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 PQS (software)

Macromolecule Content

• Total Structure Weight: 79.44 kDa 
• Atom Count: 5555 
• Modelled Residue Count: 672 
• Deposited Residue Count: 732 
• Unique protein chains: 1

1OI2

X-ray structure of the dihydroxyacetone kinase from Escherichia coli

• PDB DOI: 10.2210/pdb1OI2/pdb

• Classification: KINASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-06-04 Released: 2003-06-26 
• Deposition Author(s): Siebold, C., Garcia-Alles, L.-F., Erni, B., Baumann, U.

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Experimental Data Snapshot

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

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 U S A 100: 8188

• PubMed: 12813127 
• DOI: 10.1073/pnas.0932787100
• Primary Citation of Related Structures:  
  1OI2, 1OI3


• 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. 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.

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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
HYPOTHETICAL PROTEIN YCGT	A, B	366	Escherichia coli	Mutation(s): 0  EC: 2.7.1.29 (PDB Primary Data), 2.7.1.121 (UniProt)
UniProt
Find proteins for P76015 (Escherichia coli (strain K12)) Explore P76015  Go to UniProtKB:  P76015

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.201 
• R-Value Work: 0.172 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.509	α = 90
b = 97.408	β = 90
c = 85.963	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
SHARP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-06-04 
• Released Date: 2003-06-26 
Deposition Author(s): Siebold, C., Garcia-Alles, L.-F., Erni, B., Baumann, U.

Revision History  

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