8I0D | pdb_00008i0d

Sb3GT1 375S/Q377H mutant complex with UDP-Glc

• PDB DOI: https://doi.org/10.2210/pdb8I0D/pdb

• Classification: TRANSFERASE
• Organism(s): Scutellaria baicalensis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-01-10 Released: 2023-09-20 
• Deposition Author(s): Wang, H.T., Wang, Z.L., Ye, M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 
  0.184 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Literature

Insights into the missing apiosylation step in flavonoid apiosides biosynthesis of Leguminosae plants.

Wang, H.T., Wang, Z.L., Chen, K., Yao, M.J., Zhang, M., Wang, R.S., Zhang, J.H., Agren, H., Li, F.D., Li, J., Qiao, X., Ye, M.

(2023) Nat Commun 14: 6658-6658

• PubMed: 37863881 
• DOI: https://doi.org/10.1038/s41467-023-42393-1
• Primary Citation Related Structures: 
  8HZZ, 8I0D, 8I0E


• PubMed Abstract: 
  

  Apiose is a natural pentose containing an unusual branched-chain structure. Apiosides are bioactive natural products widely present in the plant kingdom. However, little is known on the key apiosylation reaction in the biosynthetic pathways of apiosides. In this work, we discover an apiosyltransferase GuApiGT from Glycyrrhiza uralensis. GuApiGT could efficiently catalyze 2″-O-apiosylation of flavonoid glycosides, and exhibits strict selectivity towards UDP-apiose. We further solve the crystal structure of GuApiGT, determine a key sugar-binding motif (RLGSDH) through structural analysis and theoretical calculations, and obtain mutants with altered sugar selectivity through protein engineering. Moreover, we discover 121 candidate apiosyltransferase genes from Leguminosae plants, and identify the functions of 4 enzymes. Finally, we introduce GuApiGT and its upstream genes into Nicotiana benthamiana, and complete de novo biosynthesis of a series of flavonoid apiosides. This work reports an efficient phenolic apiosyltransferase, and reveals mechanisms for its sugar donor selectivity.

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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.
Department of Physics and Astronomy, Uppsala University, SE-751 20, Uppsala, Sweden.
National Science Center for Physical Sciences at Microscale Division of Molecular & Cell Biophysics and School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China.
Department of Physics and Astronomy, Uppsala University, SE-751 20, Uppsala, Sweden. [e-mail].
State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 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].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 50.98 kDa 
• Atom Count: 3,772 
• Modeled Residue Count: 446 
• Deposited Residue Count: 458 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A	458	Scutellaria baicalensis	Mutation(s): 1  Gene Names: UGT78B4 EC: 2.4.1
UniProt
Find proteins for A0A482AQV3 (Scutellaria baicalensis) Explore A0A482AQV3  Go to UniProtKB:  A0A482AQV3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UPG (Subject of Investigation/LOI)	B [auth A]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C15 H24 N2 O17 P2 HSCJRCZFDFQWRP-JZMIEXBBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free:  0.184 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.47	α = 90
b = 74.52	β = 90
c = 128.98	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-09-20 
Deposition Author(s): Wang, H.T., Wang, Z.L., Ye, M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81891010/81891011

Revision History  

• Version 1.0: 2023-09-20
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Refinement description
• Version 1.2: 2024-04-03
  Changes: Database references