7KYD | pdb_00007kyd

Drosophila melanogaster long-chain fatty-acyl-CoA synthetase CG6178

• PDB DOI: https://doi.org/10.2210/pdb7KYD/pdb

• Classification: LIGASE
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-12-07 Released: 2022-01-05 
• Deposition Author(s): Adams, S.T., Zephyr, J., Bohn, M.F., Schiffer, C.A., Miller, S.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

FruitFire: a luciferase based on a fruit fly metabolic enzyme.

Adams, S.T., Zephyr, J., Bohn, M.F., Schiffer, C.A., Miller, S.C.

(2023) bioRxiv 

• PubMed: 37425765 
• DOI: https://doi.org/10.1101/2023.06.30.547126
• Primary Citation of Related Structures:  
  7KYD


• PubMed Abstract: 
  

  Firefly luciferase is homologous to fatty acyl-CoA synthetases from insects that are not bioluminescent. Here, we determined the crystal structure of the fruit fly fatty acyl-CoA synthetase CG6178 to 2.5 Å. Based on this structure, we mutated a steric protrusion in the active site to create the artificial luciferase FruitFire, which prefers the synthetic luciferin CycLuc2 to d-luciferin by >1000-fold. FruitFire enabled in vivo bioluminescence imaging in the brains of mice using the pro-luciferin CycLuc2-amide. The conversion of a fruit fly enzyme into a luciferase capable of in vivo imaging underscores the potential for bioluminescence with a range of adenylating enzymes from nonluminescent organisms, and the possibilities for application-focused design of enzyme-substrate pairs.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, 364 Plantation St, Worcester, MA 01605.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 60.96 kDa 
• Atom Count: 4,122 
• Modeled Residue Count: 534 
• Deposited Residue Count: 549 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Long-chain fatty-acyl-CoA synthetase CG6178	A	549	Drosophila melanogaster	Mutation(s): 0  Gene Names: Dmel\CG6178, FACL, CG6178, Dmel_CG6178 EC: 6.2.1.3 (PDB Primary Data), 1.13.12.7 (UniProt)
UniProt
Find proteins for Q9VCC6 (Drosophila melanogaster) Explore Q9VCC6  Go to UniProtKB:  Q9VCC6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C5Y (Subject of Investigation/LOI)	B [auth A]	5'-O-[(S)-hydroxy(octanoyloxy)phosphoryl]adenosine C18 H28 N5 O8 P AJYSFZDSJUTHRW-XKLVTHTNSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.851	α = 90
b = 77.778	β = 90
c = 113.315	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PHASER	phasing
Coot	model building
PDB_EXTRACT	data extraction
HKL-3000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-01-05 
Deposition Author(s): Adams, S.T., Zephyr, J., Bohn, M.F., Schiffer, C.A., Miller, S.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	F31GM116586-01A1
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)	United States	R01EB013270

Revision History  

• Version 1.0: 2022-01-05
  Type: Initial release
  
• Version 1.1: 2023-07-19
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description