6C7N

Monoclinic form of malic enzyme from sorghum at 2 angstroms resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 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: 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Malic enzyme
A, B, C, D
613Sorghum bicolorMutation(s): 0 
Gene Names: SORBI_3003G036200
UniProt
Find proteins for Q84LQ5 (Sorghum bicolor)
Explore Q84LQ5 
Go to UniProtKB:  Q84LQ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84LQ5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
E [auth A],
M [auth B],
V [auth C],
Z [auth D]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
U [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
F [auth A]
G [auth A]
AA [auth D],
BA [auth D],
CA [auth D],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
X [auth C],
Y [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
PYR
Query on PYR

Download Ideal Coordinates CCD File 
N [auth B],
O [auth B],
W [auth C]
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.1α = 90
b = 64.26β = 93.65
c = 202.72γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
TRUNCATEdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references