6U9L | pdb_00006u9l

Imidazole-triggered RAS-specific subtilisin SUBT_BACAM

• PDB DOI: https://doi.org/10.2210/pdb6U9L/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus amyloliquefaciens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-09-09 Released: 2020-09-16 
• Deposition Author(s): Toth, E.A., Bryan, P.N., Orban, J.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.173 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.147 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

Engineering subtilisin proteases that specifically degrade active RAS.

Chen, Y., Toth, E.A., Ruan, B., Choi, E.J., Simmerman, R., Chen, Y., He, Y., Wang, R., Godoy-Ruiz, R., King, H., Custer, G., Travis Gallagher, D., Rozak, D.A., Solomon, M., Muro, S., Weber, D.J., Orban, J., Fuerst, T.R., Bryan, P.N.

(2021) Commun Biol 4: 299-299

• PubMed: 33674772 
• DOI: https://doi.org/10.1038/s42003-021-01818-7
• Primary Citation Related Structures: 
  6U9L, 6UAI, 6UAO, 6UBE


• PubMed Abstract: 
  

  We describe the design, kinetic properties, and structures of engineered subtilisin proteases that degrade the active form of RAS by cleaving a conserved sequence in switch 2. RAS is a signaling protein that, when mutated, drives a third of human cancers. To generate high specificity for the RAS target sequence, the active site was modified to be dependent on a cofactor (imidazole or nitrite) and protease sub-sites were engineered to create a linkage between substrate and cofactor binding. Selective proteolysis of active RAS arises from a 2-step process wherein sub-site interactions promote productive binding of the cofactor, enabling cleavage. Proteases engineered in this way specifically cleave active RAS in vitro, deplete the level of RAS in a bacterial reporter system, and also degrade RAS in human cell culture. Although these proteases target active RAS, the underlying design principles are fundamental and will be adaptable to many target proteins.

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Organizational Affiliation: 
• Potomac Affinity Proteins, North Potomac, MD, USA.
Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.
Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA.
Center for Biomolecular Therapeutics, Rockville, MD, USA.
Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA.
National Institute of Standards and Technology and the University of Maryland, Rockville, MD, USA.
Department of Bioengineering, University of Maryland, College Park, MD, USA.
Unified Culture Collection, United States Army Research Institute of Infectious Diseases, Fort Detrick, MD, USA.
Institute for Bioengineering of Catalonia of the Barcelona Institute of Science and Technology & Institution of Catalonia for Research and Advanced Studies, Barcelona, Spain.
Institute for Bioscience and Biotechnology Research, Rockville, MD, USA. [e-mail].
Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA. [e-mail].
Institute for Bioscience and Biotechnology Research, Rockville, MD, USA. [e-mail].
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA. [e-mail].
Potomac Affinity Proteins, North Potomac, MD, USA. [e-mail].
Institute for Bioscience and Biotechnology Research, Rockville, MD, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 26.96 kDa 
• Atom Count: 2,063 
• Modeled Residue Count: 266 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUBTILISIN BPN'	A [auth S]	266	Bacillus amyloliquefaciens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth S]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
SCN	F [auth S], G [auth S], H [auth S], I [auth S], J [auth S]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M
K	B [auth S], C [auth S], D [auth S]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.173 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.147 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.65	α = 90
b = 58.65	β = 90
c = 124.75	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-09-16 
Deposition Author(s): Toth, E.A., Bryan, P.N., Orban, J.

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

Revision History  

• Version 1.0: 2020-09-16
  Type: Initial release
  
• Version 1.1: 2021-03-31
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary