7EBW

Crystal structure of Aedes aegypti Noppera-bo, glutathione S-transferase epsilon 8, in desmethylglycitein and glutathione-bound form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 

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


Literature

Molecular action of larvicidal flavonoids on ecdysteroidogenic glutathione S-transferase Noppera-bo in Aedes aegypti.

Inaba, K.Ebihara, K.Senda, M.Yoshino, R.Sakuma, C.Koiwai, K.Takaya, D.Watanabe, C.Watanabe, A.Kawashima, Y.Fukuzawa, K.Imamura, R.Kojima, H.Okabe, T.Uemura, N.Kasai, S.Kanuka, H.Nishimura, T.Watanabe, K.Inoue, H.Fujikawa, Y.Honma, T.Hirokawa, T.Senda, T.Niwa, R.

(2022) BMC Biol 20: 43-43

  • DOI: https://doi.org/10.1186/s12915-022-01233-2
  • Primary Citation of Related Structures:  
    7EBT, 7EBU, 7EBV, 7EBW

  • PubMed Abstract: 

    Mosquito control is a crucial global issue for protecting the human community from mosquito-borne diseases. There is an urgent need for the development of selective and safe reagents for mosquito control. Flavonoids, a group of chemical substances with variable phenolic structures, such as daidzein, have been suggested as potential mosquito larvicides with less risk to the environment. However, the mode of mosquito larvicidal action of flavonoids has not been elucidated. Here, we report that several flavonoids, including daidzein, inhibit the activity of glutathione S-transferase Noppera-bo (Nobo), an enzyme used for the biosynthesis of the insect steroid hormone ecdysone, in the yellow fever mosquito Aedes aegypti. The crystal structure of the Nobo protein of Ae. aegypti (AeNobo) complexed with the flavonoids and its molecular dynamics simulation revealed that Glu113 forms a hydrogen bond with the flavonoid inhibitors. Consistent with this observation, substitution of Glu113 with Ala drastically reduced the inhibitory activity of the flavonoids against AeNobo. Among the identified flavonoid-type inhibitors, desmethylglycitein (4',6,7-trihydroxyisoflavone) exhibited the highest inhibitory activity in vitro. Moreover, the inhibitory activities of the flavonoids correlated with the larvicidal activity, as desmethylglycitein suppressed Ae. aegypti larval development more efficiently than daidzein. Our study demonstrates the mode of action of flavonoids on the Ae. aegypti Nobo protein at the atomic, enzymatic, and organismal levels.


  • Organizational Affiliation

    Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutathione transferase
A, B, C, D
227Aedes aegyptiMutation(s): 0 
Gene Names: 5569853
EC: 2.5.1.18
UniProt
Find proteins for A0A1S4FIB3 (Aedes aegypti)
Explore A0A1S4FIB3 
Go to UniProtKB:  A0A1S4FIB3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S4FIB3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GSH (Subject of Investigation/LOI)
Query on GSH

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
L [auth C],
Q [auth D]
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
674 (Subject of Investigation/LOI)
Query on 674

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
M [auth C],
R [auth D]
6,7-dihydroxy-3-(4-hydroxyphenyl)-4H-chromen-4-one
C15 H10 O5
GYLUFQJZYAJQDI-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
K [auth B]
N [auth C]
O [auth C]
G [auth A],
H [auth A],
K [auth B],
N [auth C],
O [auth C],
P [auth C],
S [auth D],
T [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.314α = 90
b = 151.314β = 90
c = 146.147γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan18K19163
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan25712010
Japan Agency for Medical Research and Development (AMED)Japan20am0101001

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-26
    Type: Initial release
  • Version 1.1: 2022-04-13
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description