4HD4 | pdb_00004hd4

Crystal Structure of Tyrosinase from Bacillus megaterium V218F mutant

• PDB DOI: https://doi.org/10.2210/pdb4HD4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Priestia megaterium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-10-02 Released: 2013-01-23 
• Deposition Author(s): Goldfeder, M., Kanteev, M., Adir, N., Fishman, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.228 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Influencing the monophenolase/diphenolase activity ratio in tyrosinase.

Goldfeder, M., Kanteev, M., Adir, N., Fishman, A.

(2013) Biochim Biophys Acta 1834: 629-633

• PubMed: 23305929 
• DOI: https://doi.org/10.1016/j.bbapap.2012.12.021
• Primary Citation Related Structures: 
  4HD4, 4HD6, 4HD7


• PubMed Abstract: 
  

  Tyrosinase is a type 3 copper enzyme with great potential for production of commercially valuable diphenols from monophenols. However, the use of tyrosinase is limited by its further oxidation of diphenols to quinones. We recently determined the structure of the Bacillus megaterium tyrosinase revealing a residue, V218, which we proposed to take part in positioning of substrates within the active site. In the structure of catechol oxidase from Ipomoea batatas, the lack of monophenolase activity was attributed to the presence of F261 near CuA. Consequently, we engineered two variants, V218F and V218G. V218F was expected to have a decreased monophenolase activity, due to the bulky residue extending into the active site. Surprisingly, both V218F and V218G exhibited a 9- and 4.4-fold higher monophenolase/diphenolase activity ratio, respectively. X-ray structures of variant V218F display a flexibility of the phenylalanine residue along with an adjacent histidine, which we propose to be the source of the change in activity ratio.

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Organizational Affiliation: 
• Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 70.73 kDa 
• Atom Count: 4,956 
• Modeled Residue Count: 573 
• Deposited Residue Count: 606 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosinase	A, B	303	Priestia megaterium	Mutation(s): 2
UniProt
Find proteins for B2ZB02 (Priestia megaterium) Explore B2ZB02  Go to UniProtKB:  B2ZB02

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	C [auth A], D [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.228 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48	α = 90
b = 78.58	β = 106.13
c = 85.89	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-23 
Deposition Author(s): Goldfeder, M., Kanteev, M., Adir, N., Fishman, A.

Revision History  

• Version 1.0: 2013-01-23
  Type: Initial release
  
• Version 1.1: 2013-02-13
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations