7KZ7 | pdb_00007kz7

Crystals Structure of the Mutated Protease Domain of Botulinum Neurotoxin X (X4130B1).

• PDB DOI: https://doi.org/10.2210/pdb7KZ7/pdb

• Classification: TOXIN
• Organism(s): Clostridium botulinum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-12-10 Released: 2020-12-23 
• Deposition Author(s): Blum, T.R., Liu, H., Packer, M.S., Xiong, X., Lee, P.G., Zhang, S., Richter, M., Minasov, G., Satchell, K.J.F., Dong, M., Liu, D.R., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.185 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Phage-assisted evolution of botulinum neurotoxin proteases with reprogrammed specificity.

Blum, T.R., Liu, H., Packer, M.S., Xiong, X., Lee, P.G., Zhang, S., Richter, M., Minasov, G., Satchell, K.J.F., Dong, M., Liu, D.R.

(2021) Science 371: 803-810

• PubMed: 33602850 
• DOI: https://doi.org/10.1126/science.abf5972
• Primary Citation Related Structures: 
  7KZ7


• PubMed Abstract: 
  

  Although bespoke, sequence-specific proteases have the potential to advance biotechnology and medicine, generation of proteases with tailor-made cleavage specificities remains a major challenge. We developed a phage-assisted protease evolution system with simultaneous positive and negative selection and applied it to three botulinum neurotoxin (BoNT) light-chain proteases. We evolved BoNT/X protease into separate variants that preferentially cleave vesicle-associated membrane protein 4 (VAMP4) and Ykt6, evolved BoNT/F protease to selectively cleave the non-native substrate VAMP7, and evolved BoNT/E protease to cleave phosphatase and tensin homolog (PTEN) but not any natural BoNT protease substrate in neurons. The evolved proteases display large changes in specificity (218- to >11,000,000-fold) and can retain their ability to form holotoxins that self-deliver into primary neurons. These findings establish a versatile platform for reprogramming proteases to selectively cleave new targets of therapeutic interest.

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Organizational Affiliation: 
• Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA.
Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA.
Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA.
Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA. [e-mail] [e-mail].
Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. [e-mail] [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 51.46 kDa 
• Atom Count: 3,926 
• Modeled Residue Count: 424 
• Deposited Residue Count: 445 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Botulinum neurotoxin type X	A	445	Clostridium botulinum	Mutation(s): 6  Gene Names: CBB2_0680 EC: 3.4.24.69
UniProt
Find proteins for P0DPK1 (Clostridium botulinum) Explore P0DPK1  Go to UniProtKB:  P0DPK1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	J [auth A], K [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.185 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m37kz7

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.935	α = 90
b = 86.775	β = 90
c = 93.557	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-23 
Deposition Author(s): Blum, T.R., Liu, H., Packer, M.S., Xiong, X., Lee, P.G., Zhang, S., Richter, M., Minasov, G., Satchell, K.J.F., Dong, M., Liu, D.R., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2020-12-23
  Type: Initial release
  
• Version 1.1: 2021-12-15
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description