Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 60.84 kDa 
• Atom Count: 5011 
• Residue Count: 539 
• Unique protein chains: 1

2D1T

Crystal structure of the thermostable Japanese Firefly Luciferase red-color emission S286N mutant complexed with High-energy intermediate analogue

• DOI: 10.2210/pdb2D1T/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Luciola cruciata
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-08-31 Released: 2006-03-21 
• Deposition Author(s): Nakatsu, T., Ichiyama, S., Hiratake, J., Saldanha, A., Kobashi, N., Sakata, K., Kato, H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.182 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 

Literature

Structural basis for the spectral difference in luciferase bioluminescence.

Nakatsu, T., Ichiyama, S., Hiratake, J., Saldanha, A., Kobashi, N., Sakata, K., Kato, H.

(2006) Nature 440: 372-376

• PubMed: 16541080 
• DOI: 10.1038/nature04542
• Primary Citation of Related Structures:  
  2D1T, 2D1S, 2D1R, 2D1Q


• PubMed Abstract: 
  

Fireflies communicate with each other by emitting yellow-green to yellow-orange brilliant light. The bioluminescence reaction, which uses luciferin, Mg-ATP and molecular oxygen to yield an electronically excited oxyluciferin species, is carried out by the enzyme luciferase. Visible light is emitted during relaxation of excited oxyluciferin to its ground state. The high quantum yield of the luciferin/luciferase reaction and the change in bioluminescence colour caused by subtle structural differences in luciferase have attracted much research interest. In fact, a single amino acid substitution in luciferase changes the emission colour from yellow-green to red. Although the crystal structure of luciferase from the North American firefly (Photinus pyralis) has been described, the detailed mechanism for the bioluminescence colour change is still unclear. Here we report the crystal structures of wild-type and red mutant (S286N) luciferases from the Japanese Genji-botaru (Luciola cruciata) in complex with a high-energy intermediate analogue, 5'-O-[N-(dehydroluciferyl)-sulfamoyl]adenosine (DLSA). Comparing these structures to those of the wild-type luciferase complexed with AMP plus oxyluciferin (products) reveals a significant conformational change in the wild-type enzyme but not in the red mutant. This conformational change involves movement of the hydrophobic side chain of Ile 288 towards the benzothiazole ring of DLSA. Our results indicate that the degree of molecular rigidity of the excited state of oxyluciferin, which is controlled by a transient movement of Ile 288, determines the colour of bioluminescence during the emission reaction.

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Organizational Affiliation: 

Kinetic Crystallography Research Team, Membrane Dynamics Research Group, RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Luciferin 4-monooxygenase	A	548	Luciola cruciata	Mutation(s): 3  EC: 1.13.12.7
Find proteins for P13129 (Luciola cruciata) Explore P13129  Go to UniProtKB:  P13129

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SLU	A	5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE C21 H18 N8 O8 S3 LJLYTUYNVSHXQB-SOONXTGKSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.182 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.468	α = 90
b = 181.174	β = 90
c = 52.239	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-08-31 
• Released Date: 2006-03-21 
Deposition Author(s): Nakatsu, T., Ichiyama, S., Hiratake, J., Saldanha, A., Kobashi, N., Sakata, K., Kato, H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History 

• Version 1.0: 2006-03-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-12-25
  Changes: Data collection, Database references, Derived calculations