2QV7

Crystal Structure of Diacylglycerol Kinase DgkB in complex with ADP and Mg

• PDB DOI:  https://doi.org/10.2210/pdb2QV7/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-08-07 Released: 2008-06-17 
• Deposition Author(s): Miller, D.J., Jerga, A., Rock, C.O., White, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.246 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Literature

Analysis of the Staphylococcus aureus DgkB Structure Reveals a Common Catalytic Mechanism for the Soluble Diacylglycerol Kinases.

Miller, D.J., Jerga, A., Rock, C.O., White, S.W.

(2008) Structure 16: 1036-1046

• PubMed: 18611377 
• DOI: https://doi.org/10.1016/j.str.2008.03.019
• Primary Citation of Related Structures:  
  2QV7, 2QVL


• PubMed Abstract: 
  

Soluble diacylglycerol (DAG) kinases function as regulators of diacylglycerol metabolism in cell signaling and intermediary metabolism. We report the structure of a DAG kinase, DgkB from Staphylococcus aureus, both as the free enzyme and in complex with ADP. The molecule is a tight homodimer, and each monomer comprises two domains with the catalytic center located within the interdomain cleft. Two distinctive features of DkgB are a structural Mg2+ site and an associated Asp*water*Mg2+ network that extends toward the active site locale. Site-directed mutagenesis revealed that these features play important roles in the catalytic mechanism. The key active site residues and the components of the Asp*water*Mg2+ network are conserved in the catalytic cores of the mammalian signaling DAG kinases, indicating that these enzymes use the same mechanism and have similar structures as DgkB.

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Organizational Affiliation: 

Department of Structural Biology, St. Jude Children's Research Hospital, and Department of Molecular Sciences, University of Tennessee Health Science Center, 332 North Lauderdale Street, Memphis, TN 38105, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38.35 kDa 
• Atom Count: 2,504 
• Modelled Residue Count: 303 
• Deposited Residue Count: 337 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diacylglycerol Kinase DgkB	A	337	Staphylococcus aureus	Mutation(s): 0  Gene Names: SAR1989 EC: 2.7.1.107
UniProt
Find proteins for Q6GFF9 (Staphylococcus aureus (strain MRSA252)) Explore Q6GFF9  Go to UniProtKB:  Q6GFF9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Binding Affinity Annotations
ID	Source	Binding Affinity
ADP	PDBBind:  2QV7	Kd: 2.19e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.246 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.76	α = 90
b = 123.76	β = 90
c = 47.68	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
DgkB	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-17 
Deposition Author(s): Miller, D.J., Jerga, A., Rock, C.O., White, S.W.

Revision History  

• Version 1.0: 2008-06-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance