AtDAO1(dioxygenase for auxin oxidation 1 from Arabidopsis thaliana)

Experimental Data Snapshot

  • Resolution: 2.09 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 

Starting Models: experimental
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Crystal structure of the indole-3-acetic acid-catabolizing enzyme DAO1 from Arabidopsis thaliana.

Jin, S.H.Lee, H.Shin, Y.Kim, J.H.Rhee, S.

(2020) J Struct Biol 212: 107632-107632

  • DOI: https://doi.org/10.1016/j.jsb.2020.107632
  • Primary Citation of Related Structures:  
    6KWA, 6KWB

  • PubMed Abstract: 

    Indole-3-acetic acid (IAA), the major form of the plant hormone auxin, regulates almost every aspect of plant growth and development. Therefore, auxin homeostasis is an essential process in plants. Different metabolic routes are involved in auxin homeostasis, but the catabolic pathway has remained elusive until recent studies identified DIOXYGENASE FOR AUXIN OXIDATION (DAO) from rice and Arabidopsis thaliana. DAO, a member of the 2-oxoglutarate/Fe(II)-dependent oxygenase (2ODO) family, constitutes a major enzyme for IAA catabolism. This enzyme catalyzes, with the cosubstrate 2-oxoglutarate, the conversion of IAA into 2-oxoindole-3-acetic acid, a functionally inactive oxidative product of IAA. Here, we report a crystal structure of the unliganded DAO1 from A. thaliana (AtDAO1) and its complex with 2-oxoglutarate. AtDAO1 is structurally homologous with members of the 2ODO family but exhibits unique features in the prime substrate IAA binding site. We provide structural analyses of a putative binding site for IAA, supporting possible structural determinants for the substrate specificity of AtDAO1 toward IAA.

  • Organizational Affiliation

    Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
A, B, C
270Arabidopsis thalianaMutation(s): 0 
Gene Names: At1g14130At1g14130/F7A19_21F7A19.21F7A19_21
Find proteins for Q9XI75 (Arabidopsis thaliana)
Explore Q9XI75 
Go to UniProtKB:  Q9XI75
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XI75
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.09 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.626α = 90
b = 75.547β = 90
c = 165.318γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Rural Development AdministrationKorea, Republic Ofpj01325801
National Research Foundation (NRF, Korea)Korea, Republic Of2017r1a2b4002860

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description