7VM0 | pdb_00007vm0

Crystal structure of YojK from B.subtilis in complex with UDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.243 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Highly efficient production of rebaudioside D enabled by structure-guided engineering of bacterial glycosyltransferase YojK.

Guo, B.Hou, X.Zhang, Y.Deng, Z.Ping, Q.Fu, K.Yuan, Z.Rao, Y.

(2022) Front Bioeng Biotechnol 10: 985826-985826

  • DOI: https://doi.org/10.3389/fbioe.2022.985826
  • Primary Citation Related Structures: 
    7VM0

  • PubMed Abstract: 

    Owing to zero-calorie, high-intensity sweetness and good taste profile, the plant-derived sweetener rebaudioside D (Reb D) has attracted great interest to replace sugars. However, low content of Reb D in stevia rebaudiana Bertoni as well as low soluble expression and enzymatic activity of plant-derived glycosyltransferase in Reb D preparation restrict its commercial usage. To address these problems, a novel glycosyltransferase YojK from Bacillus subtilis 168 with the ability to glycosylate Reb A to produce Reb D was identified. Then, structure-guided engineering was performed after solving its crystal structure. A variant YojK-I241T/G327N with 7.35-fold increase of the catalytic activity was obtained, which allowed to produce Reb D on a scale preparation with a great yield of 91.29%. Moreover, based on the results from molecular docking and molecular dynamics simulations, the improvement of enzymatic activity of YojK-I241T/G327N was ascribed to the formation of new hydrogen bonds between the enzyme and substrate or uridine diphosphate glucose. Therefore, this study provides an engineered bacterial glycosyltransferase YojK-I241T/G327N with high solubility and catalytic efficiency for potential industrial scale-production of Reb D.


  • Organizational Affiliation
    • Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.

Macromolecule Content 

  • Total Structure Weight: 94.81 kDa 
  • Atom Count: 6,538 
  • Modeled Residue Count: 792 
  • Deposited Residue Count: 828 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycosyl transferase family 1
A, B
414Bacillus subtilisMutation(s): 0 
Gene Names: yojK1B4417_0117CFD21_20150
EC: 2.4.1
UniProt
Find proteins for O31853 (Bacillus subtilis (strain 168))
Explore O31853 
Go to UniProtKB:  O31853
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO31853
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.243 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.602α = 90
b = 81.053β = 91.87
c = 100.676γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateChina2018YFA0901700
Other privateChinaJUSRP12015
Other privateChina2020M671329
Other privateChina2020Z383

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release
  • Version 2.0: 2022-10-19
    Changes: Advisory, Database references, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2023-11-29
    Changes: Data collection, Refinement description