6C7N | pdb_00006c7n

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 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6C7N

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 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.

Macromolecule Content 

  • Total Structure Weight: 274.02 kDa 
  • Atom Count: 18,830 
  • Modeled Residue Count: 2,030 
  • Deposited Residue Count: 2,452 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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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 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
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