Comparison of class I aldolase binding site architecture based on the crystal structure of 2-deoxyribose-5-phosphate aldolase determined at 0.99 Angstrom resolution

Experimental Data Snapshot

  • Resolution: 0.99 Å

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Analysis of the class I aldolase binding site architecture based on the crystal structure of 2-deoxyribose-5-phosphate aldolase at 0.99A resolution.

Heine, A.Luz, J.G.Wong, C.H.Wilson, I.A.

(2004) J Mol Biol 343: 1019-1034

  • DOI: https://doi.org/10.1016/j.jmb.2004.08.066
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of the bacterial (Escherichia coli) class I 2-deoxyribose-5-phosphate aldolase (DERA) has been determined by Se-Met multiple anomalous dispersion (MAD) methods at 0.99A resolution. This structure represents the highest-resolution X-ray structure of an aldolase determined to date and enables a true atomic view of the enzyme. The crystal structure shows the ubiquitous TIM alpha/beta barrel fold. The enzyme contains two lysine residues in the active site. Lys167 forms the Schiff base intermediate, whereas Lys201, which is in close vicinity to the reactive lysine residue, is responsible for the perturbed pK(a) of Lys167 and, hence, also a key residue in the reaction mechanism. DERA is the only known aldolase that is able to use aldehydes as both aldol donor and acceptor molecules in the aldol reaction and is, therefore, of particular interest as a biocatalyst in synthetic organic chemistry. The uncomplexed DERA structure enables a detailed comparison with the substrate complexes and highlights a conformational change in the phosphate-binding site. Knowledge of the enzyme active-site environment has been the basis for exploration of catalysis of non-natural substrates and of mutagenesis of the phosphate-binding site to expand substrate specificity. Detailed comparison with other class I aldolase enzymes and DERA enzymes from different organisms reveals a similar geometric arrangement of key residues and implies a potential role for water as a general base in the catalytic mechanism.

  • Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxyribose-phosphate aldolase
A, B
260Escherichia coli K-12Mutation(s): 0 
Gene Names: b4381deoCDEOC OR DRA OR THYR OR B4381 OR C5465draJW4344thyR
Find proteins for P0A6L0 (Escherichia coli (strain K12))
Explore P0A6L0 
Go to UniProtKB:  P0A6L0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6L0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 0.99 Å
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.73α = 90
b = 42.01β = 98.53
c = 145.41γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
MAR345data collection
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-01
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-05-09
    Changes: Structure summary
  • Version 1.4: 2017-10-11
    Changes: Refinement description
  • Version 1.5: 2024-02-14
    Changes: Data collection, Database references