Ancestral luciferase AncLamp in complex with DLSA

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Resurrecting the ancient glow of the fireflies.

Oba, Y.Konishi, K.Yano, D.Shibata, H.Kato, D.Shirai, T.

(2020) Sci Adv 6

  • DOI: https://doi.org/10.1126/sciadv.abc5705
  • Primary Citation of Related Structures:  
    6K4C, 6K4D

  • PubMed Abstract: 

    The color of firefly bioluminescence is determined by the structure of luciferase. Firefly luciferase genes have been isolated from more than 30 species, producing light ranging in color from green to orange-yellow. Here, we reconstructed seven ancestral firefly luciferase genes, characterized the enzymatic properties of the recombinant proteins, and determined the crystal structures of the gene from ancestral Lampyridae. Results showed that the synthetic luciferase for the last common firefly ancestor exhibited green light caused by a spatial constraint on the luciferin molecule in enzyme, while fatty acyl-CoA synthetic activity, an original function of firefly luciferase, was diminished in exchange. All known firefly species are bioluminescent in the larvae, with a common ancestor arising approximately 100 million years ago. Combined, our findings propose that, within the mid-Cretaceous forest, the common ancestor of fireflies evolved green light luciferase via trade-off of the original function, which was likely aposematic warning display against nocturnal predation.

  • Organizational Affiliation

    Department of Environmental Biology, Chubu University, Kasugai 487-8501, Japan. yoba@isc.chubu.ac.jp t_shirai@nagahama-i-bio.ac.jp.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ancestral luciferase AncLamp545LampyridaeMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SLU (Subject of Investigation/LOI)
Query on SLU

Download Ideal Coordinates CCD File 
C21 H18 N8 O8 S3
Query on MG

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.31α = 90
b = 123.36β = 90
c = 177.39γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)Japan19am0101111j0003
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan17H01818

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-27
    Type: Initial release
  • Version 1.1: 2020-12-09
    Changes: Database references
  • Version 1.2: 2020-12-16
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description