Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 117.23 kDa 
• Atom Count: 8271 
• Modelled Residue Count: 1084 
• Deposited Residue Count: 1104 
• Unique protein chains: 1

1UN8

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

• PDB DOI: 10.2210/pdb1UN8/pdb

• Classification: TRANSFERASE
• Organism(s): Citrobacter freundii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-09-08 Released: 2003-10-10 
• Deposition Author(s): Siebold, C., Arnold, I., Garcia-Alles, L.F., Baumann, U., Erni, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.246 
• R-Value Work: 0.196 
• R-Value Observed: 0.200 

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

• PubMed: 12966101 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDROXYACETONE KINASE	A, B	552	Citrobacter freundii	Mutation(s): 0  Gene Names: dhaK EC: 2.7.1.29
UniProt
Find proteins for P45510 (Citrobacter freundii) Explore P45510  Go to UniProtKB:  P45510

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MYY	C [auth A], D [auth B]	(2R)-3-(PHOSPHONOOXY)-2-(TETRADECANOYLOXY)PROPYL PALMITATE C33 H65 O8 P GLOXZZHEZYKXNV-WJOKGBTCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 100.44	α = 90
b = 124.59	β = 90
c = 237.12	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-09-08 
• Released Date: 2003-10-10 
Deposition Author(s): Siebold, C., Arnold, I., Garcia-Alles, L.F., Baumann, U., Erni, B.

Revision History  

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