6RXA | pdb_00006rxa

EDDS lyase variant D290M/Y320M with bound formate

• PDB DOI: https://doi.org/10.2210/pdb6RXA/pdb

• Classification: LYASE
• Organism(s): Chelativorans sp. BNC1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-06-07 Released: 2019-10-30 
• Deposition Author(s): Grandi, E., Poelarends, G.J., Thunnissen, A.M.W.H.
• Funding Organization(s): European Research Council, Netherlands Organisation for Scientific Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 
  0.182 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Engineered C-N Lyase: Enantioselective Synthesis of Chiral Synthons for Artificial Dipeptide Sweeteners.

Zhang, J., Grandi, E., Fu, H., Saravanan, T., Bothof, L., Tepper, P.G., Thunnissen, A.W.H., Poelarends, G.J.

(2020) Angew Chem Int Ed Engl 59: 429-435

• PubMed: 31625664 
• DOI: https://doi.org/10.1002/anie.201910704
• Primary Citation Related Structures: 
  6RX8, 6RXA


• PubMed Abstract: 
  

  Aspartic acid derivatives with branched N-alkyl or N-arylalkyl substituents are valuable precursors to artificial dipeptide sweeteners such as neotame and advantame. The development of a biocatalyst to synthesize these compounds in a single asymmetric step is an as yet unmet challenge. Reported here is an enantioselective biocatalytic synthesis of various difficult N-substituted aspartic acids, including N-(3,3-dimethylbutyl)-l-aspartic acid and N-[3-(3-hydroxy-4-methoxyphenyl)propyl]-l-aspartic acid, precursors to neotame and advantame, respectively, using an engineered variant of ethylenediamine-N,N'-disuccinic acid (EDDS) lyase from Chelativorans sp. BNC1. This engineered C-N lyase (mutant D290M/Y320M) displayed a remarkable 1140-fold increase in activity for the selective hydroamination of fumarate compared to that of the wild-type enzyme. These results present new opportunities to develop practical multienzymatic processes for the more sustainable and step-economic synthesis of an important class of food additives.

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Organizational Affiliation: 
• Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713, AV, Groningen, The Netherlands.
Molecular Enzymology Group, Groningen Institute of Biomolecular Sciences and Biotechnology, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 56.02 kDa 
• Atom Count: 4,103 
• Modeled Residue Count: 497 
• Deposited Residue Count: 508 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Argininosuccinate lyase	A	508	Chelativorans sp. BNC1	Mutation(s): 2  Gene Names: Meso_0564 EC: 4.3.2.1
UniProt
Find proteins for Q11KV9 (Chelativorans sp. (strain BNC1)) Explore Q11KV9  Go to UniProtKB:  Q11KV9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	B [auth A], C [auth A], D [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NA	F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free:  0.182 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.892	α = 90
b = 144.936	β = 90
c = 146.13	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-10-30 
Deposition Author(s): Grandi, E., Poelarends, G.J., Thunnissen, A.M.W.H.

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Funding Organization	Location	Grant Number
European Research Council	Netherlands	713483
Netherlands Organisation for Scientific Research	Netherlands	724.016.002

Revision History  

• Version 1.0: 2019-10-30
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Database references
• Version 1.2: 2020-01-01
  Changes: Database references
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description