Crystal structure of blue fluorescent protein from metagenomic library

Experimental Data Snapshot

  • Resolution: 2.31 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

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Structure-Guided Generation of a Redox-Independent Blue Fluorescent Protein from mBFP.

Seo, P.W.Jo, E.S.You, S.H.Cheong, D.E.Kim, G.J.Kim, J.S.

(2019) J Mol Biol 431: 3191-3202

  • DOI: https://doi.org/10.1016/j.jmb.2019.06.005
  • Primary Citation of Related Structures:  
    6J7H, 6J7U

  • PubMed Abstract: 

    Fluorescent proteins, such as the green fluorescent protein, are used for detection of cellular components and events. However, green fluorescent protein and its derivatives have limited usage under anaerobic conditions and require a long maturation time. On the other hand, the NADPH-dependent blue fluorescent protein (BFP) without oxidative modification of residues is instantly functional in both aerobic and anaerobic systems. BFP proteins belong to a short-chain dehydrogenase/reductase (SDR) protein family, and their fluorescent property changes with reaction time in the presence of a substrate. With the aim of developing a better fluorescent reporter independent of redox state, we elucidated the crystal structure of a tetrameric mBFP from soil metagenomes with and without NADPH. Apart from the previously known regions, structure-guided mutational studies have identified several residues that contribute to the fluorescence of mBFP, including two aromatic residues (F97 and Y157) near the nicotinamide moiety of the bound NADPH. A single histidine mutation at Y157 (Y157H) has conferred more stabilized, time-independent fluorescence even in the presence of substrates. Furthermore, we discovered another SDR protein that can also emit blue fluorescence. These results open a new possibility for the development of BFP as a stable cellular reporter for widespread use, independent of subcellular environments.

  • Organizational Affiliation

    Department of Biological Sciences, Chonnam National University, Gwangju 61186, Republic of Korea. Electronic address: gjkim@chonnam.ac.kr.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Blue fluorescent protein
A, B, C, D
261uncultured bacteriumMutation(s): 0 
Find proteins for D6NKF4 (uncultured bacterium)
Explore D6NKF4 
Go to UniProtKB:  D6NKF4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD6NKF4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.31 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.281α = 90
b = 90.564β = 90
c = 171.526γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description