6KTH

Crystal structure of Juvenile hormone diol kinase JHDK-L2 from silkworm, Bombyx mori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.183 

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This is version 1.2 of the entry. See complete history


Literature

Structural characterization and functional analysis of juvenile hormone diol kinase from the silkworm, Bombyx mori.

Xu, H.Zhang, Y.Zhang, L.Wang, Z.Guo, P.Zhao, P.

(2021) Int J Biol Macromol 167: 570-577

  • DOI: https://doi.org/10.1016/j.ijbiomac.2020.11.138
  • Primary Citation of Related Structures:  
    6KTH

  • PubMed Abstract: 

    Juvenile hormone diol kinase (JHDK) is an important enzyme involved in the juvenile hormone metabolism pathway, which catalyzes the phosphorylation of juvenile hormone diol to form the polar metabolite JH diol phosphate. Here, we reported the first crystal structure of insect JHDK from Bombyx mori, BmJHDK-L2, determined at a resolution of 1.22 Å. The structure of BmJHDK-L2 mainly comprises of eight α-helical segments linked with loops, forming four helix-loop-helix motifs. In these four helix-loop-helix motifs with only one calcium ion bound in the first motif. Circular dichroism spectra indicated that BmJHDK-L2 has strong thermal stability, which is independent of the divalent cation. The structure of BmJHDK-L2 further allowed us to define an ATP-binding site using computational simulation and binding assays, providing a structural basis for development of inhibitor of JHDK. Moreover, the expression profile of BmJHDK-L2 indicated a predominant role in juvenile hormone metabolism in the Malpighian tubules of silkworm. Collectively, these findings expand our knowledge regarding the structural and biochemical features of insect JHDK proteins.


  • Organizational Affiliation

    State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Biological Science Research Center, Southwest University, Chongqing 400716, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Juvenile hormone diol kinase201Bombyx moriMutation(s): 0 
Gene Names: JHDK-L2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.96α = 90
b = 67.57β = 90
c = 69.47γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31502019
National Natural Science Foundation of ChinaChina31970468

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2021-04-07
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description