7S2X

Structure of SalC, a gamma-lactam-beta-lactone bicyclase for salinosporamide biosynthesis

  • Classification: BIOSYNTHETIC PROTEIN
  • Organism(s): Salinispora tropica
  • Expression System: Streptomyces coelicolor
  • Mutation(s): No 

  • Deposited: 2021-09-04 Released: 2022-04-06 
  • Deposition Author(s): Chen, P.Y.-T., Trivella, D.B.B., Bauman, K.D., Moore, B.S.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD), Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Enzymatic assembly of the salinosporamide gamma-lactam-beta-lactone anticancer warhead.

Bauman, K.D.Shende, V.V.Chen, P.Y.Trivella, D.B.B.Gulder, T.A.M.Vellalath, S.Romo, D.Moore, B.S.

(2022) Nat Chem Biol 18: 538-546

  • DOI: https://doi.org/10.1038/s41589-022-00993-w
  • Primary Citation of Related Structures:  
    7S2X

  • PubMed Abstract: 

    The marine microbial natural product salinosporamide A (marizomib) is a potent proteasome inhibitor currently in clinical trials for the treatment of brain cancer. Salinosporamide A is characterized by a complex and densely functionalized γ-lactam-β-lactone bicyclic warhead, the assembly of which has long remained a biosynthetic mystery. Here, we report an enzymatic route to the salinosporamide core catalyzed by a standalone ketosynthase (KS), SalC. Chemoenzymatic synthesis of carrier protein-tethered substrates, as well as intact proteomics, allowed us to probe the reactivity of SalC and understand its role as an intramolecular aldolase/β-lactone synthase with roles in both transacylation and bond-forming reactions. Additionally, we present the 2.85-Å SalC crystal structure that, combined with site-directed mutagenesis, allowed us to propose a bicyclization reaction mechanism. This work challenges our current understanding of the role of KS enzymes and establishes a basis for future efforts toward streamlined production of a clinically relevant chemotherapeutic.


  • Organizational Affiliation

    Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SalC
A, B, C, D
597Salinispora tropicaMutation(s): 0 
Gene Names: salC
UniProt
Find proteins for B0L7F9 (Salinispora tropica)
Explore B0L7F9 
Go to UniProtKB:  B0L7F9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0L7F9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.33α = 90
b = 218.29β = 111.014
c = 87.87γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)BrazilR01CA127622
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)BrazilR01AI047818
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)BrazilF31HD101307
Sao Paulo Research Foundation (FAPESP)Brazil2011/21358-5

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2022-05-11
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description