Structure of Polyphenol Oxidase (mutant G292N) from Thermothelomyces thermophila

Experimental Data Snapshot

  • Resolution: 1.53 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.160 

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Considerations Regarding Activity Determinants of Fungal Polyphenol Oxidases Based on Mutational and Structural Studies.

Nikolaivits, E.Valmas, A.Dedes, G.Topakas, E.Dimarogona, M.

(2021) Appl Environ Microbiol 87

  • DOI: https://doi.org/10.1128/AEM.00396-21
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Polyphenol oxidases (PPOs) are an industrially relevant family of enzymes, being involved in the postharvest browning of fruits and vegetables, as well as in human melanogenesis. Their involvement lies in their ability to oxidize phenolic or polyphenolic compounds, which subsequently form pigments. The PPO family includes tyrosinases and catechol oxidases, which, in spite of their high structural similarity, exhibit different catalytic activities. Long-standing research efforts have not yet managed to decipher the structural determinants responsible for this differentiation, as every new theory is disproved by a more recent study. In the present work, we combined biochemical along with structural data in order to better understand the function of a previously characterized PPO from Thermothelomyces thermophila ( Tt PPO). The crystal structure of a Tt PPO variant, determined at 1.55 Å resolution, represents the second known structure of an ascomycete PPO. Kinetic data for structure-guided mutants prove the implication of "gate" residue L306, residue H B1 +1 (G292), and H B2 +1 (Y296) in Tt PPO function against various substrates. Our findings demonstrate the role of L306 in the accommodation of bulky substrates and show that residue H B1 +1 is unlikely to determine monophenolase activity, as was suggested from previous studies. IMPORTANCE PPOs are enzymes of biotechnological interest. They have been extensively studied both biochemically and structurally, with a special focus on the plant-derived counterparts. Even so, explicit description of the molecular determinants of their substrate specificity is still pending. For ascomycete PPOs, only one crystal structure has been determined so far, thus limiting our knowledge on this tree branch of the family. In the present study, we report the second crystal structure of an ascomycete PPO. Combined with site-directed mutagenesis and biochemical studies, we depict the amino acids in the vicinity of the active site that affect enzyme activity and perform a detailed analysis on a variety of substrates. Our findings improve current understanding of structure-function relations of microbial PPOs, which is a prerequisite for the engineering of biocatalysts of desired properties.

  • Organizational Affiliation

    Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosinase-like protein425Thermothelomyces thermophilus ATCC 42464Mutation(s): 1 
Gene Names: MYCTH_60685
Find proteins for G2QLD3 (Thermothelomyces thermophilus (strain ATCC 42464 / BCRC 31852 / DSM 1799))
Explore G2QLD3 
Go to UniProtKB:  G2QLD3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG2QLD3
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
E [auth A]
C8 H15 N O6
Query on MPD

Download Ideal Coordinates CCD File 
C6 H14 O2
Query on SER

Download Ideal Coordinates CCD File 
G [auth A]SERINE
C3 H7 N O3
Query on GLY

Download Ideal Coordinates CCD File 
F [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
F [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
C2 H5 N O2
Query on CU

Download Ideal Coordinates CCD File 
M [auth A],
N [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.53 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.404α = 90
b = 97.177β = 90
c = 46.998γ = 90
Software Package:
Software NamePurpose
autoPROCdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Union (EU)European Union653706

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2021-10-06
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-01-24
    Changes: Data collection, Refinement description