Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

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THOUSAND-GRAIN WEIGHT 6, which is an IAA-glucose hydrolase, preferentially recognizes the structure of the indole ring.

Akabane, T.Suzuki, N.Ikeda, K.Yonezawa, T.Nagatoishi, S.Matsumura, H.Yoshizawa, T.Tsuchiya, W.Kamino, S.Tsumoto, K.Ishimaru, K.Katoh, E.Hirotsu, N.

(2024) Sci Rep 14: 6778-6778

  • DOI: https://doi.org/10.1038/s41598-024-57506-z
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    An indole-3-acetic acid (IAA)-glucose hydrolase, THOUSAND-GRAIN WEIGHT 6 (TGW6), negatively regulates the grain weight in rice. TGW6 has been used as a target for breeding increased rice yield. Moreover, the activity of TGW6 has been thought to involve auxin homeostasis, yet the details of this putative TGW6 activity remain unclear. Here, we show the three-dimensional structure and substrate preference of TGW6 using X-ray crystallography, thermal shift assays and fluorine nuclear magnetic resonance ( 19 F NMR). The crystal structure of TGW6 was determined at 2.6 Å resolution and exhibited a six-bladed β-propeller structure. Thermal shift assays revealed that TGW6 preferably interacted with indole compounds among the tested substrates, enzyme products and their analogs. Further analysis using 19 F NMR with 1,134 fluorinated fragments emphasized the importance of indole fragments in recognition by TGW6. Finally, docking simulation analyses of the substrate and related fragments in the presence of TGW6 supported the interaction specificity for indole compounds. Herein, we describe the structure and substrate preference of TGW6 for interacting with indole fragments during substrate recognition. Uncovering the molecular details of TGW6 activity will stimulate the use of this enzyme for increasing crop yields and contributes to functional studies of IAA glycoconjugate hydrolases in auxin homeostasis.

  • Organizational Affiliation

    Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura, Oura, Gunma, 374-0193, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Os06g0623700 protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
322Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: TGW6Os06g0623700OSNPB_060623700
Find proteins for Q69U01 (Oryza sativa subsp. japonica)
Explore Q69U01 
Go to UniProtKB:  Q69U01
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ69U01
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.982α = 94.14
b = 108.52β = 98.74
c = 123.071γ = 97.23
Software Package:
Software NamePurpose
Cootmodel building
BUCCANEERmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP20K05869

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-03
    Type: Initial release