1VBH

Pyruvate Phosphate Dikinase with bound Mg-PEP from Maize


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of pyruvate phosphate dikinase from maize revealed an alternative conformation in the swiveling-domain motion

Nakanishi, T.Nakatsu, T.Matsuoka, M.Sakata, K.Kato, H.

(2005) Biochemistry 44: 1136-1144

  • DOI: 10.1021/bi0484522
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pyruvate phosphate dikinase (PPDK) reversibly catalyzes the conversion of ATP, phosphate, and pyruvate into AMP, pyrophosphate, and phosphoenolpyruvate (PEP), respectively. Since the nucleotide binding site (in the N-terminal domain) and the pyruvate ...

    Pyruvate phosphate dikinase (PPDK) reversibly catalyzes the conversion of ATP, phosphate, and pyruvate into AMP, pyrophosphate, and phosphoenolpyruvate (PEP), respectively. Since the nucleotide binding site (in the N-terminal domain) and the pyruvate/PEP binding site (in the C-terminal domain) are separated by approximately 45 A, it has been proposed that an intermediary domain, called the central domain, swivels between these remote domains to transfer the phosphate. However, no direct structural evidence for the swiveling central domain has been found. In this study, the crystal structures of maize PPDK with and without PEP have been determined at 2.3 A resolution. These structures revealed that the central domain is located near the pyruvate/PEP binding C-terminal domain, in contrast to the PPDK from Clostridium symbiosum, wherein the central domain is located near the nucleotide-binding N-terminal domain. Structural comparisons between the maize and C. symbiosum PPDKs demonstrated that the swiveling motion of the central domain consists of a rotation of at least 92 degrees and a translation of 0.5 A. By comparing the maize PPDK structures with and without PEP, we have elucidated the mode of binding of PEP to the C-terminal domain and the induced conformational changes in the central domain.


    Related Citations: 
    • Primary structure of maize pyruvate, orthophosphate dikinase as deduced from cDNA sequence
      Matsuoka, M.,Ozeki, Y.,Yamamoto, N.,Hirano, H.,Kano-Murakami, Y.,Tanaka, Y.
      (1988) J.BIOL.CHEM. 263: 11080
    • Purification, crystallization and preliminary X-ray diffraction studies on pyruvate phosphate dikinase from maize
      Nakanishi, T.,Ohki, Y.,Oda, J.,Matsuoka, M.,Sakata, K.,Kato, H.
      (2004) ACTA CRYSTALLOGR.,SECT.D 60: 193


    Organizational Affiliation

    Kinetic Crystallography Research Team, Membrane Dynamics Research Group, RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
pyruvate,orthophosphate dikinase
A
876Zea maysMutation(s): 0 
Gene Names: PPDK1 (C4PPDKZM1, CYPPDKZM1, PPDK2)
EC: 2.7.9.1
Find proteins for P11155 (Zea mays)
Go to UniProtKB:  P11155
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.230 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 109.339α = 90.00
b = 100.510β = 98.48
c = 108.155γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description