7NM7

The crystal structure of the antimycin pathway standalone ketoreductase, AntM

• PDB DOI: https://doi.org/10.2210/pdb7NM7/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces albus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-02-23 Released: 2021-06-30 
• Deposition Author(s): Fazal, A., Hemsworth, G.R., Webb, M.E., Seipke, R.F.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.273 
• R-Value Work: 0.213 

Literature

A Standalone beta-Ketoreductase Acts Concomitantly with Biosynthesis of the Antimycin Scaffold.

Fazal, A., Hemsworth, G.R., Webb, M.E., Seipke, R.F.

(2021) ACS Chem Biol 16: 1152-1158

• PubMed: 34151573 
• DOI: https://doi.org/10.1021/acschembio.1c00229
• Primary Citation of Related Structures:  
  7NM7, 7NM8


• PubMed Abstract: 
  

  Antimycins are anticancer compounds produced by a hybrid nonribosomal peptide synthetase/polyketide synthase (NRPS/PKS) pathway. The biosynthesis of these compounds is well characterized, with the exception of the standalone β-ketoreductase enzyme AntM that is proposed to catalyze the reduction of the C8 carbonyl of the antimycin scaffold. Inactivation of antM and structural characterization suggested that rather than functioning as a post-PKS tailoring enzyme, AntM acts upon the terminal biosynthetic intermediate while it is tethered to the PKS acyl carrier protein. Mutational analysis identified two amino acid residues (Tyr185 and Phe223) that are proposed to serve as checkpoints controlling substrate access to the AntM active site. Aromatic checkpoint residues are conserved in uncharacterized standalone β-ketoreductases, indicating that they may also act concomitantly with synthesis of the scaffold. These data provide novel mechanistic insights into the functionality of standalone β-ketoreductases and will enable their reprogramming for combinatorial biosynthesis.

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Organizational Affiliation: 

Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 30.02 kDa 
• Atom Count: 1,829 
• Modelled Residue Count: 247 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antimycin pathway standalone ketoreductase enzyme, AntM	A [auth AAA]	286	Streptomyces albus	Mutation(s): 0  Gene Names: antM

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.273 
• R-Value Work: 0.213 
• Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.897	α = 90
b = 87.897	β = 90
c = 116.262	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-06-30 
Deposition Author(s): Fazal, A., Hemsworth, G.R., Webb, M.E., Seipke, R.F.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	--

Revision History  

• Version 1.0: 2021-06-30
  Type: Initial release
  
• Version 1.1: 2021-07-28
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Database references, Derived calculations, Refinement description