5JVN

C3-type pyruvate phosphate dikinase: intermediate state of the central domain in the swiveling mechanism


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase.

Minges, A.Ciupka, D.Winkler, C.Hoppner, A.Gohlke, H.Groth, G.

(2017) Sci Rep 7: 45389-45389

  • DOI: 10.1038/srep45389
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pyruvate phosphate dikinase (PPDK) is a vital enzyme in cellular energy metabolism catalyzing the ATP- and Pi-dependent formation of phosphoenolpyruvate from pyruvate in C4 -plants, but the reverse reaction forming ATP in bacteria and protozoa. The m ...

    Pyruvate phosphate dikinase (PPDK) is a vital enzyme in cellular energy metabolism catalyzing the ATP- and Pi-dependent formation of phosphoenolpyruvate from pyruvate in C4 -plants, but the reverse reaction forming ATP in bacteria and protozoa. The multi-domain enzyme is considered an efficient molecular machine that performs one of the largest single domain movements in proteins. However, a comprehensive understanding of the proposed swiveling domain motion has been limited by not knowing structural intermediates or molecular dynamics of the catalytic process. Here, we present crystal structures of PPDKs from Flaveria, a model genus for studying the evolution of C4 -enzymes from phylogenetic ancestors. These structures resolve yet unknown conformational intermediates and provide the first detailed view on the large conformational transitions of the protein in the catalytic cycle. Independently performed unrestrained MD simulations and configurational free energy calculations also identified these intermediates. In all, our experimental and computational data reveal strict coupling of the CD swiveling motion to the conformational state of the NBD. Moreover, structural asymmetries and nucleotide binding states in the PPDK dimer support an alternate binding change mechanism for this intriguing bioenergetic enzyme.


    Organizational Affiliation

    Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Biochemical Plant Physiology, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyruvate, phosphate dikinase, chloroplastic
A
875Flaveria pringleiMutation(s): 0 
Gene Names: PPDK (PDK)
EC: 2.7.9.1
Find proteins for Q42736 (Flaveria pringlei)
Go to UniProtKB:  Q42736
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
6NQ
Query on 6NQ

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Download CCD File 
A
2'-Bromo-2'-deoxyadenosine 5'-[beta,gamma-imide]triphosphoric acid
C10 H16 Br N6 O11 P3
GLCRVGHVCJLAHS-QYYRPYCUSA-N
 Ligand Interaction
PEP
Query on PEP

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Download CCD File 
A
PHOSPHOENOLPYRUVATE
C3 H5 O6 P
DTBNBXWJWCWCIK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 249.430α = 90.00
b = 249.430β = 90.00
c = 84.060γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
BUCCANEERmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-04-12
    Type: Database references