6IG2

Structure of mitochondrial CDP-DAG synthase Tam41 complexed with CTP, delta 74, F240A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.882 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of the Mitochondrial CDP-DAG Synthase Tam41 Suggest a Potential Lipid Substrate Pathway from Membrane to the Active Site.

Jiao, H.Yin, Y.Liu, Z.

(2019) Structure 27: 1258

  • DOI: 10.1016/j.str.2019.04.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In mitochondria, CDP-diacylglycerol (CDP-DAG) is a crucial precursor for cardiolipin biosynthesis. Mitochondrial CDP-DAG is synthesized by the translocator assembly and maintenance protein 41 (Tam41) through an elusive process. Here we show that Tam4 ...

    In mitochondria, CDP-diacylglycerol (CDP-DAG) is a crucial precursor for cardiolipin biosynthesis. Mitochondrial CDP-DAG is synthesized by the translocator assembly and maintenance protein 41 (Tam41) through an elusive process. Here we show that Tam41 adopts sequential catalytic mechanism, and report crystal structures of the bulk N-terminal region of Tam41 from Schizosaccharomyces pombe in the apo and CTP-bound state. The structure reveals that Tam41 contains a nucleotidyltransferase (NTase) domain and a winged helix domain. CTP binds to an "L"-shaped pocket sandwiched between the two domains. Rearrangement of a loop region near the active site is essential for opening the CTP-binding pocket. Docking of phosphatidic acid/CDP-DAG in the structure suggests a lipid entry/exit pathway connected to the "L"-shaped pocket. The C-terminal region of SpTam41 contains a positively charged amphipathic helix crucial for membrane association and participates in binding phospholipids. These results provide detailed insights into the mechanism of CDP-DAG biosynthesis in mitochondria.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, No. 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, No. 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China. Electronic address: liuzf@ibp.ac.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidate cytidylyltransferase, mitochondrial
A, B, C, D
313Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 1 
Gene Names: tam41
EC: 2.7.7.41
Find proteins for O74339 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O74339
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CTP
Query on CTP

Download SDF File 
Download CCD File 
D
CYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O14 P3
PCDQPRRSZKQHHS-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.882 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.216 
  • Space Group: P 21 2 2
Unit Cell:
Length (Å)Angle (°)
a = 55.266α = 90.00
b = 187.418β = 90.00
c = 186.570γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31670749
Chinese Academy of SciencesChinaXDB08020302

Revision History 

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-08-21
    Type: Data collection, Database references