6INI

a glycosyltransferase complex with UDP and the product


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Hydrophobic recognition allows the glycosyltransferase UGT76G1 to catalyze its substrate in two orientations.

Yang, T.Zhang, J.Ke, D.Yang, W.Tang, M.Jiang, J.Cheng, G.Li, J.Cheng, W.Wei, Y.Li, Q.Naismith, J.H.Zhu, X.

(2019) Nat Commun 10: 3214-3214

  • DOI: 10.1038/s41467-019-11154-4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Diets high in sugar are recognized as a serious health problem, and there is a drive to reduce their consumption. Steviol glycosides are natural zero-calorie sweeteners, but the most desirable ones are biosynthesized with low yields. UGT76G1 catalyze ...

    Diets high in sugar are recognized as a serious health problem, and there is a drive to reduce their consumption. Steviol glycosides are natural zero-calorie sweeteners, but the most desirable ones are biosynthesized with low yields. UGT76G1 catalyzes the β (1-3) addition of glucose to steviol glycosides, which gives them the preferred taste. UGT76G1 is able to transfer glucose to multiple steviol substrates yet remains highly specific in the glycosidic linkage it creates. Here, we report multiple complex structures of the enzyme combined with biochemical data, which reveal that the enzyme utilizes hydrophobic interactions for substrate recognition. The lack of a strict three-dimensional recognition arrangement, typical of hydrogen bonds, permits two different orientations for β (1-3) sugar addition. The use of hydrophobic recognition is unusual in a regio- and stereo-specific catalysis. Harnessing such non-specific hydrophobic interactions could have wide applications in the synthesis of complex glycoconjugates.


    Organizational Affiliation

    Rosalind Franklin Institute, Harwell Campus, Didcot, OX11 0FA, UK. naismith@strubi.ox.ac.uk.,State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041, Chengdu, China.,State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041, Chengdu, China. naismith@strubi.ox.ac.uk.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610064, Chengdu, China. zhuxiaofeng@scu.edu.cn.,Division of Structural Biology, Wellcome Trust Centre of Human Genomics, Oxford, OX3 7BN, UK. naismith@strubi.ox.ac.uk.,West China School of Public Health, Healthy Food Evaluation Research Center and State Key Laboratory of Biotherapy and Cancer Center, Sichuan University, 610041, Chengdu, China.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610064, Chengdu, China.,Department of Biomedical Polymers and Artificial Organs, College of Polymer Science and Engineering and State Key Laboratory of Polymer Materials Engineering, Sichuan University, 610065, Chengdu, China.,Department of Pediatrics, Obstetrics and Gynecology, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, 610041, Chengdu, China. liqintong@scu.edu.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-glycosyltransferase 76G1
A
466Stevia rebaudianaMutation(s): 0 
Gene Names: UGT76G1
EC: 2.4.1.-
Find proteins for Q6VAB4 (Stevia rebaudiana)
Go to UniProtKB:  Q6VAB4
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
AUO
Query on AUO

Download SDF File 
Download CCD File 
A
(8alpha,9beta,10alpha,13alpha)-13-{[beta-D-glucopyranosyl-(1->2)-[beta-D-glucopyranosyl-(1->3)]-beta-D-glucopyranosyl]oxy}kaur-16-en-18-oic acid
C38 H60 O18
DRSKVOAJKLUMCL-MMUIXFKXSA-N
 Ligand Interaction
UDP
Query on UDP

Download SDF File 
Download CCD File 
A
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
AQ9
Query on AQ9

Download SDF File 
Download CCD File 
A
1-O-[(8alpha,9beta,10alpha,13alpha)-13-(beta-D-glucopyranosyloxy)-18-oxokaur-16-en-18-yl]-beta-D-glucopyranose
Rubusoside
C32 H50 O13
YWPVROCHNBYFTP-OSHKXICASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.161 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 97.662α = 90.00
b = 97.662β = 90.00
c = 89.626γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata scaling
PHASERphasing
DIALSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31771910
National Natural Science Foundation of ChinaChina21534008

Revision History 

  • Version 1.0: 2019-07-31
    Type: Initial release