Biological Assembly 1  

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

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: 28.96 kDa 
• Atom Count: 2330 
• Modelled Residue Count: 258 
• Deposited Residue Count: 262 
• Unique protein chains: 1

3CT6

Crystal structure of DhaM of L. lactis

• PDB DOI: 10.2210/pdb3CT6/pdb

• Classification: TRANSFERASE
• Organism(s): Lactococcus lactis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-04-11 Released: 2008-10-21 
• Deposition Author(s): Zurbriggen, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.177 
• R-Value Observed: 0.147 

Literature

X-ray Structures of the Three Lactococcus lactis Dihydroxyacetone Kinase Subunits and of a Transient Intersubunit Complex.

Zurbriggen, A., Jeckelmann, J.M., Christen, S., Bieniossek, C., Baumann, U., Erni, B.

(2008) J Biol Chem 283: 35789-35796

• PubMed: 18957416 
• DOI: 10.1074/jbc.M804893200
• Primary Citation of Related Structures:  
  3CR3, 3CT4, 3CT6


• PubMed Abstract: 
  

Bacterial dihydroxyacetone (Dha) kinases do not exchange the ADP for ATP but utilize a subunit of the phosphoenolpyruvate carbohydrate phosphotransferase system for in situ rephosphorylation of a permanently bound ADP-cofactor. Here we report the 2.1-angstroms crystal structure of the transient complex between the phosphotransferase subunit DhaM of the phosphotransferase system and the nucleotide binding subunit DhaL of the Dha kinase of Lactococcus lactis, the 1.1-angstroms structure of the free DhaM dimer, and the 2.5-angstroms structure of the Dha-binding DhaK subunit. Conserved salt bridges and an edge-to-plane stacking contact between two tyrosines serve to orient DhaL relative to the DhaM dimer. The distance between the imidazole Nepsilon2 of the DhaM His-10 and the beta-phosphate oxygen of ADP, between which the gamma-phosphate is transferred, is 4.9 angstroms. An invariant arginine, which is essential for activity, is appropriately positioned to stabilize the gamma-phosphate in the transition state. The (betaalpha)4alpha fold of DhaM occurs a second time as a subfold in the DhaK subunit. By docking DhaL-ADP to this subfold, the nucleotide bound to DhaL and the C1-hydroxyl of Dha bound to DhaK are positioned for in-line transfer of phosphate.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit dhaM	A, B	131	Lactococcus lactis	Mutation(s): 0  Gene Names: dhaM EC: 2.7.1 (PDB Primary Data), 2.7.1.121 (UniProt)
UniProt
Find proteins for Q9CIV6 (Lactococcus lactis subsp. lactis (strain IL1403)) Explore Q9CIV6  Go to UniProtKB:  Q9CIV6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.177 
• R-Value Observed: 0.147 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.6	α = 90
b = 62.4	β = 99.6
c = 69.7	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
SOLVE	phasing
RESOLVE	phasing
SHELX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SHELX	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-04-11 
• Released Date: 2008-10-21 
Deposition Author(s): Zurbriggen, A.

Revision History  

• Version 1.0: 2008-10-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-23
  Changes: Advisory, Data collection, Source and taxonomy