8CTP

Crystal structure of engineered phospholipase D mutant superPLD 2-23


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Activity-based directed evolution of a membrane editor in mammalian cells.

Tei, R.Bagde, S.R.Fromme, J.C.Baskin, J.M.

(2023) Nat Chem 15: 1030-1039

  • DOI: https://doi.org/10.1038/s41557-023-01214-0
  • Primary Citation of Related Structures:  
    8CTP, 8CTQ

  • PubMed Abstract: 

    Cellular membranes contain numerous lipid species, and efforts to understand the biological functions of individual lipids have been stymied by a lack of approaches for controlled modulation of membrane composition in situ. Here we present a strategy for editing phospholipids, the most abundant lipids in biological membranes. Our membrane editor is based on a bacterial phospholipase D (PLD), which exchanges phospholipid head groups through hydrolysis or transphosphatidylation of phosphatidylcholine with water or exogenous alcohols. Exploiting activity-dependent directed enzyme evolution in mammalian cells, we have developed and structurally characterized a family of 'superPLDs' with up to a 100-fold enhancement in intracellular activity. We demonstrate the utility of superPLDs for both optogenetics-enabled editing of phospholipids within specific organelle membranes in live cells and biocatalytic synthesis of natural and unnatural designer phospholipids in vitro. Beyond the superPLDs, activity-based directed enzyme evolution in mammalian cells is a generalizable approach to engineer additional chemoenzymatic biomolecule editors.


  • Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phospholipase D513Streptomyces sp. PMFMutation(s): 6 
EC: 3.1.4.4
UniProt
Find proteins for P84147 (Streptomyces sp. (strain PMF))
Explore P84147 
Go to UniProtKB:  P84147
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84147
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.725α = 90
b = 73β = 90
c = 87.482γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCAREER CHE-1749919
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM136258
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124165
National Science Foundation (NSF, United States)United StatesDMR-1829070
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124166-01A1

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2023-06-07
    Changes: Database references
  • Version 1.2: 2023-07-19
    Changes: Database references
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description