8CTP | pdb_00008ctp

Crystal structure of engineered phospholipase D mutant superPLD 2-23

• PDB DOI: https://doi.org/10.2210/pdb8CTP/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces sp. PMF
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-05-16 Released: 2023-04-26 
• Deposition Author(s): Tei, R., Bagde, S.R., Fromme, J.C., Baskin, J.M.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.232 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

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

• PubMed: 37217787 
• DOI: https://doi.org/10.1038/s41557-023-01214-0
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA. [e-mail].
Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 54.81 kDa 
• Atom Count: 3,842 
• Modeled Residue Count: 480 
• Deposited Residue Count: 513 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase D	A	513	Streptomyces sp. PMF	Mutation(s): 6  EC: 3.1.4.4
UniProt
Find proteins for P84147 (Streptomyces sp. (strain PMF)) Explore P84147  Go to UniProtKB:  P84147

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	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 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.725	α = 90
b = 73	β = 90
c = 87.482	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-26 
Deposition Author(s): Tei, R., Bagde, S.R., Fromme, J.C., Baskin, J.M.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CAREER CHE-1749919
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM136258
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM124165
National Science Foundation (NSF, United States)	United States	DMR-1829070
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM124166-01A1

Revision History  

• 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
• Version 1.4: 2024-11-06
  Changes: Structure summary