PDBsum entry 3bq7

Transferase

PDB id: 3bq7

Contents

Protein chains

(+ 0 more) 68 a.a. *

* Residue conservation analysis

PDB id:

3bq7

Name:

Transferase

Title:

Sam domain of diacylglycerol kinase delta1 (e35g)

Structure:

Diacylglycerol kinase delta. Chain: a, b, c, d, e, f. Fragment: sam domain. Synonym: diglyceride kinase delta, dgk-delta, dag kinase delta, 130 kda diacylglycerol kinase. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: dgkd, kiaa0145. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: bl21 (de3).

Resolution:

2.90Å R-factor: 0.250 R-free: 0.290

Authors:

M.J.Knight,J.U.Bowie,M.R.Sawaya

Key ref:

B.T.Harada et al. (2008). Regulation of enzyme localization by polymerization: polymer formation by the SAM domain of diacylglycerol kinase delta1. Structure, 16, 380-387. PubMed id: 18334213 DOI: 10.1016/j.str.2007.12.017

Date:

19-Dec-07 Release date: 25-Mar-08

Protein chains

Q16760  (DGKD_HUMAN) -  Diacylglycerol kinase delta from Homo sapiens

Seq: 1214 a.a.

Struc: 68 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

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⁺

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

reference

DOI no: 10.1016/j.str.2007.12.017

Structure 16:380-387 (2008)

PubMed id: 18334213

Regulation of enzyme localization by polymerization: polymer formation by the SAM domain of diacylglycerol kinase delta1.

B.T.Harada, M.J.Knight, S.Imai, F.Qiao, R.Ramachander, M.R.Sawaya, M.Gingery, F.Sakane, J.U.Bowie.

ABSTRACT

The diacylglycerol kinase (DGK) enzymes function as regulators of intracellular signaling by altering the levels of the second messengers, diacylglycerol and phosphatidic acid. The DGK delta and eta isozymes possess a common protein-protein interaction module known as a sterile alpha-motif (SAM) domain. In DGK delta, SAM domain self-association inhibits the translocation of DGK delta to the plasma membrane. Here we show that DGK delta SAM forms a polymer and map the polymeric interface by a genetic selection for soluble mutants. A crystal structure reveals that DGKSAM forms helical polymers through a head-to-tail interaction similar to other SAM domain polymers. Disrupting polymerization by polymer interface mutations constitutively localizes DGK delta to the plasma membrane. Thus, polymerization of DGK delta regulates the activity of the enzyme by sequestering DGK delta in an inactive cellular location. Regulation by dynamic polymerization is an emerging theme in signal transduction.

Selected figure(s)

Figure 1.
Figure 1. Electron Micrograph of DGKSAM
Electron microscopy image of DGKSAM revealing the formation of fibers. Although most fibers are tangled, measurements of single fibers show an average width of vert, similar 80 Å. Scale bar = 25 nm.

Figure 3.
Figure 3. Crystal Structure of the DGKSAM Polymer
(A) Space-filling model of the DGKSAM polymer showing the helical structure. Every other subunit is colored green or yellow. Two of the subunits are shown as ribbon diagrams.
(B) A ribbon model showing a close-up view of the oligomeric interface. The end-helix (EH, green) surface of one SAM domain contacts the mid-loop (ML, yellow) surface of another SAM domain forming head-to-tail interaction. Side-chains important in mediating this interaction are shown and colored according to the surface on which they reside. For sequence orientation: The V52, G53, K56, E35G, and D43 in the DGKSAM structure correspond to V1148, G1149, K1152, E1131, D1139, and C1116 in the full-length DGKδ1.

The above figures are reprinted by permission from Cell Press: Structure (2008, 16, 380-387) copyright 2008.

Figures were selected by an automated process.