Crystal structure of the dihydroxyacetone kinase from E. coli in complex with glyceraldehyde

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

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Phosphoenolpyruvate- and ATP-Dependent Dihydroxyacetone Kinases: Covalent Substrate-Binding and Kinetic Mechanism

Garcia-Alles, L.F.Siebold, C.Luthi-Nyffeler, T.Flukiger-Bruhwiler, K.Schneider, P.Burgi, H.-B.Baumann, U.Erni, B.

(2004) Biochemistry 43: 13037

  • DOI: https://doi.org/10.1021/bi048575m
  • Primary Citation of Related Structures:  
    1UOD, 1UOE

  • PubMed Abstract: 

    Dihydroxyacetone (Dha) kinases are a sequence-conserved family of enzymes, which utilize two different phosphoryldonors, ATP in animals, plants, and some bacteria, and a multiphosphoprotein of the phosphoenolpyruvate carbohydrate phosphotransferase system (PTS) in most bacteria. Here, we compare the PTS-dependent kinase of Escherichia coli and the ATP-dependent kinase of Citrobacter freundii. They display 30% sequence identity. The binding constants of the E. coli kinase for eleven short-chain carbonyl compounds were determined by acetone precipitation of the enzyme-substrate complexes. They are 3.4 microM for Dha, 780 microM for Dha-phosphate (DhaP), 50 microM for D,L-glyceraldehyde (GA), and 90 microM for D,L-glyceraldehyde-3-phosphate. The k(cat) for Dha of the PTS-dependent kinase is 290 min(-1), and that of the ATP-dependent kinase is 1050 min(-1). The Km for Dha of both kinases is <6 microM. The X-ray structures of the enzyme-GA and the enzyme-DhaP complex show that substrates as well as products are bound in hemiaminal linkage to an active-site histidine. Quantum-mechanical calculations offer no indication for activation of the reacting hydroxyl group by the formation of the hemiaminal. However, the formation of the hemiaminal bond allows selection for short-chain carbonyl compounds and discrimination against structurally similar polyols. The Dha kinase remains fully active in the presence of 2 M glycerol, and phosphorylates trace impurities of carbonyl compounds present in glycerol.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry and Laboratory for Chemical and Mineralogical Crystallography, University of Berne, CH-3012 Berne, Switzerland.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
366Escherichia coliMutation(s): 0 
Find proteins for P76015 (Escherichia coli (strain K12))
Explore P76015 
Go to UniProtKB:  P76015
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76015
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.54α = 90
b = 97.315β = 90
c = 85.997γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance