8S1Y | pdb_00008s1y

ThaOS V79A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.192 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.159 (Depositor), 0.159 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Rational engineering of a thermostable alpha-oxoamine synthase biocatalyst expands the substrate scope and synthetic applicability.

Ashley, B.Mathew, S.Sajjad, M.Zhu, Y.Novikovs, N.Basle, A.Marles-Wright, J.Campopiano, D.J.

(2025) Commun Chem 8: 78-78

  • DOI: https://doi.org/10.1038/s42004-025-01448-8
  • Primary Citation Related Structures: 
    8S1Y

  • PubMed Abstract: 

    Carbon-carbon bond formation is one of the key pillars of organic synthesis. Green, selective and efficient biocatalytic methods for such are therefore highly desirable. The α-oxoamine synthases (AOSs) are a class of pyridoxal 5'-phosphate (PLP)-dependent, irreversible, carbon-carbon bond-forming enzymes, which have been limited previously by their narrow substrate specificity and requirement of acyl-CoA thioester substrates. We recently characterized a thermophilic enzyme from Thermus thermophilus (ThAOS) with a much broader substrate scope and described its use in a chemo-biocatalytic cascade process to generate pyrroles in good yields and timescales. Herein, we report the structure-guided engineering of ThAOS to arrive at variants able to use a greatly expanded range of amino acid and simplified N-acetylcysteamine (SNAc) acyl-thioester substrates. The crystal structure of the improved ThAOS V79A variant with a bound PLP:L-penicillamine external aldimine ligand, provides insight into the properties of the engineered biocatalyst.


  • Organizational Affiliation
    • School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, UK.

Macromolecule Content 

  • Total Structure Weight: 94.58 kDa 
  • Atom Count: 6,812 
  • Modeled Residue Count: 793 
  • Deposited Residue Count: 842 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A ligase
A, B
421Thermus thermophilusMutation(s): 1 
Gene Names: TTHA1582
EC: 2.3.1.29 (PDB Primary Data), 2.3.1.47 (PDB Primary Data)
UniProt
Find proteins for Q5SHZ8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHZ8 
Go to UniProtKB:  Q5SHZ8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHZ8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H4V
(Subject of Investigation/LOI)

Query on A1H4V



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B]
(2~{R},4~{R})-5,5-dimethyl-2-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]-1,3-thiazolidine-4-carboxylic acid
C13 H19 N2 O7 P S
YADZKSQVDLLMOU-GHMZBOCLSA-N
MPD

Query on MPD



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
F [auth B]
G [auth B]
H [auth B]
C [auth A],
D [auth A],
F [auth B],
G [auth B],
H [auth B],
I [auth B]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.192 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.159 (Depositor), 0.159 (DCC) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.43α = 64.8
b = 63.94β = 70.29
c = 65.97γ = 68.18
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
xia2data reduction
XDSdata reduction
PHASERphasing
MolProbitymodel building
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/J01446X/1

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Database references