7E5V | pdb_00007e5v

Crystal structure of Phm7 in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb7E5V/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Pyrenochaetopsis sp.
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-02-20 Released: 2021-06-30 
• Deposition Author(s): Fujiyama, K., Kato, N., Kinugasa, K., Hino, T., Takahashi, S., Nagano, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.211 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.192 (DCC) 

Starting Model: experimental

Literature

Molecular Basis for Two Stereoselective Diels-Alderases that Produce Decalin Skeletons*.

Fujiyama, K., Kato, N., Re, S., Kinugasa, K., Watanabe, K., Takita, R., Nogawa, T., Hino, T., Osada, H., Sugita, Y., Takahashi, S., Nagano, S.

(2021) Angew Chem Int Ed Engl 60: 22401-22410

• PubMed: 34121297 
• DOI: https://doi.org/10.1002/anie.202106186
• Primary Citation Related Structures: 
  7E5T, 7E5U, 7E5V


• PubMed Abstract: 
  

  Enzymes catalyzing [4+2] cycloaddition have attracted increasing attention because of their key roles in natural product biosynthesis. Here, we solved the X-ray crystal structures of a pair of decalin synthases, Fsa2 and Phm7, that catalyze intramolecular [4+2] cycloadditions to form enantiomeric decalin scaffolds during biosynthesis of the HIV-1 integrase inhibitor equisetin and its stereochemical opposite, phomasetin. Computational modeling, using molecular dynamics simulations as well as quantum chemical calculations, demonstrates that the reactions proceed through synergetic conformational constraints assuring transition state-like substrates folds and their stabilization by specific protein-substrate interactions. Site-directed mutagenesis experiments verified the binding models. Intriguingly, the flexibility of bound substrates is largely different in two enzymes, suggesting the distinctive mechanism of dynamics regulation behind these stereoselective reactions. The proposed reaction mechanism herein deepens the basic understanding how these enzymes work but also provides a guiding principle to create artificial enzymes.

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Organizational Affiliation: 
• Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-cho, Minami, Tottori, 680-8552, Japan.
Current address: Dormancy and Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
Natural Product Biosynthesis Research Unit, RIKEN Center for Sustainable Research Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
Faculty of Agriculture, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka, 573-0101, Japan.
Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health, and Nutrition, 7-6-8, Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan.
Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
Chemical Biology Research Group, RIKEN Center for Sustainable Research Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
Center for Research on Green Sustainable Chemistry, Tottori University, 4-101 Koyama-cho, Minami, Tottori, 680-8552, Japan.
Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 128.21 kDa 
• Atom Count: 9,454 
• Modeled Residue Count: 1,116 
• Deposited Residue Count: 1,167 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diels-Alderase	A, B, C	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HZC (Subject of Investigation/LOI)	D [auth A], I [auth B], J [auth B], K [auth B], S [auth C], T [auth C], U [auth C]	[(1S,2S,5R)-5-methyl-2-propan-2-yl-cyclohexyl]methanamine C11 H23 N BMNCNNYYLCTHDB-MXWKQRLJSA-N
SO4	BA [auth C], CA [auth C], H [auth A], O [auth B], P [auth B], Q [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	AA [auth C], E [auth A], F [auth A], G [auth A], L [auth B], M [auth B], N [auth B], R [auth B], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.211 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.192 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.052	α = 90
b = 149.881	β = 97.119
c = 99.27	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
pointless	data scaling
Aimless	data scaling
MLPHARE	phasing
Coot	model building
REFMAC	refinement
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-06-30 
Deposition Author(s): Fujiyama, K., Kato, N., Kinugasa, K., Hino, T., Takahashi, S., Nagano, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	19H04665
Japan Society for the Promotion of Science (JSPS)	Japan	19H05780
Japan Society for the Promotion of Science (JSPS)	Japan	19H04658

Revision History  

• Version 1.0: 2021-06-30
  Type: Initial release
  
• Version 1.1: 2021-10-13
  Changes: Database references
• Version 1.2: 2024-04-03
  Changes: Data collection, Derived calculations, Refinement description