Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 13.86 kDa 
• Atom Count: 1042 
• Modelled Residue Count: 110 
• Deposited Residue Count: 115 
• Unique protein chains: 1

4EEP

Crystal structure of LOV2 domain of Arabidopsis thaliana phototropin 2

• PDB DOI: 10.2210/pdb4EEP/pdb

• Classification: SIGNALING PROTEIN, flavoprotein
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-28 Released: 2012-05-16 
• Deposition Author(s): Hitomi, K., Christie, J.M., Arvai, A.S., Hartfield, K.A., Pratt, A.J., Tainer, J.A., Getzoff, E.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.238 
• R-Value Work: 0.213 
• R-Value Observed: 0.214 

Literature

Structural Tuning of the Fluorescent Protein iLOV for Improved Photostability.

Christie, J.M., Hitomi, K., Arvai, A.S., Hartfield, K.A., Mettlen, M., Pratt, A.J., Tainer, J.A., Getzoff, E.D.

(2012) J Biol Chem 287: 22295-22304

• PubMed: 22573334 
• DOI: 10.1074/jbc.M111.318881
• Primary Citation of Related Structures:  
  4EEP, 4EER, 4EES, 4EET, 4EEU


• PubMed Abstract: 
  

Fluorescent proteins derived from light, oxygen, or voltage (LOV) domains offer advantages over green fluorescent protein (GFP) from their small size and efficacy under anaerobic conditions. The flavoprotein improved LOV (iLOV) was engineered from the blue light receptor phototropin as a reporter of viral infection. To inform the molecular basis for the improved, photoreversible, fluorescent properties of iLOV, we employed directed evolution and determined five LOV crystallographic structures. Comparative structural analyses between iLOV and its progenitors reveal mutation-induced constraints in the environment of the flavin mononucleotide (FMN) chromophore; in iLOV, the methyl group of Thr-394 "crowds" the FMN isoalloxazine ring, Leu-470 triggers side chain "flipping" of Leu-472, and the terminal FMN phosphate shows increased anchoring. We further engineered iLOV variants that are readily detectable in bacterial and mammalian cells due to order-of-magnitude photostability increases. Structure determination of a resulting representative photostable iLOV (phiLOV) variant reveals additional constraints on the chromophore. Aromatic residues Tyr-401 and Phe-485 in phiLOV sandwich the FMN isoalloxazine ring from both sides, whereas Ser-390 anchors the side chain of FMN-interacting Gln-489 Our combined structural and mutational results reveal that constraining the FMN fluorophore yields improved photochemical properties for iLOV and its new photostable derivative. These findings provide a framework for structural fine-tuning of LOV scaffold proteins to maximize their potential as oxygen-independent fluorescent reporters.

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Organizational Affiliation: 

Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phototropin-2	A	115	Arabidopsis thaliana	Mutation(s): 0  Gene Names: PHOT2, CAV1, KIN7, NPL1, At5g58140, K21L19.6 EC: 2.7.11.1
UniProt
Find proteins for P93025 (Arabidopsis thaliana) Explore P93025  Go to UniProtKB:  P93025

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.238 
• R-Value Work: 0.213 
• R-Value Observed: 0.214 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.502	α = 90
b = 40.502	β = 90
c = 127.315	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-03-28 
• Released Date: 2012-05-16 
Deposition Author(s): Hitomi, K., Christie, J.M., Arvai, A.S., Hartfield, K.A., Pratt, A.J., Tainer, J.A., Getzoff, E.D.

Revision History  

• Version 1.0: 2012-05-16
  Type: Initial release
  
• Version 1.1: 2012-06-06
  Changes: Database references
• Version 1.2: 2012-07-11
  Changes: Database references
• Version 1.3: 2018-01-24
  Changes: Structure summary