8RA0

Crystal structure of CysF

  • Classification: BIOSYNTHETIC PROTEIN
  • Organism(s): Kitasatospora cystarginea
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-11-30 Released: 2024-06-26 
  • Deposition Author(s): Levy, C.W.
  • Funding Organization(s): Engineering and Physical Sciences Research Council, Biotechnology and Biological Sciences Research Council (BBSRC), European Commission

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryptic enzymatic assembly of peptides armed with beta-lactone warheads.

Xu, G.Torri, D.Cuesta-Hoyos, S.Panda, D.Yates, L.R.L.Zallot, R.Bian, K.Jia, D.Iorgu, A.I.Levy, C.Shepherd, S.A.Micklefield, J.

(2024) Nat Chem Biol 20: 1371-1379

  • DOI: https://doi.org/10.1038/s41589-024-01657-7
  • Primary Citation of Related Structures:  
    8RA0

  • PubMed Abstract: 

    Nature has evolved biosynthetic pathways to molecules possessing reactive warheads that inspired the development of many therapeutic agents, including penicillin antibiotics. Peptides armed with electrophilic warheads have proven to be particularly effective covalent inhibitors, providing essential antimicrobial, antiviral and anticancer agents. Here we provide a full characterization of the pathways that nature deploys to assemble peptides with β-lactone warheads, which are potent proteasome inhibitors with promising anticancer activity. Warhead assembly involves a three-step cryptic methylation sequence, which is likely required to reduce unfavorable electrostatic interactions during the sterically demanding β-lactonization. Amide-bond synthetase and adenosine triphosphate (ATP)-grasp enzymes couple amino acids to the β-lactone warhead, generating the bioactive peptide products. After reconstituting the entire pathway to β-lactone peptides in vitro, we go on to deliver a diverse range of analogs through enzymatic cascade reactions. Our approach is more efficient and cleaner than the synthetic methods currently used to produce clinically important warhead-containing peptides.


  • Organizational Affiliation

    Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AMP-dependent synthetase499Kitasatospora cystargineaMutation(s): 0 
Gene Names: cysF
UniProt
Find proteins for A0A1W6R555 (Kitasatospora cystarginea)
Explore A0A1W6R555 
Go to UniProtKB:  A0A1W6R555
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1W6R555
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CXM
Query on CXM
A
L-PEPTIDE LINKINGC6 H11 N O4 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.052α = 90
b = 68.776β = 96.833
c = 75.399γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2024-06-26 
  • Deposition Author(s): Levy, C.W.

Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited KingdomEP/V048929/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/V016083/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/V008552/1
European CommissionEuropean UnionEP/Y023714/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release
  • Version 1.1: 2024-07-10
    Changes: Database references
  • Version 1.2: 2024-10-09
    Changes: Database references, Structure summary