PDBsum entry 2qv7

Transferase

PDB id: 2qv7

Contents

Protein chain

303 a.a. *

Ligands

ADP

Metals

_MG

Waters ×152

* Residue conservation analysis

PDB id:

2qv7

Name:

Transferase

Title:

Crystal structure of diacylglycerol kinase dgkb in complex with adp and mg

Structure:

Diacylglycerol kinase dgkb. Chain: a. Engineered: yes

Source:

Staphylococcus aureus. Gene: sar1989. Expressed in: escherichia coli.

Resolution:

2.30Å R-factor: 0.208 R-free: 0.246

Authors:

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

Key ref:

D.J.Miller et al. (2008). Analysis of the Staphylococcus aureus DgkB structure reveals a common catalytic mechanism for the soluble diacylglycerol kinases. Structure, 16, 1036-1046. PubMed id: 18611377 DOI: 10.1016/j.str.2008.03.019

Date:

07-Aug-07 Release date: 17-Jun-08

Protein chain

Q6GFF9  (DAGK_STAAR) -  Diacylglycerol kinase from Staphylococcus aureus (strain MRSA252)

Seq: 315 a.a.

Struc: 303 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.1.107 - diacylglycerol kinase (ATP).
• Reaction: a 1,2-diacyl-sn-glycerol + ATP = a 1,2-diacyl-sn-glycero-3-phosphate + ADP + H⁺

1,2-diacyl-sn-glycerol + ATP = 1,2-diacyl-sn-glycero-3-phosphate + ADP (Bound ligand (Het Group name = ADP) corresponds exactly) + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.str.2008.03.019

Structure 16:1036-1046 (2008)

PubMed id: 18611377

Analysis of the Staphylococcus aureus DgkB structure reveals a common catalytic mechanism for the soluble diacylglycerol kinases.

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

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.

Selected figure(s)

Figure 1.
Figure 1. Overall Structure of DgkB and a Close-Up of the Nucleotide-Binding Site
(A) Cartoon diagram of the DgkB monomer in the asymmetric unit. α helices are gray, and β strands and loops are green. ADP carbons and Mg1 (sphere) are cyan. Secondary structure elements are labeled. Disordered residues 145–157 are absent in the final model and are indicated with a broken line. The predicted locations of the insertions in human diacylglycerol kinases (see Figure 2) are labeled IN1–3.
(B) Stereo cartoon of the YegS structure (PDB code: 2BON, chain A) superimposed on DgkB. The orientations of domains 1 and 2 differ slightly in the two structures, and, to highlight their structural similarity, each domain of YegS was superimposed independently onto the DgkB structure. DgkB is colored as shown in (A), and YegS is tan. Disordered residues are indicated with broken lines. Significant differences reside in the predicted DgkB substrate-binding region (β8-α6 loop), which is highlighted in bright green, and the corresponding YegS region is brown.
(C) Stereo close-up view of the DgkB nucleotide-binding site with omit electron density for ADP contoured to 3σ. Bound waters are shown as red spheres. Hydrogen bonds are indicated by broken lines.

Figure 3.
Figure 3. Properties of the DgkB Dimer
(A) Gel-filtration chromatography of DgkB with a Sephadex-200 10/300 GL column. DgkB eluted with a Stokes radius (Rs) of 41 Å based on calibration of the column with eight protein standards (left inset). SDS gel electrophoresis (right inset) showed the presence of a single protein with an apparent subunit molecular weight of 42 kDa. The molecular weight calculated from the DNA sequence was 37,333.
(B) Sedimentation velocity analysis of DgkB. The protein characteristics determined from the velocity sedimentation experiment are shown as an inset in the figure.
(C) The structure of the DgkB dimer. The green monomer is the observed molecule in the asymmetric unit shown in Figure 1A, tilted backward 45°. The sand-colored monomer is generated by two-fold symmetry. ADP carbons and Mg1 (sphere) are cyan.
(D) The conserved DgkB dimerization interface. Only the residues involved in salt bridges are shown as sticks. Hydrogen bonds are indicated with broken lines.
(E) A representative sequence alignment of the amino-terminal residues in known bacterial DgkBs involved in dimer formation. Residues responsible for salt bridges and van der Waals interactions are indicated with an “x” and black spheres, respectively.

The above figures are reprinted by permission from Cell Press: Structure (2008, 16, 1036-1046) copyright 2008.

Figures were selected by an automated process.