1OI2

X-ray structure of the dihydroxyacetone kinase from Escherichia coli

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

A Mechanism of Covalent Substrate Binding in the X-Ray Structure of Subunit K of the Escherichia Coli Dihydroxyacetone Kinase

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

(2003) Proc.Natl.Acad.Sci.USA 100: 8188

  • DOI: 10.1073/pnas.0932787100
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Dihydroxyacetone (Dha) kinases are homologous proteins that use different phosphoryl donors, a multiphosphoryl protein of the phosphoenolpyruvate-dependent carbohydrate:phosphotransferase system in bacteria, ATP in animals, plants, and some bacteria. ...

    Dihydroxyacetone (Dha) kinases are homologous proteins that use different phosphoryl donors, a multiphosphoryl protein of the phosphoenolpyruvate-dependent carbohydrate:phosphotransferase system in bacteria, ATP in animals, plants, and some bacteria. The Dha kinase of Escherichia coli consists of three subunits, DhaK and DhaL, which are colinear to the ATP-dependent Dha kinases of eukaryotes, and the multiphosphoryl protein DhaM. Here we show the crystal structure of the DhaK subunit in complex with Dha at 1.75 A resolution. DhaK is a homodimer with a fold consisting of two six-stranded mixed beta-sheets surrounded by nine alpha-helices and a beta-ribbon covering the exposed edge strand of one sheet. The core of the N-terminal domain has an alpha/beta fold common to subunits of carbohydrate transporters and transcription regulators of the phosphoenolpyruvate-dependent carbohydrate:phosphotransferase system. The core of the C-terminal domain has a fold similar to the C-terminal domain of the cell-division protein FtsZ. A molecule of Dha is covalently bound in hemiaminal linkage to the N epsilon 2 of His-230. The hemiaminal does not participate in covalent catalysis but is the chemical basis for discrimination between short-chain carbonyl compounds and polyols. Paralogs of Dha kinases occur in association with transcription regulators of the TetR/QacR and the SorC families, pointing to their biological role as sensors in signaling.

    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
HYPOTHETICAL PROTEIN YCGT
A, B
366Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: dhaK (ycgT)
EC: 2.7.1.121
Find proteins for P76015 (Escherichia coli (strain K12))
Go to UniProtKB:  P76015
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 96.509α = 90.00
b = 97.408β = 90.00
c = 85.963γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SHARPphasing
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance