6HQJ

apo-form of polyphenol oxidase from Solanum lycopersicum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


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Literature

Biochemical and structural characterization of tomato polyphenol oxidases provide novel insights into their substrate specificity.

Kampatsikas, I.Bijelic, A.Rompel, A.

(2019) Sci Rep 9: 4022-4022

  • DOI: 10.1038/s41598-019-39687-0
  • Primary Citation of Related Structures:  
    6HQI, 6HQJ

  • PubMed Abstract: 
  • Polyphenol oxidases (PPOs) contain the structurally similar enzymes tyrosinases (TYRs) and catechol oxidases (COs). Two cDNAs encoding pro-PPOs from tomato (Solanum lycopersicum) were cloned and heterologously expressed in Escherichia coli. The two pro-PPOs (SlPPO1-2) differ remarkably in their activity as SlPPO1 reacts with the monophenols tyramine (k cat  = 7 ...

    Polyphenol oxidases (PPOs) contain the structurally similar enzymes tyrosinases (TYRs) and catechol oxidases (COs). Two cDNAs encoding pro-PPOs from tomato (Solanum lycopersicum) were cloned and heterologously expressed in Escherichia coli. The two pro-PPOs (SlPPO1-2) differ remarkably in their activity as SlPPO1 reacts with the monophenols tyramine (k cat  = 7.94 s -1 ) and phloretin (k cat  = 2.42 s -1 ) and was thus characterized as TYR, whereas SlPPO2 accepts only diphenolic substrates like dopamine (k cat  = 1.99 s -1 ) and caffeic acid (k cat  = 20.33 s -1 ) rendering this enzyme a CO. This study, for the first time, characterizes a plant TYR and CO originating from the same organism. Moreover, X-ray structure analysis of the latent holo- and apo-SlPPO1 (PDB: 6HQI and 6HQJ) reveals an unprecedented high flexibility of the gatekeeper residue phenylalanine (Phe270). Docking studies showed that depending on its orientation the gatekeeper residue could either stabilize and correctly position incoming substrates or hinder their entrance into the active site. Furthermore, phloretin, a substrate of SIPPO1 (K m  = 0.11 mM), is able to approach the active centre of SlPPO1 with both phenolic rings. Kinetic and structural results indicate that phloretin could act as a natural substrate and connote the participation of PPOs in flavonoid-biosynthesis.


    Organizational Affiliation

    Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Wien, Austria. annette.rompel@univie.ac.at.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polyphenol oxidase A, chloroplasticA506Solanum lycopersicumMutation(s): 0 
EC: 1.10.3.1
UniProt
Find proteins for Q08303 (Solanum lycopersicum)
Explore Q08303 
Go to UniProtKB:  Q08303
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08303
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.8α = 90
b = 54.14β = 101.08
c = 69.77γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustria29144

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release