8J0A

Robust design of effective allosteric activator UbV R4 for Rsp5 E3 ligase using the machine-learning tool ProteinMPNN

• PDB DOI: https://doi.org/10.2210/pdb8J0A/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-04-10 Released: 2023-08-09 
• Deposition Author(s): Lin, Y.-F., Hsieh, Y.-J., Kao, H.-W., Ko, T.-P., Wu, K.-P.
• Funding Organization(s): Academia Sinica (Taiwan), Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.237 
• R-Value Work: 0.223 
• R-Value Observed: 0.224 

Literature

Robust Design of Effective Allosteric Activators for Rsp5 E3 Ligase Using the Machine Learning Tool ProteinMPNN.

Kao, H.W., Lu, W.L., Ho, M.R., Lin, Y.F., Hsieh, Y.J., Ko, T.P., Danny Hsu, S.T., Wu, K.P.

(2023) ACS Synth Biol 12: 2310-2319

• PubMed: 37556858 
• DOI: https://doi.org/10.1021/acssynbio.3c00042
• Primary Citation of Related Structures:  
  8J0A


• PubMed Abstract: 
  

  We used the deep learning tool ProteinMPNN to redesign ubiquitin (Ub) as a specific and functionally stimulating/enhancing binder of the Rsp5 E3 ligase. We generated 20 extensively mutated─up to 37 of 76 residues─recombinant Ub variants (UbVs), named R1 to R20, displaying well-folded structures and high thermal stabilities. These UbVs can also form stable complexes with Rsp5, as predicted using AlphaFold2. Three of the UbVs bound to Rsp5 with low micromolar affinity, with R4 and R12 effectively enhancing the Rsp5 activity six folds. AlphaFold2 predicts that R4 and R12 bind to Rsp5's exosite in an identical manner to the Rsp5-Ub template, thereby allosterically activating Rsp5-Ub thioester formation. Thus, we present a virtual solution for rapidly and cost-effectively designing UbVs as functional modulators of Ub-related enzymes.

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Organizational Affiliation: 

Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 23.62 kDa 
• Atom Count: 1,308 
• Modelled Residue Count: 157 
• Deposited Residue Count: 206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin variant R4	A, B	103	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth B], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.237 
• R-Value Work: 0.223 
• R-Value Observed: 0.224 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.111	α = 90
b = 133.111	β = 90
c = 46.934	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-09 
Deposition Author(s): Lin, Y.-F., Hsieh, Y.-J., Kao, H.-W., Ko, T.-P., Wu, K.-P.

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Funding Organization	Location	Grant Number
Academia Sinica (Taiwan)	Taiwan	AS-CDA-110-L03
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	110-2311-B-001-046 to KPW

Revision History  

• Version 1.0: 2023-08-09
  Type: Initial release
  
• Version 1.1: 2023-08-16
  Changes: Data collection, Database references
• Version 1.2: 2023-08-30
  Changes: Database references