5HP7

Crystal structures of RidA in the apo form

  • 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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 

wwPDB Validation   3D Report Full Report


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Literature

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: 10.1038/srep30494
  • Primary Citation of Related Structures:  
    5HP8, 5HP7

  • 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) ...

    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

    Center for Cellular &Structural biology, The Sun Yat-Sen University, 132 E. Circle Rd., University City, Guangzhou, Guangdong 510006, People's Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Reactive Intermediate Deaminase A, chloroplasticA124Arabidopsis thalianaMutation(s): 0 
Gene Names: RIDAAt3g20390MQC12.15
EC: 3.5.99.10
UniProt
Find proteins for Q94JQ4 (Arabidopsis thaliana)
Explore Q94JQ4 
Go to UniProtKB:  Q94JQ4
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.907α = 90
b = 76.907β = 90
c = 40.298γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-01-20 
  • Released Date: 2016-10-12 
  • Deposition Author(s): Xie, W., Liu, X.

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