1MXS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

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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 D Biol Crystallogr 59: 1454-1458

  • DOI: 10.1107/s0907444903013192
  • Primary Citation of Related Structures:  
    1MXS

  • 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 to a crystallographic residual R = 17 ...

    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
    • 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 U S A 98: 3679
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
KDPG AldolaseA225Pseudomonas putidaMutation(s): 0 
Gene Names: eda
EC: 4.1.2.14
UniProt
Find proteins for P00885 (Pseudomonas putida)
Explore P00885 
Go to UniProtKB:  P00885
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00885
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.3α = 90
b = 103.3β = 90
c = 103.3γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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