2KDC | pdb_00002kdc

NMR Solution Structure of E. coli diacylglycerol kinase (DAGK) in DPC micelles

• PDB DOI: https://doi.org/10.2210/pdb2KDC/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2009-01-06 Released: 2009-07-07 
• Deposition Author(s): Van Horn, W.D., Kim, H., Ellis, C.D., Hadziselimovic, A., Sulistijo, E.S., Karra, M.D., Tian, C., Sonnichsen, F.D., Sanders, C.R.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 48 
• Conformers Submitted: 16 
• Selection Criteria: structures with the lowest energy 

Literature

Solution nuclear magnetic resonance structure of membrane-integral diacylglycerol kinase

Van Horn, W.D., Kim, H.J., Ellis, C.D., Hadziselimovic, A., Sulistijo, E.S., Karra, M.D., Tian, C., Sonnichsen, F.D., Sanders, C.R.

(2009) Science 324: 1726-1729

• PubMed: 19556511 
• DOI: https://doi.org/10.1126/science.1171716
• Primary Citation Related Structures: 
  2KDC


• PubMed Abstract: 
  

  Escherichia coli diacylglycerol kinase (DAGK) represents a family of integral membrane enzymes that is unrelated to all other phosphotransferases. We have determined the three-dimensional structure of the DAGK homotrimer with the use of solution nuclear magnetic resonance. The third transmembrane helix from each subunit is domain-swapped with the first and second transmembrane segments from an adjacent subunit. Each of DAGK's three active sites resembles a portico. The cornice of the portico appears to be the determinant of DAGK's lipid substrate specificity and overhangs the site of phosphoryl transfer near the water-membrane interface. Mutations to cysteine that caused severe misfolding were located in or near the active site, indicating a high degree of overlap between sites responsible for folding and for catalysis.

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Organizational Affiliation: 
• Department of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 39.37 kDa 
• Atom Count: 2,769 
• Modeled Residue Count: 363 
• Deposited Residue Count: 363 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diacylglycerol kinase	A, B, C	121	Escherichia coli K-12	Mutation(s): 0  Gene Names: dgkA, b4042, JW4002 EC: 2.7.1.107 Membrane Entity: Yes
UniProt
Find proteins for P0ABN1 (Escherichia coli (strain K12)) Explore P0ABN1  Go to UniProtKB:  P0ABN1

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 48 
• Conformers Submitted: 16 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-07 
Deposition Author(s): Van Horn, W.D., Kim, H., Ellis, C.D., Hadziselimovic, A., Sulistijo, E.S., Karra, M.D., Tian, C., Sonnichsen, F.D., Sanders, C.R.

Revision History  

• Version 1.0: 2009-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-16
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-05-22
  Changes: Data collection