3BQ7

SAM domain of Diacylglycerol Kinase delta1 (E35G)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.254 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Regulation of Enzyme Localization by Polymerization: Polymer Formation by the SAM Domain of Diacylglycerol Kinase delta1

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

(2008) Structure 16: 380-387

  • DOI: https://doi.org/10.1016/j.str.2007.12.017
  • Primary Citation of Related Structures:  
    3BQ7

  • PubMed 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.


  • Organizational Affiliation

    Molecular Biology Institute, University of California, Los Angeles, Boyer Hall, Los Angeles, CA 90095-1570, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diacylglycerol kinase delta
A, B, C, D, E
A, B, C, D, E, F
81Homo sapiensMutation(s): 1 
Gene Names: DGKDKIAA0145
EC: 2.7.1.107
UniProt & NIH Common Fund Data Resources
Find proteins for Q16760 (Homo sapiens)
Explore Q16760 
Go to UniProtKB:  Q16760
PHAROS:  Q16760
GTEx:  ENSG00000077044 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16760
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.254 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.079α = 90
b = 108.079β = 90
c = 33.513γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
BOSdata collection
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Advisory, Refinement description
  • Version 1.3: 2021-10-20
    Changes: Advisory, Database references
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description