9E97 | pdb_00009e97

L-allo-threonine aldolase from Thermotoga maritima N308E-Y87A-R122G-P121D Mutant with a 2-(aminomethyl)pyridine PLP modification


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 
    0.186 (Depositor), 0.183 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Nucleophilic alpha-Functionalization of Benzyl Amines Using an Engineered Threonine Aldolase.

Ouyang, Y.Wang, S.Sorigue, D.Hyster, T.K.

(2025) J Am Chem Soc 147: 25184-25190

  • DOI: https://doi.org/10.1021/jacs.5c04097
  • Primary Citation of Related Structures:  
    9E97, 9E9J

  • PubMed Abstract: 

    Chiral amines are ubiquitous in pharmaceuticals and agrochemicals, making their efficient and selective synthesis a significant synthetic challenge. Threonine aldolases synthesize chiral amines via stereoselective C-C bond formation; however, they are restricted to small amino acids as pro-nucleophiles, limiting their utility in chemical synthesis. Here, we report an engineered threonine aldolase capable of α-functionalizing benzylamines. The evolved enzyme has excellent catalytic efficiency and accepts a broad range of (heterocyclic)benzyl amines and structurally diverse aldehydes to yield single-enantiomers of 1,2-amino alcohols in high-yield and diastereoselectivity. Mechanistic and crystallographic studies provide a rationale for how these mutations enable this previously unknown function. Moreover, beneficial mutations can be transferred to a related pyridoxal-dependent protein, highlighting the generality of these insights.


  • Organizational Affiliation
    • Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-allo-threonine aldolase
A, B
349Thermotoga maritimaMutation(s): 6 
Gene Names: TM_1744
UniProt
Find proteins for Q9X266 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X266 
Go to UniProtKB:  Q9X266
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X266
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BGC (Subject of Investigation/LOI)
Query on A1BGC

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
{5-hydroxy-6-methyl-4-[(E)-{[(pyridin-2-yl)methyl]imino}methyl]pyridin-3-yl}methyl dihydrogen phosphate
C14 H16 N3 O5 P
DLZFMIJJITXVAE-OVCLIPMQSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
E [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
L [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
M [auth B],
N [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free:  0.186 (Depositor), 0.183 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.208α = 90
b = 166.022β = 90
c = 93.978γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionEuropean Union101063280
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR12GM146043

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-23
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Database references