6JJS | pdb_00006jjs

Crystal structure of an enzyme from Penicillium herquei in condition2

• PDB DOI: https://doi.org/10.2210/pdb6JJS/pdb

• Classification: TRANSFERASE
• Organism(s): Penicillium herquei
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-02-26 Released: 2020-01-01 
• Deposition Author(s): Fen, Y., Huang, J.W., Liu, W.D., Chen, C.C., Guo, R.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.202 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.185 (Depositor) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Crystal structure and proposed mechanism of an enantioselective hydroalkoxylation enzyme from Penicillium herquei.

Feng, Y., Yu, X., Huang, J.W., Liu, W., Li, Q., Hu, Y., Yang, Y., Chen, Y., Jin, J., Li, H., Chen, C.C., Guo, R.T.

(2019) Biochem Biophys Res Commun 516: 801-805

• PubMed: 31256936 
• DOI: https://doi.org/10.1016/j.bbrc.2019.06.100
• Primary Citation Related Structures: 
  6JJS, 6JJT


• PubMed Abstract: 
  

  Hydroalkoxylation is a useful and efficient reaction which generates C-O bond and produces cyclic ethers, the common structural elements of natural products. The dedicative enzyme which can catalyze enantioselective hydroalkoxylation named PhnH was recently identified in the herqueinone biosynthetic gene from Penicillium herquei. It catalyzes addition of a phenol to the terminal olefin on substrate to produce a dihydrobenzofuran. Here, the crystal structure of PhnH is reported and the putative substrate-binding pocket is illustrated. Through docking experiment, possible substrate-binding poses are displayed and the catalytic mechanism is therefore proposed. Our findings form the basis for further studies of enantioselective hydroalkoxylation enzymes.

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Organizational Affiliation: 
• Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China.
Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China; Tobacco Research Institute of Hubei Province, Wuhan, 430030, China.
School of Pharmaceutical Sciences, Jiangnan University, Wuxi, Jiangsu, 214122, China.
Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China. Electronic address: [e-mail].
State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China. Electronic address: [e-mail].
State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 16.28 kDa 
• Atom Count: 1,187 
• Modeled Residue Count: 130 
• Deposited Residue Count: 149 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PhnH	A	149	Penicillium herquei	Mutation(s): 0  Gene Names: phnH EC: 4
UniProt
Find proteins for A0A1S6PUA4 (Penicillium herquei) Explore A0A1S6PUA4  Go to UniProtKB:  A0A1S6PUA4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	B [auth A], C [auth A], D [auth A], E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.202 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.185 (Depositor) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.617	α = 90
b = 74.617	β = 90
c = 108.926	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-01-01 
Deposition Author(s): Fen, Y., Huang, J.W., Liu, W.D., Chen, C.C., Guo, R.T.

Revision History  

• Version 1.0: 2020-01-01
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description