7CS5

IiPLR1 with NADP+ and (-)pinoresinol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

Starting Model: experimental
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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-lariciresinol reductase317Isatis tinctoriaMutation(s): 0 
UniProt
Find proteins for I6LRS1 (Isatis tinctoria)
Explore I6LRS1 
Go to UniProtKB:  I6LRS1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6LRS1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP (Subject of Investigation/LOI)
Query on NDP

Download Ideal Coordinates CCD File 
H [auth E]
J [auth A]
L [auth F]
N [auth D]
P [auth C]
H [auth E],
J [auth A],
L [auth F],
N [auth D],
P [auth C],
R [auth B]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
GEF (Subject of Investigation/LOI)
Query on GEF

Download Ideal Coordinates CCD File 
G [auth E]
I [auth A]
K [auth F]
M [auth D]
O [auth C]
G [auth E],
I [auth A],
K [auth F],
M [auth D],
O [auth C],
Q [auth B]
4-[(3R,3aS,6R,6aS)-6-(3-methoxy-4-oxidanyl-phenyl)-1,3,3a,4,6,6a-hexahydrofuro[3,4-c]furan-3-yl]-2-methoxy-phenol
C20 H22 O6
HGXBRUKMWQGOIE-NSMLZSOPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 244.953α = 90
b = 244.953β = 90
c = 75.744γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
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