9E97 | pdb_00009e97

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

PDB DOI: https://doi.org/10.2210/pdb9E97/pdb

Classification: LYASE
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-11-07 Released: 2025-07-23
Deposition Author(s): Wang, S., Jeffrey, P.D., Sorigue, D., Hyster, T.K.
Funding Organization(s): H2020 Marie Curie Actions of the European Commission, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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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wwPDB Validation 3D Report Full Report

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

PubMed: 40631863 Search on PubMed
DOI: https://doi.org/10.1021/jacs.5c04097
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 78.22 kDa
Atom Count: 5,830
Modeled Residue Count: 688
Deposited Residue Count: 698
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-allo-threonine aldolase	A, B	349	Thermotoga maritima	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X266
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BGC (Subject of Investigation/LOI) Query on A1BGC Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	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		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B]	D [auth A], K [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	F [auth A], G [auth A], L [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	H [auth A], I [auth A], M [auth B], N [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B]

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 = 94.208	α = 90
b = 166.022	β = 90
c = 93.978	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-23

Deposition Author(s):

Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	European Union	101063280
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R12GM146043