1UN8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1074/jbc.M305942200
  • Primary Citation of Related Structures:  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 i ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIHYDROXYACETONE KINASE
A, B
552Citrobacter freundiiGene Names: dhaK
EC: 2.7.1.29
Find proteins for P45510 (Citrobacter freundii)
Go to UniProtKB:  P45510
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYY
Query on MYY

Download SDF File 
Download CCD File 
A, B
(2R)-3-(PHOSPHONOOXY)-2-(TETRADECANOYLOXY)PROPYL PALMITATE
C33 H65 O8 P
GLOXZZHEZYKXNV-WJOKGBTCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.196 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 100.440α = 90.00
b = 124.590β = 90.00
c = 237.120γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

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