Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 57.22 kDa 
• Atom Count: 4191 
• Modelled Residue Count: 471 
• Deposited Residue Count: 506 
• Unique protein chains: 1

6HQJ

apo-form of polyphenol oxidase from Solanum lycopersicum

• PDB DOI: 10.2210/pdb6HQJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Solanum lycopersicum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-09-25 Released: 2019-03-20 
• Deposition Author(s): Kampatsikas, I., Bijelic, A., Rompel, A.
• Funding Organization(s): Austrian Science Fund

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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 

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

• PubMed: 30858490 
• 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  = 7.94 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.

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Organizational Affiliation: 

Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Wien, Austria. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyphenol oxidase A, chloroplastic	A	506	Solanum lycopersicum	Mutation(s): 0  EC: 1.10.3.1
UniProt
Find proteins for Q08303 (Solanum lycopersicum) Explore Q08303  Go to UniProtKB:  Q08303

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 = 60.8	α = 90
b = 54.14	β = 101.08
c = 69.77	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-09-25 
• Released Date: 2019-03-20 
Deposition Author(s): Kampatsikas, I., Bijelic, A., Rompel, A.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	29144

Revision History  

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