2YII

Manipulating the regioselectivity of phenylalanine aminomutase: new insights into the reaction mechanism of MIO-dependent enzymes from structure-guided directed evolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

Starting Models: experimental
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This is version 2.1 of the entry. See complete history. 


Literature

Mechanism-Inspired Engineering of Phenylalanine Aminomutase for Enhanced Beta-Regioselective Asymmetric Amination of Cinnamates.

Wu, B., Szymanski, W., Wybenga, G.G., Heberling, M.M., Bartsch, S., De Wildeman, S., Poelarends, G.J., Feringa, B.L., Dijkstra, B.W., Janssen, D.B.

(2012) Angew Chem Int Ed Engl 51: 482

  • DOI: https://doi.org/10.1002/anie.201106372
  • Primary Citation of Related Structures:  
    2YII

  • PubMed Abstract: 

    Turn to switch: A mutant of phenylalanine aminomutase was engineered that can catalyze the regioselective amination of cinnamate derivatives (see scheme, red) to, for example, β-amino acids. This regioselectivity, along with the X-ray crystal structures, suggests two distinct carboxylate binding modes differentiated by C(β)-C(ipso) bond rotation, which determines if β- (see scheme) or α-addition takes place.

    • Organizational Affiliation: 

    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHENYLALANINE AMMONIA-LYASE
A, B, C, D
705Taxus chinensisMutation(s): 1 
EC: 5.4.3 (PDB Primary Data), 4.3.1.24 (PDB Primary Data), 5.4.3.10 (UniProt)
UniProt
Find proteins for Q68G84 (Taxus chinensis)
Explore Q68G84 
Go to UniProtKB:  Q68G84
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ68G84
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
J [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME
Query on BME
Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth B]
I [auth B]
L [auth C]
E [auth A],
F [auth A],
H [auth B],
I [auth B],
L [auth C],
M [auth C],
O [auth D],
P [auth D]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
FMT
Query on FMT
Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
N [auth C],
Q [auth D]		FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MDO
Query on MDO
A, B, C, D
L-PEPTIDE LINKINGC8 H11 N3 O3ALA, SER, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.454α = 90
b = 145.999β = 99.51
c = 99.68γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-09
    Type: Initial release
  • Version 1.1: 2012-01-25
    Changes: Other
  • Version 1.2: 2013-01-30
    Changes: Database references
  • Version 1.3: 2019-10-23
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2023-12-20
    Changes: Refinement description