5WSF

Crystal structure of a cupin protein (tm1459) in osmium (Os)-substituted form II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.11 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A Well-Defined Osmium-Cupin Complex: Hyperstable Artificial Osmium Peroxygenase

Fujieda, N.Nakano, T.Taniguchi, Y.Ichihashi, H.Sugimoto, H.Morimoto, Y.Nishikawa, Y.Kurisu, G.Itoh, S.

(2017) J. Am. Chem. Soc. --: --

  • DOI: 10.1021/jacs.7b00675
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Thermally stable TM1459 cupin superfamily protein from Thermotoga maritima was repurposed as an osmium (Os) peroxygenase by metal-substitution strategy employing the metal-binding promiscuity. This novel artificial metalloenzyme bears a datively boun ...

    Thermally stable TM1459 cupin superfamily protein from Thermotoga maritima was repurposed as an osmium (Os) peroxygenase by metal-substitution strategy employing the metal-binding promiscuity. This novel artificial metalloenzyme bears a datively bound Os ion supported by the 4-histidine motif. The well-defined Os center is responsible for not only the catalytic activity but also the thermodynamic stability of the protein folding, leading to the robust biocatalyst (T m ≈ 120 °C). The spectroscopic analysis and atomic resolution X-ray crystal structures of Os-bound TM1459 revealed two types of donor sets to Os center with octahedral coordination geometry. One includes trans-dioxide, OH, and mer-three histidine imidazoles (O 3 N 3 donor set), whereas another one has four histidine imidazoles plus OH and water molecule in a cis position (O 2 N 4 donor set). The Os-bound TM1459 having the latter donor set (O 2 N 4 donor set) was evaluated as a peroxygenase, which was able to catalyze cis-dihydroxylation of several alkenes efficiently. With the low catalyst loading (0.01% mol), up to 9100 turnover number was achieved for the dihydroxylation of 2-methoxy-6-vinyl-naphthalene (50 mM) using an equivalent of H 2 O 2 as oxidant at 70 °C for 12 h. When octene isomers were dihydroxylated in a preparative scale for 5 h (2% mol cat.), the terminal alkene octene isomers was converted to the corresponding diols in a higher yield as compared with the internal alkenes. The result indicates that the protein scaffold can control the regioselectivity by the steric hindrance. This protein scaffold enhances the efficiency of the reaction by suppressing disproportionation of H 2 O 2 on Os reaction center. Moreover, upon a simple site-directed mutagenesis, the catalytic activity was enhanced by about 3-fold, indicating that Os-TM1459 is evolvable nascent osmium peroxygenase.


    Organizational Affiliation

    Institute for Protein Research, Osaka University , 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan.,Department of Material and Life Science, Graduate School of Engineering, Osaka University , 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein tm1459
A, B, C, D
118Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 0 
Find proteins for R4P0Z5 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  R4P0Z5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OS
Query on OS

Download SDF File 
Download CCD File 
A, B, C, D
OSMIUM ION
Os
XQBKHDFIPARBOX-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A, B, C, D
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.11 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.147 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 35.488α = 65.45
b = 49.014β = 83.58
c = 64.431γ = 78.79
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
SHELXphasing
SHELXL-97refinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and TechnologyJapanJP15H01066
Ministry of Education, Culture, Sports, Science and TechnologyJapanJP16H01025

Revision History 

  • Version 1.0: 2017-05-31
    Type: Initial release