical interest, malate shuttled into the bundle sheath cells is decarboxylated mainly by nicotinamide adenine dinucleotide phosphate (NADP)-malic enzyme (C <sub>4 </sub>-NADP-ME). The activity of C <sub>4 </sub>-NA ...

    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

    Institute for Computer Science and Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Centro de Estudios Fotosinteticos y Bioquimicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, University of Rosario, Rosario, Argentina.,Plant Molecular Physiology and Biotechnology Group, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Institut of Complex Systems, Structural Biochemistry (ICS-6), Jülich, Germany.,Cluster of Excellence on Plant Sciences, Düsseldorf, Germany. veronica.maurino@uni-duesseldorf.de.,Institut für Physikalische Biologie, Heinrich Heine University, Düsseldorf, Germany.,Cluster of Excellence on Plant Sciences, Düsseldorf, Germany.,Center for Structural Studies, Hreinrich Heine University Düsseldorf, Düsseldorf, Germany.,Integrative Microbiology of Zoonotic Agents, Department of Microbiology, Institut Pasteur, Paris, France.,Plant Molecular Physiology and Biotechnology Group, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, Düsseldorf, Germany. veronica.maurino@uni-duesseldorf.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Malic enzyme
A, B, C, D
576Zea maysMutation(s): 0 
Gene Names: MOD1 (ME1)
EC: 1.1.1.40
Find proteins for P16243 (Zea mays)
Go to UniProtKB:  P16243
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.160 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 135.961α = 90.00
b = 147.155β = 90.00
c = 261.615γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2019-07-31
    Type: Data collection, Database references