8PPP

Amide bond synthetase from Streptomyces hindustanus K492H mutant in complex with AMP-CPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.215 

Starting Model: experimental
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Literature

Broad Spectrum Enantioselective Amide Bond Synthetase from Streptoalloteichus hindustanus.

Tang, Q.Petchey, M.Rowlinson, B.Burden, T.J.Fairlamb, I.J.S.Grogan, G.

(2024) ACS Catal 14: 1021-1029

  • DOI: https://doi.org/10.1021/acscatal.3c05656
  • Primary Citation of Related Structures:  
    8PPP, 8PYX, 8PYY

  • PubMed Abstract: 

    The synthesis of amide bonds is one of the most frequently performed reactions in pharmaceutical synthesis, but the requirement for stoichiometric quantities of coupling agents and activated substrates in established methods has prompted interest in biocatalytic alternatives. Amide Bond Synthetases (ABSs) actively catalyze both the ATP-dependent adenylation of carboxylic acid substrates and their subsequent amidation using an amine nucleophile, both within the active site of the enzyme, enabling the use of only a small excess of the amine partner. We have assessed the ability of an ABS from Streptoalloteichus hindustanus (ShABS) to couple a range of carboxylic acid substrates and amines to form amine products. ShABS displayed superior activity to a previously studied ABS, McbA, and a remarkable complementary substrate specificity that included the enantioselective formation of a library of amides from racemic acid and amine coupling partners. The X-ray crystallographic structure of ShABS has permitted mutational mapping of the carboxylic acid and amine binding sites, revealing key roles for L207 and F246 in determining the enantioselectivity of the enzyme with respect to chiral acid and amine substrates. ShABS was applied to the synthesis of pharmaceutical amides, including ilepcimide, lazabemide, trimethobenzamide, and cinepazide, the last with 99% conversion and 95% isolated yield. These findings provide a blueprint for enabling a contemporary pharmaceutical synthesis of one of the most significant classes of small molecule drugs using biocatalysis.


  • Organizational Affiliation

    Department of Chemistry, University of York, Heslington, York YO10 5DD, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fatty-acyl-CoA synthase
A, B
504Streptoalloteichus hindustanusMutation(s): 1 
Gene Names: SAMN05444320_10350
UniProt
Find proteins for A0A1M5ABR5 (Streptoalloteichus hindustanus)
Explore A0A1M5ABR5 
Go to UniProtKB:  A0A1M5ABR5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1M5ABR5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
APC (Subject of Investigation/LOI)
Query on APC

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.7α = 90
b = 95.7β = 117.8
c = 87.2γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited KingdomEP/T01430X/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release