8ZYG | pdb_00008zyg

Crystal structure of a cupin protein (tm1459, I49C-4py/H52A/C106D mutant) in copper (Cu) substituted form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 
    0.171 (Depositor), 0.164 (DCC) 
  • R-Value Work: 
    0.141 (Depositor), 0.132 (DCC) 
  • R-Value Observed: 
    0.142 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A thiopyridine-bound mirror-image copper center in an artificial non-heme metalloenzyme.

Morita, Y.Kubo, H.Matsumoto, R.Fujieda, N.

(2024) J Inorg Biochem 260: 112694-112694

  • DOI: https://doi.org/10.1016/j.jinorgbio.2024.112694
  • Primary Citation of Related Structures:  
    8ZYG, 8ZYH

  • PubMed Abstract: 

    Artificial metalloenzymes, in which a metal complex and protein matrix are combined, have been synthesized to catalyze stereoselective reactions using the chiral environment provided by the protein cavity. Artificial metalloenzymes can be engineered by the chemical modification and mutagenesis of the protein matrix. We developed artificial non-heme metalloenzymes using a cupin superfamily protein (TM1459) with a 4-His tetrad-metal-binding motif. The Cu-bound H52A/C106D mutant with 3-His triad showed a S-enantioselective Michael addition of nitromethane to α,β-unsaturated ketone, 2-aza-chalcone 1. In this study, we demonstrated a chemical modification near the copper-binding site of this mutant to reverse its enantioselectivity. For chemical modification, the amino acid on the Si-face of the binding state of 1 to the copper center was replaced with Cys, followed by reaction with 4,4'-dithiopyridine (4-PDS) to form S-(pyridin-4-ylthio)cysteine (Cys-4py). Cu-bound I49C-4py/H52A/C106D showed reversal of the enantioselectivity from S-form to R-form (ee = 71%, (R)). The effect of steric hindrance of the amino acids at position 49 on enantioselectivity was investigated using I49X/H52A/C106D mutants (X = A, C, I, F, and W). Additionally, chemical modification with 2,2'-dithiopyridine (2-PDS) produced I49-2py/H52A/C106D, which showed lower R-enantioselectivity than I49-4py/H52A/C106D. Among the mutants, the 4py-modification on the Si-face was the most effective in reversing the enantioselectivity. By tuning the Re-face side, the H54A mutation introduced into the I49C-4py/H52A/C106D increased the R-enantioselectivity (ee = 88%, (R)). X-ray crystallography revealed a coordinated structure with ligation of thiopyridine in Cu-bound I49C-4py/H52A/H54A/C106D.


  • Organizational Affiliation
    • Graduate School of Agriculture, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai-shi, Osaka 599-8531, Japan. Electronic address: yoshi.morita@omu.ac.jp.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cupin type-2 domain-containing protein
A, B
118Thermotoga maritima MSB8Mutation(s): 3 
Gene Names: TM_1459
UniProt
Find proteins for Q9X1H0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X1H0 
Go to UniProtKB:  Q9X1H0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X1H0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free:  0.171 (Depositor), 0.164 (DCC) 
  • R-Value Work:  0.141 (Depositor), 0.132 (DCC) 
  • R-Value Observed: 0.142 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.67α = 90
b = 57.57β = 90
c = 75.87γ = 90
Software Package:
Software NamePurpose
PHASERphasing
SHELXL-97refinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan21KK0249
Japan Society for the Promotion of Science (JSPS)Japan23K13764
Japan Society for the Promotion of Science (JSPS)JapanJP21H01954
Japan Society for the Promotion of Science (JSPS)Japan24K01503

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Structure summary
  • Version 1.2: 2025-03-19
    Changes: Database references