6J7U

Crystal structure of blue fluorescent protein from metagenomic library in complex with NADPH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation 3D Report Full Report



Literature

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

  • 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 ...

    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 Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea. Electronic address: jsunkim@chonnam.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Blue fluorescent proteinA, B, C, D261uncultured bacteriumMutation(s): 0 
EC: 1.2.4.4
Find proteins for D6NKF4 (uncultured bacterium)
Explore D6NKF4 
Go to UniProtKB:  D6NKF4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download CCD File 
A, B, C, D
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.662α = 90
b = 96.792β = 90
c = 168.937γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-01-18 
  • Released Date: 2019-09-18 
  • Deposition Author(s): Seo, P.W., Kim, J.S.

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

Revision History 

  • Version 1.0: 2019-09-18
    Type: Initial release