8H8I | pdb_00008h8i

Triterpenoid saponin acetyltransferase, AmAT7-3

• PDB DOI: https://doi.org/10.2210/pdb8H8I/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Astragalus membranaceus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-10-22 Released: 2023-09-13 
• Deposition Author(s): Wang, L.L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 
  0.245 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Characterization and structure-based protein engineering of a regiospecific saponin acetyltransferase from Astragalus membranaceus.

Wang, L., Jiang, Z., Zhang, J., Chen, K., Zhang, M., Wang, Z., Wang, B., Ye, M., Qiao, X.

(2023) Nat Commun 14: 5969-5969

• PubMed: 37749089 
• DOI: https://doi.org/10.1038/s41467-023-41599-7
• Primary Citation Related Structures: 
  8H8I, 8HBT


• PubMed Abstract: 
  

  Acetylation contributes to the bioactivity of numerous medicinally important natural products. However, little is known about the acetylation on sugar moieties. Here we report a saponin acetyltransferase from Astragalus membranaceus. AmAT7-3 is discovered through a stepwise gene mining approach and characterized as the xylose C3'/C4'-O-acetyltransferse of astragaloside IV (1). To elucidate its catalytic mechanism, complex crystal structures of AmAT7-3/1 and AmAT7-3 _A310G /1 are obtained, which reveal a large active pocket decided by a specific sequence AADAG. Combining with QM/MM computation, the regiospecificity of AmAT7-3 is determined by sugar positioning modulated by surrounding amino acids including #A310 and #L290. Furthermore, a small mutant library is built using semi-rational design, where variants A310G and A310W are found to catalyze specific C3'-O and C4'-O acetylation, respectively. AmAT7-3 and its variants are also employed to acetylate other bioactive saponins. This work expands the understanding of saponin acetyltransferases, and provide efficient catalytic tools for saponin acetylation.

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Organizational Affiliation: 
• State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China.
State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, China.
State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, China. [e-mail].
State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China. [e-mail].
Peking University-Yunnan Baiyao International Medical Research Center, 38 Xueyuan Road, Beijing, 100191, China. [e-mail].
State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China. [e-mail].
Peking University-Yunnan Baiyao International Medical Research Center, 38 Xueyuan Road, Beijing, 100191, China. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 50.77 kDa 
• Atom Count: 3,568 
• Modeled Residue Count: 431 
• Deposited Residue Count: 446 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AmAT7-3	A	446	Astragalus membranaceus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KZO	B [auth A]	Astragaloside IV C41 H68 O14 QMNWISYXSJWHRY-RDWDXCDVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free:  0.245 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.63	α = 90
b = 135.63	β = 90
c = 192.18	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	refinement
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-09-13 
Deposition Author(s): Wang, L.L.

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Funding Organization	Location	Grant Number
Not funded	China	--

Revision History  

• Version 1.0: 2023-09-13
  Type: Initial release
  
• Version 1.1: 2024-02-14
  Changes: Database references