Crystal structures of RidA in complex with pyruvate

  • Classification: HYDROLASE
  • Organism(s): Arabidopsis thaliana
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2016-01-20 Released: 2016-10-12 
  • Deposition Author(s): Xie, W., Liu, X.
  • Funding Organization(s): Science and Technology Program of Guangzhou, Guangdong Innovative Research Team, Fundamental Research Funds for the Central Universities

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report

This is version 2.0 of the entry. See complete history


Crystal structures of RidA, an important enzyme for the prevention of toxic side products

Liu, X.Zeng, J.Chen, X.Xie, W.

(2016) Sci Rep 6: 30494-30494

  • DOI: https://doi.org/10.1038/srep30494
  • Primary Citation of Related Structures:  
    5HP7, 5HP8

  • PubMed Abstract: 

    The YjgF/YER057c/UK114 family proteins are highly conserved across all three domains of life, and most of them currently have no clearly defined biological roles. In vitro, these proteins were found to hydrolyze the enamine/imine intermediates generated from serine or threonine, and were renamed Reactive Intermediate Deaminase A (RidA). RidA was recently discovered in Arabidopsis thaliana, and by deaminating the toxic enamine/imine intermediates, it prevents the inactivation of many functionally important pyridoxal 5'-phosphate (PLP)-containing enzymes in plants such as branched-chain aminotransferase BCAT (IlvE). In this study, we determined the crystal structure of Arabidopsis thaliana RidA in the apo form, as well as RidA complexed with the ligand pyruvate. RidA forms the trimeric, barrel-like quaternary structure and inter-subunit cavities, and resembles most RidA family members. Each pyruvate molecule binds to the interface between two subunits, and the recognition of pyruvate is achieved by the interactions with R165 and T167. From sequence alignment and structural superposition, we identified a series of key residues responsible for the trimer assembly, whose importance was confirmed by enzymatic assays. This study provides structural insight into RidA functions in plants.

  • Organizational Affiliation

    State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, 135 W. Xingang Rd., Guangzhou, Guangdong 510275, People's Republic of China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reactive Intermediate Deaminase A, chloroplastic
A, B, C
124Arabidopsis thalianaMutation(s): 0 
Gene Names: RIDAAt3g20390MQC12.15
Find proteins for Q94JQ4 (Arabidopsis thaliana)
Explore Q94JQ4 
Go to UniProtKB:  Q94JQ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ94JQ4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.325α = 111.44
b = 46.251β = 107.74
c = 46.375γ = 106.26
Software Package:
Software NamePurpose
CrysalisProdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Science and Technology Program of GuangzhouChina201504010025
Guangdong Innovative Research TeamChina2011Y038
Fundamental Research Funds for the Central UniversitiesChina15lgjc15

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection