7PGX | pdb_00007pgx

Structure of dark-adapted AsLOV2 wild type

• PDB DOI: https://doi.org/10.2210/pdb7PGX/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Avena sativa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-08-16 Released: 2022-05-11 
• Deposition Author(s): Gelfert, R., Weyand, M., Moeglich, A.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 
  0.147 (Depositor), 0.149 (DCC) 
• R-Value Work: 
  0.114 (Depositor), 0.117 (DCC) 

Starting Model: experimental

Literature

Signal transduction in light-oxygen-voltage receptors lacking the active-site glutamine.

Dietler, J., Gelfert, R., Kaiser, J., Borin, V., Renzl, C., Pilsl, S., Ranzani, A.T., Garcia de Fuentes, A., Gleichmann, T., Diensthuber, R.P., Weyand, M., Mayer, G., Schapiro, I., Moglich, A.

(2022) Nat Commun 13: 2618-2618

• PubMed: 35552382 
• DOI: https://doi.org/10.1038/s41467-022-30252-4
• Primary Citation Related Structures: 
  7PGX, 7PGY, 7PGZ, 7PH0


• PubMed Abstract: 
  

  In nature as in biotechnology, light-oxygen-voltage photoreceptors perceive blue light to elicit spatiotemporally defined cellular responses. Photon absorption drives thioadduct formation between a conserved cysteine and the flavin chromophore. An equally conserved, proximal glutamine processes the resultant flavin protonation into downstream hydrogen-bond rearrangements. Here, we report that this glutamine, long deemed essential, is generally dispensable. In its absence, several light-oxygen-voltage receptors invariably retained productive, if often attenuated, signaling responses. Structures of a light-oxygen-voltage paradigm at around 1 Å resolution revealed highly similar light-induced conformational changes, irrespective of whether the glutamine is present. Naturally occurring, glutamine-deficient light-oxygen-voltage receptors likely serve as bona fide photoreceptors, as we showcase for a diguanylate cyclase. We propose that without the glutamine, water molecules transiently approach the chromophore and thus propagate flavin protonation downstream. Signaling without glutamine appears intrinsic to light-oxygen-voltage receptors, which pertains to biotechnological applications and suggests evolutionary descendance from redox-active flavoproteins.

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Organizational Affiliation: 
• Department of Biochemistry, University of Bayreuth, 95447, Bayreuth, Germany.
Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.
Life and Medical Sciences (LIMES), University of Bonn, 53121, Bonn, Germany.
Biophysical Chemistry, Humboldt-University Berlin, 10115, Berlin, Germany.
Center of Aptamer Research & Development, University of Bonn, 53121, Bonn, Germany.
Department of Biochemistry, University of Bayreuth, 95447, Bayreuth, Germany. [e-mail].
Biophysical Chemistry, Humboldt-University Berlin, 10115, Berlin, Germany. [e-mail].
Bayreuth Center for Biochemistry & Molecular Biology, Universität Bayreuth, 95447, Bayreuth, Germany. [e-mail].
North-Bavarian NMR Center, Universität Bayreuth, 95447, Bayreuth, Germany. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 18.7 kDa 
• Atom Count: 1,877 
• Modeled Residue Count: 146 
• Deposited Residue Count: 146 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NPH1-1	A [auth AAA]	146	Avena sativa	Mutation(s): 0  Gene Names: NPH1-1 EC: 2.7.11.1
UniProt
Find proteins for O49003 (Avena sativa) Explore O49003  Go to UniProtKB:  O49003

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN (Subject of Investigation/LOI)	S [auth AAA]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
PEG (Subject of Investigation/LOI)	N [auth AAA], O [auth AAA]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	D [auth AAA], E [auth AAA], F [auth AAA], G [auth AAA], H [auth AAA], I [auth AAA], J [auth AAA], K [auth AAA], L [auth AAA], M [auth AAA]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	P [auth AAA], Q [auth AAA]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	R [auth AAA]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	B [auth AAA]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	C [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free:  0.147 (Depositor), 0.149 (DCC) 
• R-Value Work:  0.114 (Depositor), 0.117 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.5	α = 90
b = 56.42	β = 90
c = 66.66	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-05-11 
Deposition Author(s): Gelfert, R., Weyand, M., Moeglich, A.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	MO2192/8-1

Revision History  

• Version 1.0: 2022-05-11
  Type: Initial release
  
• Version 1.1: 2022-05-25
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Derived calculations, Refinement description