8A6X | pdb_00008a6x

Crystal structure of a chimeric LOV-Histidine kinase SB2F1 (asymmetrical variant, trigonal form with long c axis)

PDB DOI: https://doi.org/10.2210/pdb8A6X/pdb

Classification: SIGNALING PROTEIN
Organism(s): Pseudomonas putida KT2440, Bradyrhizobium diazoefficiens USDA 110
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-06-20 Released: 2024-01-10
Deposition Author(s): Arinkin, V., Granzin, J., Batra-Safferling, R.
Funding Organization(s): German Federal Ministry for Education and Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.267 (Depositor), 0.280 (DCC)
R-Value Work:
0.226 (Depositor), 0.237 (DCC)
R-Value Observed:
0.228 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Dimer asymmetry in signaling of blue light sensor histidine kinases.

Arinkin, V., Stadler, A.M., Meier, S.S.M., Jaeger, K.E., Moglich, A., Krauss, U., Batra-Safferling, R.

(2026) Sci Adv 12: eaed8943-eaed8943

PubMed: 42384803 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.aed8943
Primary Citation Related Structures:
8A3U, 8A52, 8A6X, 8A7F, 8A7H

PubMed Abstract:
Photoreceptor sensory histidine kinases (SHKs) couple light absorption to conformational changes regulating two-component signaling. Despite their importance and widespread use in optogenetics, the underlying structural signaling mechanisms remain poorly understood. Here, we engineered dimeric SHKs based on Pseudomonas putida short light-oxygen-voltage (LOV) proteins, determined their crystal structures, and investigated their signaling mechanisms. Regardless of illumination, the structures adopted a light-state like LOV-LOV dimer with symmetric/straight kinase modules. In contrast, small-angle x-ray scattering together with functional assays revealed pronounced light-dependent rearrangements in solution and allowed the assignment of the kinase-ON dark state to an asymmetric/kinked conformation, whereas the light state adopts a symmetric/straight structure. Comparative analyses of natural and engineered SHKs identified conserved motifs linking light-induced LOV domain rotation to kinase activity. The findings highlight the central role of dimer asymmetry and flexibility in SHK signaling, thereby not least informing the engineering of new light-responsive signaling systems.

Organizational Affiliation

Institut für Biologische Informationsprozesse (IBI), Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany.

Macromolecule Content

Total Structure Weight: 88.66 kDa
Atom Count: 5,811
Modeled Residue Count: 732
Deposited Residue Count: 776
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative Sensory box protein,Sensor protein FixL	A, B	388	Pseudomonas putida KT2440, Bradyrhizobium diazoefficiens USDA 110 This entity is chimeric	Mutation(s): 0 Gene Names: PP_2739, fixL, bll2760 EC: 2.7.13.3
UniProt
Find proteins for P23222 (Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)) Explore P23222 Go to UniProtKB: P23222
Find proteins for Q88JB0 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88JB0 Go to UniProtKB: Q88JB0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P23222 Q88JB0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
FMN (Subject of Investigation/LOI) Query on FMN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.267 (Depositor), 0.280 (DCC)
R-Value Work: 0.226 (Depositor), 0.237 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.794	α = 90
b = 138.794	β = 90
c = 96.084	γ = 120

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
SHELXD	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-01-10

Deposition Author(s):

Arinkin, V.

Granzin, J.

Batra-Safferling, R.

Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	FKZ 031A16

Revision History (Full details and data files)

Version 1.0: 2024-01-10
Type: Initial release
Version 1.1: 2024-10-16
Changes: Structure summary
Version 1.2: 2026-04-01
Changes: Database references, Refinement description
Version 1.3: 2026-07-15
Changes: Database references