7DMO | pdb_00007dmo

Crystal structures of two pericyclases catalyzing [4+2] cycloadditions

• PDB DOI: https://doi.org/10.2210/pdb7DMO/pdb

• Classification: ISOMERASE
• Organism(s): Pyrenochaetopsis sp.
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2020-12-04 Released: 2021-10-06 
• Deposition Author(s): Wang, Z.D., Chi, C.B., Ma, M.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.210 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.173 (Depositor) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Crystal Structures of Fsa2 and Phm7 Catalyzing [4 + 2] Cycloaddition Reactions with Reverse Stereoselectivities in Equisetin and Phomasetin Biosynthesis.

Chi, C., Wang, Z., Liu, T., Zhang, Z., Zhou, H., Li, A., Jin, H., Jia, H., Yin, F., Yang, D., Ma, M.

(2021) ACS Omega 6: 12913-12922

• PubMed: 34056443 
• DOI: https://doi.org/10.1021/acsomega.1c01593
• Primary Citation Related Structures: 
  7DMN, 7DMO


• PubMed Abstract: 
  

  Fsa2 and Phm7 are a unique pair of pericyclases catalyzing [4 + 2] cycloaddition reactions with reverse stereoselectivities in the biosynthesis of equisetin and phomasetin, both of which are potent HIV-1 integrase inhibitors. We here solve the crystal structures of Fsa2 and Phm7, both of which possess unusual "two-β barrel" folds. Different residues are evident between the active sites of Fsa2 and Phm7, and modeling experiments provide key structural information determining the reverse stereoselectivities. These results provide a better understanding of how natural pericyclases control the catalytic stereoselectivities and benefit the protein engineering in future.

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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.
Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 239 Zhangheng Road, Pudong District, Shanghai 201204, China.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 250.51 kDa 
• Atom Count: 18,922 
• Modeled Residue Count: 2,247 
• Deposited Residue Count: 2,334 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diels-Alderase	A, B, C, D, E, F	389	Pyrenochaetopsis sp.	Mutation(s): 0  Gene Names: phm7 EC: 5.5.1
UniProt
Find proteins for A0A2Z5XAU0 (Pyrenochaetopsis sp) Explore A0A2Z5XAU0  Go to UniProtKB:  A0A2Z5XAU0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.210 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.173 (Depositor) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.196	α = 90
b = 150.533	β = 96.94
c = 100.047	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-10-06 
Deposition Author(s): Wang, Z.D., Chi, C.B., Ma, M.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2019YFC0312502

Revision History  

• Version 1.0: 2021-10-06
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description