6T74 | pdb_00006t74

New antiparallel dimer of aureochrome 1a LOV domain mutants from Phaeodactylum tricornutum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.175 (Depositor), 0.175 (DCC) 
  • R-Value Work: 
    0.154 (Depositor), 0.155 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6T74

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

An Optogenetic Tool for Induced Protein Stabilization Based on the Phaeodactylum tricornutum Aureochrome 1a Light-Oxygen-Voltage Domain.

Hepp, S.Trauth, J.Hasenjager, S.Bezold, F.Essen, L.O.Taxis, C.

(2020) J Mol Biology 432: 1880-1900

  • DOI: https://doi.org/10.1016/j.jmb.2020.02.019
  • Primary Citation Related Structures: 
    6T73, 6T74

  • PubMed Abstract: 

    Control of cellular events by optogenetic tools is a powerful approach to manipulate cellular functions in a minimally invasive manner. A common problem posed by the application of optogenetic tools is to tune the activity range to be physiologically relevant. Here, we characterized a photoreceptor of the light-oxygen-voltage (LOV) domain family of Phaeodactylum tricornutum aureochrome 1a (AuLOV) as a tool for increasing protein stability under blue light conditions in budding yeast. Structural studies of AuLOV wt , the variants AuLOV M254 , and AuLOV W349 revealed alternative dimer association modes for the dark state, which differ from previously reported AuLOV dark-state structures. Rational design of AuLOV-dimer interface mutations resulted in an optimized optogenetic tool that we fused to the photoactivatable adenylyl cyclase from Beggiatoa sp. This synergistic light-regulation approach using two photoreceptors resulted in an optimized, photoactivatable adenylyl cyclase with a cyclic adenosine monophosphate production activity that matches the physiological range of Saccharomyces cerevisiae. Overall, we enlarged the optogenetic toolbox for yeast and demonstrated the importance of fine-tuning the optogenetic tool activity for successful application in cells.


  • Organizational Affiliation
    • Unit for Structural Biochemistry, Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany; Center of Synthetic Microbiology, Philipps Universität Marburg, Hans-Meerwein- Strasse 4, 35032 Marburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 38.12 kDa 
  • Atom Count: 2,718 
  • Modeled Residue Count: 281 
  • Deposited Residue Count: 324 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ptaureo1a lov2 domain
A, B
162Phaeodactylum tricornutumMutation(s): 0 
UniProt
Find proteins for A0A140UHJ0 (Phaeodactylum tricornutum)
Explore A0A140UHJ0 
Go to UniProtKB:  A0A140UHJ0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140UHJ0
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN

Query on FMN



Download:Ideal Coordinates CCD File
C [auth A],
H [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
D [auth A],
F [auth A],
I [auth B]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
MLI

Query on MLI



Download:Ideal Coordinates CCD File
K [auth B]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth A],
L [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.175 (Depositor), 0.175 (DCC) 
  • R-Value Work:  0.154 (Depositor), 0.155 (DCC) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.746α = 90
b = 100.746β = 90
c = 120.57γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACrefinement
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyES152/16-1; TA320/7-1

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Database references
  • Version 1.2: 2020-05-20
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description