7PJD | pdb_00007pjd

The X-ray structure of juvenile hormone diol kinase from the silk worm Bombyx mori.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 
    0.248 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

The X-ray structure of juvenile hormone diol kinase from the silkworm Bombyx mori.

Guo, J.Keegan, R.M.Rigden, D.J.Erskine, P.T.Wood, S.P.Li, S.Cooper, J.B.

(2021) Acta Crystallogr F Struct Biol Commun 77: 465-472

  • DOI: https://doi.org/10.1107/S2053230X21012012
  • Primary Citation Related Structures: 
    7PJD

  • PubMed Abstract: 

    Insect juvenile hormones (JHs) are a family of sesquiterpenoid molecules that are secreted into the haemolymph. JHs have multiple roles in insect development, metamorphosis and sexual maturation. A number of pesticides work by chemically mimicking JHs, thus preventing insects from developing and reproducing normally. The haemolymph levels of JH are governed by the rates of its biosynthesis and degradation. One enzyme involved in JH catabolism is JH diol kinase (JHDK), which uses ATP (or GTP) to phosphorylate JH diol to JH diol phosphate, which can be excreted. The X-ray structure of JHDK from the silkworm Bombyx mori has been determined at a resolution of 2.0 Å with an R factor of 19.0% and an R free of 24.8%. The structure possesses three EF-hand motifs which are occupied by calcium ions. This is in contrast to the recently reported structure of the JHDK-like-2 protein from B. mori (PDB entry 6kth), which possessed only one calcium ion. Since JHDK is known to be inhibited by calcium ions, it is likely that our structure represents the calcium-inhibited form of the enzyme. The electrostatic surface of the protein suggests a binding site for the triphosphate of ATP close to the N-terminal end of the molecule in a cavity between the N- and C-terminal domains. Superposition with a number of calcium-activated photoproteins suggests that there may be parallels between the binding of JH diol to JHDK and the binding of luciferin to aequorin.


  • Organizational Affiliation
    • Division of Medicine, UCL, Gower Street, London WC1E 6BT, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 125.79 kDa 
  • Atom Count: 9,287 
  • Modeled Residue Count: 1,092 
  • Deposited Residue Count: 1,104 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Juvenile hormone diol kinase
A, B, C, D, E
A, B, C, D, E, F
184Bombyx moriMutation(s): 0 
Gene Names: JHDK
UniProt
Find proteins for Q6URH4 (Bombyx mori)
Explore Q6URH4 
Go to UniProtKB:  Q6URH4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6URH4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
(Subject of Investigation/LOI)

Query on CA



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth B]
K [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth C],
N [auth C],
O [auth C],
P [auth D],
Q [auth D],
R [auth D],
S [auth E],
T [auth E],
U [auth E],
V [auth F],
W [auth F],
X [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.64α = 90
b = 79.43β = 91.6
c = 100.93γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
xia2data reduction
MrBUMPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-22
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-16
    Changes: Structure summary