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)

Experimental Data Snapshot

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

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1101/2023.06.30.547126
Primary Citation 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.

Organizational Affiliation

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

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9VCC6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C5Y (Subject of Investigation/LOI) Query on C5Y Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	5'-O-[(S)-hydroxy(octanoyloxy)phosphoryl]adenosine C₁₈ H₂₈ N₅ O₈ P AJYSFZDSJUTHRW-XKLVTHTNSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-01-05

Deposition Author(s):

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