1YTM

Crystal structure of phosphoenolpyruvate carboxykinase of Anaerobiospirillum succiniciproducens complexed with ATP, oxalate, magnesium and manganese ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of Anaerobiospirillum succiniciproducens PEP carboxykinase reveals an important active site loop

Cotelesage, J.J.H.Prasad, L.Zeikus, J.G.Laivenieks, M.Delbaere, L.T.J.

(2005) Int.J.Biochem.Cell Biol. 37: 1829-1837

  • DOI: 10.1016/j.biocel.2005.03.008
  • Primary Citation of Related Structures:  1YVY

  • PubMed Abstract: 
  • The 2.2 Angstroms resolution crystal structure of the enzyme phosphoenolpyruvate carboxykinase (PCK) from the bacterium Anaerobiospirillum succiniciproducens complexed with ATP, Mg(2+), Mn(2+) and the transition state analogue oxalate has been solved ...

    The 2.2 Angstroms resolution crystal structure of the enzyme phosphoenolpyruvate carboxykinase (PCK) from the bacterium Anaerobiospirillum succiniciproducens complexed with ATP, Mg(2+), Mn(2+) and the transition state analogue oxalate has been solved. The 2.4 Angstroms resolution native structure of A. succiniciproducens PCK has also been determined. It has been found that upon binding of substrate, PCK undergoes a conformational change. Two domains of the molecule fold towards each other, with the substrates and metal ions held in a cleft formed between the two domains. This domain movement is believed to accelerate the reaction PCK catalyzes by forcing bulk solvent molecules out of the active site. Although the crystal structure of A. succiniciproducens PCK with bound substrate and metal ions is related to the structures of PCK from Escherichia coli and Trypanosoma cruzi, it is the first crystal structure from this class of enzymes that clearly shows an important surface loop (residues 383-397) from the C-terminal domain, hydrogen bonding with the peptide backbone of the active site residue Arg60. The interaction between the surface loop and the active site backbone, which is a parallel beta-sheet, seems to be a feature unique of A. succiniciproducens PCK. The association between the loop and the active site is the third type of interaction found in PCK that is thought to play a part in the domain closure. This loop also appears to help accelerate catalysis by functioning as a 'lid' that shields water molecules from the active site.


    Organizational Affiliation

    Department of Biochemistry, University of Saskatchewan, Saskatoon, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
phosphoenolpyruvate carboxykinase [ATP]
A, B
532Anaerobiospirillum succiniciproducensGene Names: pckA
EC: 4.1.1.49
Find proteins for O09460 (Anaerobiospirillum succiniciproducens)
Go to UniProtKB:  O09460
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
OXD
Query on OXD

Download SDF File 
Download CCD File 
A, B
OXALIC ACID
C2 H2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 194.871α = 90.00
b = 123.219β = 90.00
c = 48.463γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
AMoREphasing
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-24
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance