7Y87 | pdb_00007y87

class I diterpene synthase mutant (CyS-C59A) from Streptomyces cattleya

• PDB DOI: https://doi.org/10.2210/pdb7Y87/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Streptantibioticus cattleyicolor
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-06-23 Released: 2022-12-21 
• Deposition Author(s): Xing, B., Ma, M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.235 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure Based Mutagenesis of Cattleyene Synthase Leads to the Generation of Rearranged Polycyclic Diterpenes.

Xing, B., Xu, H., Li, A., Lou, T., Xu, M., Wang, K., Xu, Z., Dickschat, J.S., Yang, D., Ma, M.

(2022) Angew Chem Int Ed Engl 61: e202209785-e202209785

• PubMed: 35819825 
• DOI: https://doi.org/10.1002/anie.202209785
• Primary Citation Related Structures: 
  7Y50, 7Y87, 7Y88


• PubMed Abstract: 
  

  The crystal structures of cattleyene synthase (apo-CyS), and CyS complexed with geranylgeranyl pyrophosphate (GGPP) were solved. The CyS ^C59A variant exhibited an increased production of cattleyene and other diterpenes with diverse skeletons. Its structure showed a widened active site cavity explaining the relaxed selectivity. Isotopic labeling experiments revealed a remarkable cyclization mechanism involving several skeletal rearrangements for one of the novel diterpenes.

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Organizational Affiliation: 
• State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China.
Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.02 kDa 
• Atom Count: 3,049 
• Modeled Residue Count: 352 
• Deposited Residue Count: 378 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative glutamate dehydrogenase/leucine dehydrogenase	A	378	Streptantibioticus cattleyicolor	Mutation(s): 1  Gene Names: SCATT_p16530 EC: 4.2.3.225
UniProt
Find proteins for F8JK18 (Streptantibioticus cattleyicolor (strain ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057)) Explore F8JK18  Go to UniProtKB:  F8JK18

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.235 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.284	α = 90
b = 112.628	β = 90
c = 137.382	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-12-21 
Deposition Author(s): Xing, B., Ma, M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21877002, 22077007

Revision History  

• Version 1.0: 2022-12-21
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description