2-dehydro-3-deoxy-galactarate aldolase from Escherichia coli

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

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Crystal Structures of the Metal-Dependent 2-Dehydro-3-Deoxy-Galactarate Aldolase Suggest a Novel Reaction Mechanism.

Izard, T.Blackwell, N.C.

(2000) EMBO J 19: 3849

  • DOI: https://doi.org/10.1093/emboj/19.15.3849
  • Primary Citation of Related Structures:  
    1DXE, 1DXF

  • PubMed Abstract: 

    Carbon-carbon bond formation is an essential reaction in organic chemistry and the use of aldolase enzymes for the stereochemical control of such reactions is an attractive alternative to conventional chemical methods. Here we describe the crystal structures of a novel class II enzyme, 2-dehydro-3-deoxy-galactarate (DDG) aldolase from Escherichia coli, in the presence and absence of substrate. The crystal structure was determined by locating only four Se sites to obtain phases for 506 protein residues. The protomer displays a modified (alpha/beta)(8) barrel fold, in which the eighth alpha-helix points away from the beta-barrel instead of packing against it. Analysis of the DDG aldolase crystal structures suggests a novel aldolase mechanism in which a phosphate anion accepts the proton from the methyl group of pyruvate.

  • Organizational Affiliation

    Department of Biochemistry, University of Leicester, Leicester LE1 7RH, UK. Tina.Izard@stjude.org

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
256Escherichia coliMutation(s): 0 
Find proteins for P23522 (Escherichia coli (strain K12))
Explore P23522 
Go to UniProtKB:  P23522
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23522
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.07α = 90
b = 129.07β = 90
c = 167.96γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-08-25
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations