8A7H | pdb_00008a7h

Classification: SIGNALING PROTEIN
Organism(s): Pseudomonas putida KT2440, Bradyrhizobium diazoefficiens USDA 110
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Experimental Data Snapshot

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

(2026) Sci Adv 12: eaed8943-eaed8943

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

Find similar proteins by:

| 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): 1 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

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]
JGC (Subject of Investigation/LOI) Query on JGC Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	Flavin mononucleotide (semi-quinone intermediate) C₁₇ H₂₃ N₄ O₉ P JNFNEOXSUODPSY-DGAVXFQQSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]