7S2X | pdb_00007s2x

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

• PDB DOI: https://doi.org/10.2210/pdb7S2X/pdb

• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.230 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

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

• PubMed: 35314816 
• DOI: https://doi.org/10.1038/s41589-022-00993-w
• Primary Citation 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.

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Organizational Affiliation: 
• Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
Morphic Therapeutics, Waltham, MA, USA.
Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil.
Institute of Chemistry, University of Campinas, Campinas, Brazil.
Chair of Technical Biochemistry, Technical University of Dresden, Dresden, Germany.
Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA.
Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA. [e-mail].
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 259.92 kDa 
• Atom Count: 17,986 
• Modeled Residue Count: 2,350 
• Deposited Residue Count: 2,388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SalC	A, B, C, D	597	Salinispora tropica	Mutation(s): 0  Gene Names: salC
UniProt
Find proteins for B0L7F9 (Salinispora tropica) Explore B0L7F9  Go to UniProtKB:  B0L7F9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	I [auth D]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
K	E [auth A], F [auth B], G [auth B], H [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.230 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.33	α = 90
b = 218.29	β = 111.014
c = 87.87	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-04-06 
Deposition Author(s): Chen, P.Y.-T., Trivella, D.B.B., Bauman, K.D., Moore, B.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	Brazil	R01CA127622
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	Brazil	R01AI047818
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	Brazil	F31HD101307
Sao Paulo Research Foundation (FAPESP)	Brazil	2011/21358-5

Revision History  

• 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