9H40 | pdb_00009h40

Pinoresinol hydroxylase from Pseudomonas sp.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.228 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: in silico
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Literature

Biochemical and structural insights into pinoresinol hydroxylase from Pseudomonas sp.

Guerriere, T.B.Fraaije, M.W.Mattevi, A.

(2024) Arch Biochem Biophys 764: 110247-110247

  • DOI: https://doi.org/10.1016/j.abb.2024.110247
  • Primary Citation of Related Structures:  
    9H40

  • PubMed Abstract: 

    The vanillyl alcohol oxidase/p-cresol methylhydroxylase (VAO/PCMH) flavoprotein family comprises a broad spectrum of enzymes capable of catalyzing the oxidative bioconversions of various substrates. Among them, pinoresinol hydroxylase (PinH) from the 4-alkylphenol oxidizing subgroup initiates the oxidative degradation of (+)-pinoresinol, a lignan important for both lignin structure and plant defense. In this study, we present a detailed biochemical and structural characterization of PinH from Pseudomonas sp., with focus on its substrate specificity and product formation. PinH was expressed in E. coli and purified as FAD-containing, soluble protein. The flavoenzyme catalyzes the hydroxylation of both (+)-pinoresinol and eugenol. Structural analysis reveals its dimeric form, non-covalent flavin binding, and a large active site. AlphaFold models of the PinH-cytochrome complex demonstrate cytochrome's dual role in electron transfer and modulating PinH's conformation. A distinctive feature of PinH is a large cavity that hosts its multi-ring (+)-pinoresinol substrate. The capability of converting bulky lignans is particularly attractive for biotechnological applications aimed at producing high-value compounds from phenolic precursors. These insights expand our knowledge on the structure and mechanism of the VAO/PCMH flavoenzyme family members.


  • Organizational Affiliation
    • Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
p-cresol methylhydroxylaseA,
B [auth C]
557Pseudomonas sp.Mutation(s): 0 
Gene Names: CQ065_22110
UniProt
Find proteins for A0A6I3XBB3 (Pseudoduganella dura)
Explore A0A6I3XBB3 
Go to UniProtKB:  A0A6I3XBB3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6I3XBB3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.228 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.214α = 90
b = 131.809β = 90
c = 137.458γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXmodel building
REFMACrefinement
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentItaly2020CW39SJ

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release