8URT | pdb_00008urt

Cholinephosphotransferase in complex with selective inhibitor chelerythrine


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis for catalysis and selectivity of phospholipid synthesis by eukaryotic choline-phosphotransferase.

Roberts, J.R.Horibata, Y.Kwarcinski, F.E.Lam, V.Raczkowski, A.M.Hubbard, A.White, B.Sugimoto, H.Tall, G.G.Ohi, M.D.Maeda, S.

(2025) Nat Commun 16: 111-111

  • DOI: https://doi.org/10.1038/s41467-024-55673-1
  • Primary Citation of Related Structures:  
    8UL9, 8URP, 8URT

  • PubMed Abstract: 

    Phospholipids are the most abundant component in lipid membranes and are essential for the structural and functional integrity of the cell. In eukaryotic cells, phospholipids are primarily synthesized de novo through the Kennedy pathway that involves multiple enzymatic processes. The terminal reaction is mediated by a group of cytidine-5'-diphosphate (CDP)-choline /CDP-ethanolamine-phosphotransferases (CPT/EPT) that use 1,2-diacylglycerol (DAG) and CDP-choline or CDP-ethanolamine to produce phosphatidylcholine (PC) or phosphatidylethanolamine (PE) that are the main phospholipids in eukaryotic cells. Here we present the structure of the yeast CPT1 in multiple substrate-bound states. Structural and functional analysis of these binding-sites reveal the critical residues for the DAG acyl-chain preference and the choline/ethanolamine selectivity. Additionally, we present the structure in complex with a potent inhibitor characterized in this study. The ensemble of structures allows us to propose the reaction mechanism for phospholipid biosynthesis by the family of CDP-alcohol phosphotransferases (CDP-APs).


  • Organizational Affiliation

    Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cholinephosphotransferase 1
A, B
393Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: CPT1
EC: 2.7.8.2
Membrane Entity: Yes 
UniProt
Find proteins for P17898 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P17898 
Go to UniProtKB:  P17898
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17898
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PCW
Query on PCW

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth A]
I [auth A]
J [auth B]
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
CTI (Subject of Investigation/LOI)
Query on CTI

Download Ideal Coordinates CCD File 
G [auth A],
N [auth B]
1,2-dimethoxy-12-methyl[1,3]benzodioxolo[5,6-c]phenanthridin-12-ium
C21 H18 N O4
LLEJIEBFSOEYIV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
K [auth B],
L [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.2.1
MODEL REFINEMENTPHENIX1.20.1-4487

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Source and taxonomy
  • Version 1.2: 2024-11-20
    Changes: Data collection
  • Version 1.3: 2024-11-27
    Changes: Data collection, Data processing
  • Version 1.4: 2025-01-15
    Changes: Data collection, Database references, Structure summary