6PXS

Crystal structure of iminodiacetate oxidase (IdaA) from Chelativorans sp. BNC1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

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This is version 1.3 of the entry. See complete history


Literature

Structural and biochemical characterization of iminodiacetate oxidase from Chelativorans sp. BNC1.

Kang, C.Jun, S.Y.Bravo, A.G.Vargas, E.M.Liu, H.Lewis, K.M.Xun, L.

(2019) Mol Microbiol 112: 1863-1874

  • DOI: https://doi.org/10.1111/mmi.14399
  • Primary Citation of Related Structures:  
    6PXS

  • PubMed Abstract: 

    Ethylenediaminetetraacetate (EDTA) is the most abundant organic pollutant in surface water because of its extensive usage and the recalcitrance of stable metal-EDTA complexes. A few bacteria including Chelativorans sp. BNC1 can degrade EDTA with a monooxygenase to ethylenediaminediacetate (EDDA) and then use iminodiacetate oxidase (IdaA) to further degrade EDDA into ethylenediamine in a two-step oxidation. To alleviate EDTA pollution into the environment, deciphering the mechanisms of the metabolizing enzymes is an imperative prerequisite for informed EDTA bioremediation. Although IdaA cannot oxidize glycine, the crystal structure of IdaA shows its tertiary and quaternary structures similar to those of glycine oxidases. All confirmed substrates, EDDA, ethylenediaminemonoacetate, iminodiacetate and sarcosine are secondary amines with at least one N-acetyl group. Each substrate was bound at the re-side face of the isoalloxazine ring in a solvent-connected cavity. The carboxyl group of the substrate was bound by Arg 265 and Arg 307 . The catalytic residue, Tyr 250 , is under the hydrogen bond network to facilitate its deprotonation acting as a general base, removing an acetate group of secondary amines as glyoxylate. Thus, IdaA is a secondary amine oxidase, and our findings improve understanding of molecular mechanism involved in the bioremediation of EDTA and the metabolism of secondary amines.


  • Organizational Affiliation

    State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, 266237, P.R. China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FAD dependent oxidoreductase
A, B, C, D
379Chelativorans sp. BNC1Mutation(s): 0 
Gene Names: Meso_1828
UniProt
Find proteins for Q11HA4 (Chelativorans sp. (strain BNC1))
Explore Q11HA4 
Go to UniProtKB:  Q11HA4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ11HA4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.457α = 90
b = 113.457β = 90
c = 266.119γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE 1804699
National Science Foundation (NSF, United States)United StatesDBI 0959778

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.2: 2019-12-25
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description