8WU7

Structure of a cis-Geranylfarnesyl Diphosphate Synthase from Streptomyces clavuligerus

• PDB DOI: https://doi.org/10.2210/pdb8WU7/pdb

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


• Deposited: 2023-10-20 Released: 2024-05-08 
• Deposition Author(s): Li, F.R., Wang, Q.L., Pan, X.M., Dong, L.B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.230 
• R-Value Work: 0.187 
• R-Value Observed: 0.191 

Literature

Discovery, Structure, and Engineering of a cis-Geranylfarnesyl Diphosphate Synthase.

Li, F.R., Wang, Q., Pan, X., Xu, H.M., Dong, L.B.

(2024) Angew Chem Int Ed Engl : e202401669-e202401669

• PubMed: 38651244 
• DOI: https://doi.org/10.1002/anie.202401669
• Primary Citation of Related Structures:  
  8WU6, 8WU7, 8YLZ


• PubMed Abstract: 
  

  cis-Prenyltransferases (cis-PTs) catalyze the sequential head-to-tail condensation of isopentenyl diphosphate (IPP) to allylic diphosphates, producing mixed E-Z prenyl diphosphates of varying lengths; yet, the specific enzymes synthesizing cis-C25 prenyl diphosphates have not been identified. In this study, we present the discovery and characterization of a cis-geranylfarnesyl diphosphate synthase (ScGFPPS) from Streptomyces clavuligerus. This enzyme demonstrates high catalytic proficiency in generating six distinct cis-polyisoprenoids, including three C25 and three C20 variants. We further determine the crystal structure of ScGFPPS. Additionally, we unveil the crystal structure of nerylneryl diphosphate synthase (NNPS), known for synthesizing an all-cis-C20 polyisoprenoid. Comparative structural analysis of ScGFPPS and NNPS has identified key differences that influence product specificity. Through site-directed mutagenesis, we have identified eight single mutations that significantly refine ScGFPPS's selectivity for cis-polyisoprenoids. Our findings not only expand the functional spectrum of cis-PTs but also provide a structural comparison strategy in cis-PTs engineering.

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Organizational Affiliation: 

China Pharmaceutical University, School of Traditional Chinese Pharmacy, CHINA.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 32.48 kDa 
• Atom Count: 1,818 
• Modelled Residue Count: 214 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoprenyl transferase	A	306	Streptomyces clavuligerus	Mutation(s): 0  Gene Names: uppS2
UniProt
Find proteins for D5SL65 (Streptomyces clavuligerus) Explore D5SL65  Go to UniProtKB:  D5SL65

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.230 
• R-Value Work: 0.187 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.59	α = 90
b = 61.17	β = 90
c = 84.37	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-08 
Deposition Author(s): Li, F.R., Wang, Q.L., Pan, X.M., Dong, L.B.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82073746

Revision History  

• Version 1.0: 2024-05-08
  Type: Initial release