9E6M | pdb_00009e6m

Crystal structure of the G200R mutant from the maize chloroplastic photosynthetic NADP(+)-dependent malic enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.296 (Depositor), 0.302 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.252 (DCC) 
  • R-Value Observed: 
    0.242 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

A milestone in C4 carbon concentration mechanism evolution: structural remodeling of NADP-malic enzyme in Poaceae.

Bohm, J.M.Willms, S.Ferrao, O.Buitrago-Arango, M.Hudig, M.Poschmann, G.Fazelnia, N.Nagel-Steger, L.Klinke, S.Drakonaki, A.Gatsogiannis, C.Tronconi, M.A.Alvarez, C.E.Maurino, V.G.

(2026) Mol Biol Evol 43

  • DOI: https://doi.org/10.1093/molbev/msag056
  • Primary Citation Related Structures: 
    9E6M

  • PubMed Abstract: 

    The evolution of C4 photosynthesis required extensive modification of ancestral enzymes enabling the development of an efficient carbon concentrating mechanism. A key example is NADP-malic enzyme (NADP-ME), which, in maize and sorghum-members of the same C4 lineage-underwent gene duplication and neofunctionalization, resulting in 2 plastidic isoforms with distinct oligomeric states: a tetrameric C4-specific isoform and a dimeric housekeeping (nonC4) isoform. In this study, we resolve the structural basis of this oligomeric divergence using X-ray crystallography, cryo-electron microscopy, and molecular modeling combined with targeted biochemical analysis. Our findings demonstrate that the N-terminal region of nonC4-NADP-ME is involved in its oligomeric organization, whereas a suite of adaptive substitutions at the dimer interface drives the transition to the stable tetramer characteristic of the C4 isoform. Moreover, the C-terminal region stabilizes the oligomeric states of C4- and nonC4-NADP-ME through specific interactions with adaptive residues. We propose that tetramerization mitigates aggregation at the high expression levels demanded by the C4 cycle and likely creates a scaffold for the emergence of regulatory properties. Collectively, the data show that remodeling of terminal domains and inter-subunit interfaces rewires the quaternary architecture of the enzymes, illustrating how subtle structural changes can drive the evolution of complex innovations such as C4 photosynthesis.


  • Organizational Affiliation
    • Molecular Plant Physiology, Institute for Cellular and Molecular Botany (IZMB), University of Bonn, Kirschallee 1, Bonn 53115, Germany.

Macromolecule Content 

  • Total Structure Weight: 255.51 kDa 
  • Atom Count: 17,498 
  • Modeled Residue Count: 2,235 
  • Deposited Residue Count: 2,304 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Malic enzyme
A, B, C, D
576Zea maysMutation(s): 1 
EC: 1.1.1.40
UniProt
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.296 (Depositor), 0.302 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.252 (DCC) 
  • R-Value Observed: 0.242 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.679α = 90
b = 124.161β = 90
c = 189.472γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
MrBUMPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyGrant MA2379/20-1 to VM
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)ArgentinaPICT-2019-00079

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-15
    Type: Initial release
  • Version 1.1: 2026-04-29
    Changes: Database references