4G37

Structure of cross-linked firefly luciferase in second catalytic conformation

• PDB DOI: https://doi.org/10.2210/pdb4G37/pdb

• Classification: LIGASE
• Organism(s): Photinus pyralis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-07-13 Released: 2012-08-15 
• Deposition Author(s): Sundlov, J.A., Branchini, B.R., Gulick, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.259 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 

Starting Model: experimental

Literature

Crystal structure of firefly luciferase in a second catalytic conformation supports a domain alternation mechanism.

Sundlov, J.A., Fontaine, D.M., Southworth, T.L., Branchini, B.R., Gulick, A.M.

(2012) Biochemistry 51: 6493-6495

• PubMed: 22852753 
• DOI: https://doi.org/10.1021/bi300934s
• Primary Citation of Related Structures:  
  4G36, 4G37


• PubMed Abstract: 
  

  Beetle luciferases catalyze a two-step reaction that includes the initial adenylation of the luciferin substrate, followed by an oxidative decarboxylation that ultimately produces light. Evidence for homologous acyl-CoA synthetases supports a domain alternation catalytic mechanism in which these enzymes' C-terminal domain rotates by ~140° to adopt two conformations that are used to catalyze the two partial reactions. While many structures exist of acyl-CoA synthetases in both conformations, to date only biochemical evidence supports domain alternation with luciferase. We have determined the structure of a cross-linked luciferase enzyme that is trapped in the second conformation. This new structure supports the role of the second catalytic conformation and provides insights into the biochemical mechanism of the luciferase oxidative step.

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Organizational Affiliation: 

Hauptman-Woodward Institute, 700 Ellicott Street, Buffalo, NY 14203, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 124.21 kDa 
• Atom Count: 8,395 
• Modelled Residue Count: 1,072 
• Deposited Residue Count: 1,110 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Luciferin 4-monooxygenase	A, B	555	Photinus pyralis	Mutation(s): 11  EC: 1.13.12.7
UniProt
Find proteins for P08659 (Photinus pyralis) Explore P08659  Go to UniProtKB:  P08659

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SLU	C [auth A], G [auth B]	5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE C21 H18 N8 O8 S3 LJLYTUYNVSHXQB-SOONXTGKSA-N
XLX	D [auth A], H [auth B]	4,4'-(ethylenediimino)bis[4-oxobutyrate] C11 H18 N2 O6 JUHMDCQKNGDTCV-UHFFFAOYSA-N
SO4	E [auth A], F [auth A], J [auth B], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.259 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.638	α = 90
b = 184.091	β = 90
c = 170.53	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-15 
Deposition Author(s): Sundlov, J.A., Branchini, B.R., Gulick, A.M.

Revision History  

• Version 1.0: 2012-08-15
  Type: Initial release
  
• Version 1.1: 2012-10-31
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description