Crystal structure of the dihydroxyacetone kinase of C. freundii (native form)

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 

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Crystal Structure of the Citrobacter Freundii Dihydroxyacetone Kinase Reveals an Eight-Stranded Alpha-Helical Barrel ATP-Binding Domain

Siebold, C.Arnold, I.Garcia-Alles, L.F.Baumann, U.Erni, B.

(2003) J Biol Chem 278: 48236

  • DOI: https://doi.org/10.1074/jbc.M305942200
  • Primary Citation of Related Structures:  
    1UN8, 1UN9

  • PubMed Abstract: 

    Dihydroxyacetone 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 in bacteria. Here we report the 2.5-A crystal structure of the homodimeric Citrobacter freundii dihydroxyacetone kinase complex with an ATP analogue and dihydroxyacetone. The N-terminal domain consists of two alpha/beta-folds with a molecule of dihydroxyacetone covalently bound in hemiaminal linkage to the N epsilon 2 of His-220. The C-terminal domain consists of a regular eight-helix alpha-barrel. The eight helices form a deep pocket, which includes a tightly bound phospholipid. Only the lipid headgroup protrudes from the surface. The nucleotide is bound on the top of the barrel across from the entrance to the lipid pocket. The phosphate groups are coordinated by two Mg2+ ions to gamma-carboxyl groups of aspartyl residues. The ATP binding site does not contain positively charged or aromatic groups. Paralogues of dihydroxyacetone kinase also occur in association with transcription regulators and proteins of unknown function pointing to biological roles beyond triose metabolism.

  • Organizational Affiliation

    Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
552Citrobacter freundiiMutation(s): 0 
Find proteins for P45510 (Citrobacter freundii)
Explore P45510 
Go to UniProtKB:  P45510
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45510
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MYY

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C33 H65 O8 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.44α = 90
b = 124.59β = 90
c = 237.12γ = 90
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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance