Complex between a UDP-glucosyltransferase from Polygonum tinctorium capable of glucosylating indoxyl and indoxyl sulfate

Experimental Data Snapshot

  • Resolution: 2.14 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

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This is version 1.3 of the entry. See complete history


Employing a biochemical protecting group for a sustainable indigo dyeing strategy.

Hsu, T.M.Welner, D.H.Russ, Z.N.Cervantes, B.Prathuri, R.L.Adams, P.D.Dueber, J.E.

(2018) Nat Chem Biol 14: 256-261

  • DOI: https://doi.org/10.1038/nchembio.2552
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Indigo is an ancient dye uniquely capable of producing the signature tones in blue denim; however, the dyeing process requires chemical steps that are environmentally damaging. We describe a sustainable dyeing strategy that not only circumvents the use of toxic reagents for indigo chemical synthesis but also removes the need for a reducing agent for dye solubilization. This strategy utilizes a glucose moiety as a biochemical protecting group to stabilize the reactive indigo precursor indoxyl to form indican, preventing spontaneous oxidation to crystalline indigo during microbial fermentation. Application of a β-glucosidase removes the protecting group from indican, resulting in indigo crystal formation in the cotton fibers. We identified the gene coding for the glucosyltransferase PtUGT1 from the indigo plant Polygonum tinctorium and solved the structure of PtUGT1. Heterologous expression of PtUGT1 in Escherichia coli supported high indican conversion, and biosynthesized indican was used to dye cotton swatches and a garment.

  • Organizational Affiliation

    Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
indoxyl UDP-glucosyltransferase
A, B
478Persicaria tinctoriaMutation(s): 0 
EC: 2.4.1
Find proteins for A0A2R2JFJ4 (Persicaria tinctoria)
Explore A0A2R2JFJ4 
Go to UniProtKB:  A0A2R2JFJ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2R2JFJ4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.14 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121α = 90
b = 172.82β = 90
c = 48.41γ = 90
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-AC02-05CH11231
Bakar Fellows ProgramUnited States--
National Science Foundation (NSF, United States)United States1605465
Department of Defense (DOD, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references
  • Version 1.2: 2022-03-30
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2024-01-17
    Changes: Data collection, Refinement description