4Q2E

CRYSTAL STRUCTURE OF AN INTRAMEMBRANE CDP-DAG SYNTHETASE CENTRAL FOR PHOSPHOLIPID BIOSYNTHESIS (S200C/S258C, active mutant)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.299 
  • R-Value Observed: 0.299 

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This is version 1.2 of the entry. See complete history. 


Literature

Structure and mechanism of an intramembrane liponucleotide synthetase central for phospholipid biosynthesis

Liu, X., Yin, Y., Wu, J., Liu, Z.

(2014) Nat Commun 5: 4244-4244

  • DOI: 10.1038/ncomms5244
  • Primary Citation of Related Structures:  
    4Q2E, 4Q2G

  • PubMed Abstract: 

    • Phospholipids are elemental building-block molecules for biological membranes. Biosynthesis of phosphatidylinositol, phosphatidylglycerol and phosphatidylserine requires a central liponucleotide intermediate named cytidine-diphosphate diacylglycerol (CDP-DAG) ...

    Phospholipids are elemental building-block molecules for biological membranes. Biosynthesis of phosphatidylinositol, phosphatidylglycerol and phosphatidylserine requires a central liponucleotide intermediate named cytidine-diphosphate diacylglycerol (CDP-DAG). The CDP-DAG synthetase (Cds) is an integral membrane enzyme catalysing the formation of CDP-DAG, an essential step for phosphoinositide recycling during signal transduction. Here we report the structure of the Cds from Thermotoga maritima (TmCdsA) at 3.4 Å resolution. TmCdsA forms a homodimer and each monomer contains nine transmembrane helices arranged into a novel fold with three domains. An unusual funnel-shaped cavity penetrates half way into the membrane, allowing the enzyme to simultaneously accept hydrophilic substrate (cytidine 5'-triphosphate (CTP)/deoxy-CTP) from cytoplasm and hydrophobic substrate (phosphatidic acid) from membrane. Located at the bottom of the cavity, a Mg(2+)-K(+) hetero-di-metal centre coordinated by an Asp-Asp dyad serves as the cofactor of TmCdsA. The results suggest a two-metal-ion catalytic mechanism for the Cds-mediated synthesis of CDP-DAG at the membrane-cytoplasm interface.

    Organizational Affiliation: 

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidate cytidylyltransferaseA, B290Thermotoga maritima MSB8Mutation(s): 2 
Gene Names: cdsA, TM_1397
EC: 2.7.7.41
Membrane Entity: Yes 
UniProt
Find proteins for Q9X1B7 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X1B7 
Go to UniProtKB:  Q9X1B7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X1B7
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.299 
  • R-Value Observed: 0.299 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.08α = 90
b = 142.08β = 90
c = 198.373γ = 120
Software Package:
Software NamePurpose
SERGUIdata collection
PHENIXmodel building
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2014-07-30
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description