PDBsum entry: 2bon

Transferase

PDB id: 2bon

Contents

Protein chains

287 a.a. *

265 a.a. *

Metals

_MG ×2

Waters ×71

* Residue conservation analysis

PDB id:

2bon

Name:

Transferase

Title:

Structure of an escherichia coli lipid kinase (yegs)

Structure:

Lipid kinase. Chain: a, b. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 469008. Strain: k12. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.90Å R-factor: 0.222 R-free: 0.267

Authors:

H.M.Bakali,K.A.Johnson,B.M.Hallberg,M.D.Herman,P.Nordlund

Key ref:

H.M.Bakali et al. (2007). Crystal structure of YegS, a homologue to the mammalian diacylglycerol kinases, reveals a novel regulatory metal binding site. J Biol Chem, 282, 19644-19652. PubMed id: 17351295 DOI: 10.1074/jbc.M604852200

Date:

12-Apr-05 Release date: 18-Oct-06

Protein chain

P76407  (YEGS_ECOLI) -  Lipid kinase YegS

Seq: 299 a.a.

Struc: 287 a.a.

Protein chain

P76407  (YEGS_ECOLI) -  Lipid kinase YegS

Seq: 299 a.a.

Struc: 265 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: phospholipid biosynthetic process (4 terms)
• Biochemical function: nucleotide binding (8 terms)

DOI no: 10.1074/jbc.M604852200

J Biol Chem 282:19644-19652 (2007)

PubMed id: 17351295

Crystal structure of YegS, a homologue to the mammalian diacylglycerol kinases, reveals a novel regulatory metal binding site.

H.M.Bakali, M.D.Herman, K.A.Johnson, A.A.Kelly, A.Wieslander, B.M.Hallberg, P.Nordlund.

ABSTRACT

The human lipid kinase family controls cell proliferation, differentiation, and tumorigenesis and includes diacylglycerol kinases, sphingosine kinases, and ceramide kinases. YegS is an Escherichia coli protein with significant sequence homology to the catalytic domain of the human lipid kinases. We have solved the crystal structure of YegS and shown that it is a lipid kinase with phosphatidylglycerol kinase activity. The crystal structure reveals a two-domain protein with significant structural similarity to a family of NAD kinases. The active site is located in the interdomain cleft formed by four conserved sequence motifs. Surprisingly, the structure reveals a novel metal binding site composed of residues conserved in most lipid kinases.

Selected figure(s)

Figure 4.
FIGURE 4. Conserved key residues and the metal binding site. A, the conserved aspartic acid residues of the lipid kinases and the location of the metal site. Mutations of all five conserved aspartic acids in porcine DGK show diminished activity. Mutation of the residues equivalent to YegS Asp-125 and Asp-269 also attenuate Ca^2+ activation. Water molecules and Mg^2+ are shown in blue and red spheres. Asp-98 and Asp-269 are localized at the domain interface, making stabilizing hydrogen bonds to main chain amide groups. B, the refined model of residues involved in metal coordination shown in 2 F[o] - F[c] map, contoured at 2.5 . Leu-215 and Leu-220 are contributing to coordinating the Mg^2+ along with water molecules (W1–3). The octahedral coordination is completed by Asp-218, while Asp-125 provides a second sphere coordination of a water molecule.

Figure 5.
FIGURE 5. The dependence of the YegS kinase activity on Ca^2+ and Mg^2+ concentrations.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 19644-19652) copyright 2007.

Figures were selected by an automated process.