6LZX

Structure of Phytolacca americana UGT3 with 15-crown-5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.203 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Crown-ether-mediated crystal structures of the glycosyltransferase PaGT3 from Phytolacca americana.

Maharjan, R.Fukuda, Y.Nakayama, T.Nakayama, T.Hamada, H.Ozaki, S.I.Inoue, T.

(2020) Acta Crystallogr D Struct Biol 76: 521-530

  • DOI: https://doi.org/10.1107/S2059798320005306
  • Primary Citation of Related Structures:  
    6LZX, 6LZY

  • PubMed Abstract: 

    Uridine diphosphate glycosyltransferases (UGTs) are ubiquitous enzymes that are involved in the glycosylation of small molecules. As glycosylation improves the water solubility and stability of hydrophobic compounds, interest in the use of UGTs for the synthesis of glycosides of poorly soluble compounds is increasing. While sugar-donor recognition in UGTs is conserved with the presence of a plant secondary product glycosyltransferase (PSPG) motif, the basis of the recognition of the sugar acceptor and the regioselectivity of the products is poorly understood owing to low sequence identity around the acceptor-binding region. PaGT3, a glycosyltransferase from the plant Phytolacca americana, can glycosylate a range of acceptors. To illustrate the structure-function relationship of PaGT3, its crystal structure was determined. The sugar-donor and sugar-acceptor binding pockets in PaGT3 were recognized by comparison of its structure with those of other UGTs. The key feature of PaGT3 was the presence of longer loop regions around the hydrophobic acceptor-binding pocket, which resulted in a flexible and wider acceptor binding pocket. In this study, PaGT3 crystals were grown by co-crystallization with 18-crown-6 ether or 15-crown-5 ether. The crown-ether molecule in the asymmetric unit was observed to form a complex with a metal ion, which was coordinated on two sides by the main-chain O atoms of Glu238 from two molecules of the protein. The crown ether-metal complex resembles a molecular glue that sticks two molecules of PaGT3 together to enhance crystal growth. Thus, this result provides an insight into the substrate-recognition strategy in PaGT3 for the study of glycosyltransferases. Additionally, it is shown that crown ether-metal ion complexes can be used as a molecular glue for the crystallization of proteins.


  • Organizational Affiliation

    Graduate School of Pharmaceutical Science, Osaka University, Suita, Osaka 565-0871, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycosyltransferase
A, B
505Phytolacca americanaMutation(s): 0 
Gene Names: PaGT3
EC: 2.4.1
UniProt
Find proteins for B5MGN9 (Phytolacca americana)
Explore B5MGN9 
Go to UniProtKB:  B5MGN9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5MGN9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EYO
Query on EYO

Download Ideal Coordinates CCD File 
C [auth A]1,4,7,10,13-pentaoxacyclopentadecane
C10 H20 O5
VFTFKUDGYRBSAL-UHFFFAOYSA-N
BR
Query on BR

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth B],
H [auth B]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.173α = 90
b = 103.298β = 90
c = 110.383γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
BALBESphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-10
    Type: Initial release
  • Version 1.1: 2020-06-17
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Derived calculations, Refinement description