9JPL | pdb_00009jpl

Crystal structure of DhdR inducer binding domain in complex with inducer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 
    0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Development of D2HG biosensors inspired by the molecular mechanism of D2HG regulation of DhdR.

Wang, B.Luo, S.Sun, P.

(2025) Cell Chem Biol 32: 1397-1411.e7

  • DOI: https://doi.org/10.1016/j.chembiol.2025.10.004
  • Primary Citation of Related Structures:  
    9JPJ, 9JPK, 9JPL, 9VKN

  • PubMed Abstract: 

    Mutant isocitrate dehydrogenases (IDH1/IDH2) catalyze the conversion of α-ketoglutarate (αKG) to D-2-hydroxyglutarate (D2HG), a hallmark of many lower-grade gliomas. Elevated D2HG levels promote tumorigenesis through epigenetic reprogramming and immunosuppressive mechanisms, although paradoxically, D2HG can also inhibit tumor growth. To explore D2HG's biological functions, we developed genetically encoded D2HG biosensors (DHsers) based on the prokaryotic transcriptional regulator DhdR. Structural analysis of DhdR, including its apo form, D2HG-bound complex, and DNA-bound complex, revealed that D2HG binding induces DhdR conformational changes that regulate DNA interaction. Leveraging these insights, we engineered biosensors (DHsers) that detect a wide range of concentrations of D2HG (0.3-30 mM) with high sensitivity. We also established a standardized protocol for quantifying subcellular D2HG levels in living cells. Notably, STING activation promotes D2HG production, suggesting a role of D2HG in immune modulation. Our findings reveal D2HG-induced transcriptional regulation in prokaryotes, offering a platform for studying the role of D2HG in cellular metabolism and tumorigenesis.


  • Organizational Affiliation
    • Research Center of Neurobiology, Shanxi University of Chinese Medicine, Jinzhong 030619, China; Basic Laboratory of Integrated Traditional Chinese and Western Medicine, Shanxi University of Chinese Medicine, Jinzhong 030619, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate dehydrogenase complex repressor
A, B
238Achromobacter denitrificans NBRC 15125Mutation(s): 0 
Gene Names: FOC81_30220
UniProt
Find proteins for A0A6N0JVZ6 (Achromobacter denitrificans)
Explore A0A6N0JVZ6 
Go to UniProtKB:  A0A6N0JVZ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6N0JVZ6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128α = 90
b = 128β = 90
c = 42.95γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release
  • Version 1.1: 2025-11-19
    Changes: Database references
  • Version 1.2: 2025-12-03
    Changes: Database references