8J66

Crystal structure of glycosyltransferase SgUGT94-289-3 in complex with M3, state 2

  • Classification: TRANSFERASE
  • Organism(s): Siraitia grosvenorii
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-04-24 Released: 2024-05-29 
  • Deposition Author(s): Li, M., Zhang, S., Cui, S.
  • Funding Organization(s): Chinese Academy of Sciences, National Natural Science Foundation of China (NSFC), CAMS Innovation Fund for Medical Sciences (CIFMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

Starting Model: experimental
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Literature

Structural insights into the catalytic selectivity of glycosyltransferase SgUGT94-289-3 towards mogrosides.

Cui, S.Zhang, S.Wang, N.Su, X.Luo, Z.Ma, X.Li, M.

(2024) Nat Commun 15: 6423-6423

  • DOI: https://doi.org/10.1038/s41467-024-50662-w
  • Primary Citation of Related Structures:  
    8HJF, 8HJG, 8HJH, 8HJK, 8HJL, 8HJN, 8HJO, 8HJP, 8HJQ, 8J66

  • PubMed Abstract: 

    Mogrosides constitute a series of natural sweeteners extracted from Siraitia grosvenorii fruits. These mogrosides are glucosylated to different degrees, with mogroside V (M5) and siamenoside I (SIA) being two mogrosides with high intensities of sweetness. SgUGT94-289-3 constitutes a uridine diphosphate (UDP)-dependent glycosyltransferase (UGT) responsible for the biosynthesis of M5 and SIA, by continuously catalyzing glucosylation on mogroside IIe (M2E) and on the subsequent intermediate mogroside products. However, the mechanism of its promiscuous substrate recognition and multiple catalytic modes remains unclear. Here, we report multiple complex structures and the enzymatic characterization of the glycosyltransferase SgUGT94-289-3. We show that SgUGT94-289-3 adopts a dual-pocket organization in its active site, which allows the two structurally distinct reactive ends of mogrosides to be presented from different pockets to the active site for glucosylation reaction, thus enabling both substrate promiscuity and catalytic regioselectivity. We further identified a structural motif that is essential to catalytic activity and regioselectivity, and generated SgUGT94-289-3 mutants with greatly improved M5/SIA production from M2E in an in vitro one-pot setup.


  • Organizational Affiliation

    Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, 100193, Beijing, PR China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycosyltransferase459Siraitia grosvenoriiMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M2Q (Subject of Investigation/LOI)
Query on M2Q

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
(2S,3S,4S,5R,6R)-2-(hydroxymethyl)-6-[[(2R,3S,4S,5R,6S)-6-[(3R,6S)-6-[(3S,8S,9R,10R,11S,13R,14S,17S)-3-[(2R,3R,4S,5S,6S)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,4,9,13,14-pentamethyl-11-oxidanyl-2,3,7,8,10,11,12,15,16,17-decahydro-1H-cyclopenta[a]phenanthren-17-yl]-2-methyl-2-oxidanyl-heptan-3-yl]oxy-3,4,5-tris(oxidanyl)oxan-2-yl]methoxy]oxane-3,4,5-triol
C48 H82 O19
KYVIPFHNYCKOMQ-YDYRNPCOSA-N
UDP (Subject of Investigation/LOI)
Query on UDP

Download Ideal Coordinates CCD File 
B [auth A]URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.068α = 90
b = 78.127β = 90
c = 94.653γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
autoPROCdata processing
Aimlessdata scaling
PHENIXphasing
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDB27020106
National Natural Science Foundation of China (NSFC)ChinaU20A2004
Chinese Academy of SciencesChina#YSBR-015
CAMS Innovation Fund for Medical Sciences (CIFMS)United Kingdom2021-I2M-1-071

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-29
    Type: Initial release
  • Version 1.1: 2024-08-14
    Changes: Database references