Crystal structure of EDDS lyase in complex with formate

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 

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This is version 1.4 of the entry. See complete history


Structural Basis for the Catalytic Mechanism of Ethylenediamine- N, N'-disuccinic Acid Lyase, a Carbon-Nitrogen Bond-Forming Enzyme with a Broad Substrate Scope.

Poddar, H.de Villiers, J.Zhang, J.Puthan Veetil, V.Raj, H.Thunnissen, A.W.H.Poelarends, G.J.

(2018) Biochemistry 57: 3752-3763

  • DOI: https://doi.org/10.1021/acs.biochem.8b00406
  • Primary Citation of Related Structures:  
    6G3D, 6G3E, 6G3F, 6G3G, 6G3H, 6G3I

  • PubMed Abstract: 

    The natural aminocarboxylic acid product ethylenediamine- N, N'-disuccinic acid [( S, S)-EDDS] is able to form a stable complex with metal ions, making it an attractive biodegradable alternative for the synthetic metal chelator ethylenediaminetetraacetic acid (EDTA), which is currently used on a large scale in numerous applications. Previous studies have demonstrated that biodegradation of ( S, S)-EDDS may be initiated by an EDDS lyase, converting ( S, S)-EDDS via the intermediate N-(2-aminoethyl)aspartic acid (AEAA) into ethylenediamine and two molecules of fumarate. However, current knowledge of this enzyme is limited because of the absence of structural data. Here, we describe the identification and characterization of an EDDS lyase from Chelativorans sp. BNC1, which has a broad substrate scope, accepting various mono- and diamines for addition to fumarate. We report crystal structures of the enzyme in an unliganded state and in complex with formate, succinate, fumarate, AEAA, and ( S, S)-EDDS. The structures reveal a tertiary and quaternary fold that is characteristic of the aspartase/fumarase superfamily and support a mechanism that involves general base-catalyzed, sequential two-step deamination of ( S, S)-EDDS. This work broadens our understanding of mechanistic diversity within the aspartase/fumarase superfamily and will aid in the optimization of EDDS lyase for asymmetric synthesis of valuable (metal-chelating) aminocarboxylic acids.

  • Organizational Affiliation

    Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy , University of Groningen , Antonius Deusinglaan 1 , 9713 AV Groningen , The Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Argininosuccinate lyase508Chelativorans sp. BNC1Mutation(s): 0 
Gene Names: Meso_0564
Find proteins for Q11KV9 (Chelativorans sp. (strain BNC1))
Explore Q11KV9 
Go to UniProtKB:  Q11KV9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ11KV9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.44α = 90
b = 144.33β = 90
c = 145.81γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research CouncilNetherlands242293

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2018-05-23
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-30
    Changes: Data collection, Database references
  • Version 1.3: 2018-07-11
    Changes: Data collection, Database references
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Refinement description