1MXS

Crystal structure of 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase from Pseudomonas putida.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase from Pseudomonas putida.

Bell, B.J.Watanabe, L.Rios-Steiner, J.L.Tulinsky, A.Lebioda, L.Arni, R.K.

(2003) Acta Crystallogr.,Sect.D 59: 1454-1458


  • PubMed Abstract: 
  • 2-Keto-3-deoxy-6-phosphogluconate (KDPG) aldolase from Pseudomonas putida is a key enzyme in the Entner-Doudoroff pathway which catalyses the cleavage of KDPG via a class I Schiff-base mechanism. The crystal structure of this enzyme has been refined ...

    2-Keto-3-deoxy-6-phosphogluconate (KDPG) aldolase from Pseudomonas putida is a key enzyme in the Entner-Doudoroff pathway which catalyses the cleavage of KDPG via a class I Schiff-base mechanism. The crystal structure of this enzyme has been refined to a crystallographic residual R = 17.1% (R(free) = 21.4%). The N-terminal helix caps one side of the torus of the (betaalpha)(8)-barrel and the active site is located on the opposite, carboxylic side of the barrel. The Schiff-base-forming Lys145 is coordinated by a sulfate (or phosphate) ion and two solvent water molecules. The interactions that stabilize the trimer are predominantly hydrophobic, with the exception of the cyclically permuted bonds formed between Glu132 OE1 of one molecule and Thr129 OG1 of a symmetry-equivalent molecule. Except for the N-terminal helix, the structure of KDPG aldolase from P. putida closely resembles the structure of the homologous enzyme from Escherichia coli.


    Related Citations: 
    • Directed evolution of a new catalytic site in 2-keto-3-deoxy-6-phosphogluconate aldolase from Escherichia coli.
      Wymer, N.,Buchanan, L.V.,Henderson, D.,Mehta, N.,Botting, C.H.,Pocivavsek, L.,Fierke, C.A.,Toone, E.J.,Naismith, J.H.
      (2001) Structure 9: 1
    • Structure of 2-keto-3-deoxy-6-phosphogluconate aldolase at 2.8A resolution
      Mavridis, I.M.,Hatada, M.H.,Tulinsky, A.,Lebioda, L.
      (1982) J.Mol.Biol. 162: 419
    • The folding and quaternary structure of trimeric 2-keto-3-deoxy-6-phosphogluconic aldolase at 3.5-A resolution.
      Mavridis, I.M.,Tulinsky, A.
      (1976) Biochemistry 15: 4410
    • Covalent intermediate trapped in 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase structure at 1.95-A resolution
      Allard, J.,Grochulski, P.,Sygusch, J.
      (2001) Proc.Natl.Acad.Sci.USA 98: 3679


    Organizational Affiliation

    Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
KDPG Aldolase
A
225Pseudomonas putidaGene Names: eda
EC: 4.1.2.14
Find proteins for P00885 (Pseudomonas putida)
Go to UniProtKB:  P00885
Small Molecules
Ligands 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.171 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 103.300α = 90.00
b = 103.300β = 90.00
c = 103.300γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-16
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description