8SMS | pdb_00008sms

Crosslinked Crystal Structure of Type II Fatty Acid Synthase, FabB, and cerulenin crosslinker-crypto Acyl Carrier Protein, AcpP

• PDB DOI: https://doi.org/10.2210/pdb8SMS/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Escherichia coli K-12, Atlantibacter hermannii NBRC 105704
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2023-04-26 Released: 2023-09-27 
• Deposition Author(s): Jiang, Z., Chen, A., Chen, J., Sekhon, A., Louie, G.V., Noel, J.P., La Clair, J.J., Burkart, M.D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.255 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Masked cerulenin enables a dual-site selective protein crosslink.

Jiang, Z., Chen, A., Chen, J., Sekhon, A., Louie, G.V., Noel, J.P., La Clair, J.J., Burkart, M.D.

(2023) Chem Sci 14: 10925-10933

• PubMed: 37829009 
• DOI: https://doi.org/10.1039/d3sc02864j
• Primary Citation of Related Structures:  
  8SMS


• PubMed Abstract: 
  

  Protein-reactive natural products such as the fungal metabolite cerulenin are recognized for their value as therapeutic candidates, due to their ability to selectively react with catalytic residues within a protein active site or a complex of protein domains. Here, we explore the development of fatty-acid and polyketide-synthase probes by synthetically modulating cerulenin's functional moieties. Using a mechanism-based approach, we reveal unique reactivity within cerulenin and adapt it for fluorescent labeling and crosslinking of fatty-acid and iterative type-I polyketide synthases. We also describe two new classes of silylcyanohydrin and silylhemiaminal masked crosslinking probes that serve as new tools for activity and structure studies of these biosynthetic pathways.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA [e-mail].
The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics La Jolla CA 92037 USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: cross-linking

Macromolecule Content 

• Total Structure Weight: 103.33 kDa 
• Atom Count: 7,603 
• Modeled Residue Count: 964 
• Deposited Residue Count: 966 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] synthase 1	A, B	406	Escherichia coli K-12	Mutation(s): 0  Gene Names: fabB, fabC, b2323, JW2320 EC: 2.3.1.41
UniProt
Find proteins for P0A953 (Escherichia coli (strain K12)) Explore P0A953  Go to UniProtKB:  P0A953

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl carrier protein	C, D	77	Atlantibacter hermannii NBRC 105704	Mutation(s): 0  Gene Names: acpP
UniProt
Find proteins for H5V184 (Atlantibacter hermannii NBRC 105704) Explore H5V184  Go to UniProtKB:  H5V184

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G7U (Subject of Investigation/LOI)	E [auth C], F [auth D]	N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-{2-[(2R)-2-hydroxy-4-oxododecanamido]ethyl}-beta-alaninamide C23 H44 N3 O10 P BTRNTPSBBUMIHA-QUCCMNQESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.255 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.03	α = 90
b = 100.23	β = 109.34
c = 78.31	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-27 
Deposition Author(s): Jiang, Z., Chen, A., Chen, J., Sekhon, A., Louie, G.V., Noel, J.P., La Clair, J.J., Burkart, M.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2023-09-27
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Database references
• Version 1.2: 2024-10-23
  Changes: Structure summary