4P6S

Crystal Structure of tyrosinase from Bacillus megaterium with L-DOPA in the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Determination of tyrosinase substrate-binding modes reveals mechanistic differences between type-3 copper proteins.

Goldfeder, M.Kanteev, M.Isaschar-Ovdat, S.Adir, N.Fishman, A.

(2014) Nat Commun 5: 4505-4505

  • DOI: https://doi.org/10.1038/ncomms5505
  • Primary Citation of Related Structures:  
    4P6R, 4P6S, 4P6T

  • PubMed Abstract: 

    Tyrosinase is responsible for the two initial enzymatic steps in the conversion of tyrosine to melanin. Many tyrosinase mutations are the leading cause of albinism in humans, and it is a prominent biotechnology and pharmaceutical industry target. Here we present crystal structures that show that both monophenol hydroxylation and diphenol oxidation occur at the same site. It is suggested that concurrent presence of a phenylalanine above the active site and a restricting thioether bond on the histidine coordinating CuA prevent hydroxylation of monophenols by catechol oxidases. Furthermore, a conserved water molecule activated by E195 and N205 is proposed to mediate deprotonation of the monophenol at the active site. Overall, the structures reveal precise steps in the enzymatic catalytic cycle as well as differences between tyrosinases and other type-3 copper enzymes.


  • Organizational Affiliation

    1] Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel [2].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosinase
A, B
287Priestia megateriumMutation(s): 0 
EC: 1.14.18.1
UniProt
Find proteins for B2ZB02 (Priestia megaterium)
Explore B2ZB02 
Go to UniProtKB:  B2ZB02
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2ZB02
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DAH
Query on DAH

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
J [auth B],
L [auth B]
3,4-DIHYDROXYPHENYLALANINE
C9 H11 N O4
WTDRDQBEARUVNC-LURJTMIESA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
H [auth B]
I [auth B]
C [auth A],
D [auth A],
E [auth A],
H [auth B],
I [auth B],
K [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.88α = 90
b = 81.55β = 90
c = 84.06γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael193/11

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2014-08-06
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.3: 2018-03-21
    Changes: Data collection
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Refinement description