7CSA

AtPrR1 with NADP+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure-based engineering of substrate specificity for pinoresinol-lariciresinol reductases.

Xiao, Y.Shao, K.Zhou, J.Wang, L.Ma, X.Wu, D.Yang, Y.Chen, J.Feng, J.Qiu, S.Lv, Z.Zhang, L.Zhang, P.Chen, W.

(2021) Nat Commun 12: 2828-2828

  • DOI: https://doi.org/10.1038/s41467-021-23095-y
  • Primary Citation of Related Structures:  
    7CS2, 7CS3, 7CS4, 7CS5, 7CS6, 7CS7, 7CS8, 7CS9, 7CSA, 7CSB, 7CSC, 7CSD, 7CSE, 7CSF, 7CSG, 7CSH

  • PubMed Abstract: 

    Pinoresinol-lariciresinol reductases (PLRs) are enzymes involved in the lignan biosynthesis after the initial dimerization of two monolignols, and this represents the entry point for the synthesis of 8-8' lignans and contributes greatly to their structural diversity. Of particular interest has been the determination of how differing substrate specificities are achieved with these enzymes. Here, we present crystal structures of IiPLR1 from Isatis indigotica and pinoresinol reductases (PrRs) AtPrR1 and AtPrR2 from Arabidopsis thaliana, in the apo, substrate-bound and product-bound states. Each structure contains a head-to-tail homodimer, and the catalytic pocket comprises structural elements from both monomers. β4 loop covers the top of the pocket, and residue 98 from the loop governs catalytic specificity. The substrate specificities of IiPLR1 and AtPrR2 can be switched via structure-guided mutagenesis. Our study provides insight into the molecular mechanism underlying the substrate specificity of PLRs/PrRs and suggests an efficient strategy for the large-scale commercial production of the pharmaceutically valuable compound lariciresinol.


  • Organizational Affiliation

    Research and Development Center of Chinese Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pinoresinol reductase 1
A, B, C, D
317Arabidopsis thalianaMutation(s): 0 
Gene Names: PRR1PLR1At1g32100F3C3.10
EC: 1.23.1.1 (PDB Primary Data), 1.23.1.3 (PDB Primary Data)
UniProt
Find proteins for Q9FVQ6 (Arabidopsis thaliana)
Explore Q9FVQ6 
Go to UniProtKB:  Q9FVQ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FVQ6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.265α = 90
b = 144.311β = 116.278
c = 77.26γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description