3ZVH | pdb_00003zvh

Methylaspartate ammonia lyase from Clostridium tetanomorphum mutant Q73A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 
    0.249 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3ZVH

This is version 1.3 of the entry. See complete history

Literature

Engineering Methylaspartate Ammonia Lyase for the Asymmetric Synthesis of Unnatural Amino Acids.

Raj, H.Szymanski, W.De Villiers, J.Rozeboom, H.J.Veetil, V.P.Reis, C.R.De Villiers, M.Dekker, F.J.De Wildeman, S.Quax, W.J.Thunnissen, A.M.W.H.Feringa, B.L.Janssen, D.B.Poelarends, G.J.

(2012) Nat Chem 4: 478

  • DOI: https://doi.org/10.1038/nchem.1338
  • Primary Citation Related Structures: 
    3ZVH, 3ZVI

  • PubMed Abstract: 

    The redesign of enzymes to produce catalysts for a predefined transformation remains a major challenge in protein engineering. Here, we describe the structure-based engineering of methylaspartate ammonia lyase (which in nature catalyses the conversion of 3-methylaspartate to ammonia and 2-methylfumarate) to accept a variety of substituted amines and fumarates and catalyse the asymmetric synthesis of aspartic acid derivatives. We obtained two single-active-site mutants, one exhibiting a wide nucleophile scope including structurally diverse linear and cyclic alkylamines and one with broad electrophile scope including fumarate derivatives with alkyl, aryl, alkoxy, aryloxy, alkylthio and arylthio substituents at the C2 position. Both mutants have an enlarged active site that accommodates the new substrates while retaining the high stereo- and regioselectivity of the wild-type enzyme. As an example, we demonstrate a highly enantio- and diastereoselective synthesis of threo-3-benzyloxyaspartate (an important inhibitor of neuronal excitatory glutamate transporters in the brain).


  • Organizational Affiliation
    • Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 97.48 kDa 
  • Atom Count: 7,001 
  • Modeled Residue Count: 830 
  • Deposited Residue Count: 876 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
METHYLASPARTATE AMMONIA-LYASE438Clostridium tetanomorphumMutation(s): 1 
EC: 4.3.1.2
UniProt
Find proteins for Q05514 (Clostridium tetanomorphum)
Explore Q05514 
Go to UniProtKB:  Q05514
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05514
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
METHYLASPARTATE AMMONIA-LYASE438Clostridium tetanomorphumMutation(s): 1 
EC: 4.3.1.2
UniProt
Find proteins for Q05514 (Clostridium tetanomorphum)
Explore Q05514 
Go to UniProtKB:  Q05514
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05514
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
J [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
OCS
Query on OCS
B
L-PEPTIDE LINKINGC3 H7 N O5 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free:  0.249 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.788α = 90
b = 109.705β = 90
c = 110.096γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2012-07-25
    Changes: Database references
  • Version 1.2: 2017-07-05
    Changes: Data collection
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description