6ELT | pdb_00006elt

C-terminal domain of MdPPO1 upon self-cleavage (Ccleaved-domain)

• PDB DOI: https://doi.org/10.2210/pdb6ELT/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Malus domestica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-09-29 Released: 2019-03-20 
• Deposition Author(s): Kampatsikas, I., Bijelic, A., Pretzler, M., Rompel, A.
• Funding Organization(s): Austrian Science Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.201 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: other

Literature

A Peptide-Induced Self-Cleavage Reaction Initiates the Activation of Tyrosinase.

Kampatsikas, I., Bijelic, A., Pretzler, M., Rompel, A.

(2019) Angew Chem Int Ed Engl 58: 7475-7479

• PubMed: 30825403 
• DOI: https://doi.org/10.1002/anie.201901332
• Primary Citation Related Structures: 
  6ELS, 6ELT, 6ELV


• PubMed Abstract: 
  

  The conversion of inactive pro-polyphenol oxidases (pro-PPOs) into the active enzyme results from the proteolytic cleavage of its C-terminal domain. Herein, a peptide-mediated cleavage process that activates pro-MdPPO1 (Malus domestica) is reported. Mass spectrometry, mutagenesis studies, and X-ray crystal-structure analysis of pro-MdPPO1 (1.35 Å) and two separated C-terminal domains, one obtained upon self-cleavage of pro-MdPPO1 and the other one produced independently, were applied to study the observed self-cleavage. The sequence Lys 355-Val 370 located in the linker between the active and the C-terminal domain is indispensable for the self-cleavage. Partial introduction (Lys 352-Ala 360) of this peptide into the sequence of two other PPOs, MdPPO2 and aurone synthase (CgAUS1), triggered self-cleavage in the resulting mutants. This is the first experimental proof of a self-cleavage-inducing peptide in PPOs, unveiling a new mode of activation for this enzyme class that is independent of any external protease.

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Organizational Affiliation: 
• Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstraße 14, 1090, Wien, Austria.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 15.07 kDa 
• Atom Count: 1,260 
• Modeled Residue Count: 133 
• Deposited Residue Count: 136 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyphenol oxidase, chloroplastic	A	136	Malus domestica	Mutation(s): 0  EC: 1.10.3.1
UniProt
Find proteins for P43309 (Malus domestica) Explore P43309  Go to UniProtKB:  P43309

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.201 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.23	α = 90
b = 50.14	β = 90
c = 50.72	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

• Released Date: 2019-03-20 
Deposition Author(s): Kampatsikas, I., Bijelic, A., Pretzler, M., Rompel, A.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	P25217
Austrian Science Fund	Austria	P29144

Revision History  

• Version 1.0: 2019-03-20
  Type: Initial release
  
• Version 1.1: 2019-04-24
  Changes: Data collection, Database references
• Version 1.2: 2019-05-29
  Changes: Data collection, Database references
• Version 1.3: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Refinement description