9CSW

Streptavidin-E101Q-S112A-K121Y bound to Cu(II)-biotin-ethyl-dipicolylamine cofactor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Selective oxidation of active site aromatic residues in engineered Cu proteins.

Uyeda, K.S.Follmer, A.H.Borovik, A.S.

(2024) Chem Sci 

  • DOI: https://doi.org/10.1039/d4sc06667g
  • Primary Citation of Related Structures:  
    9CST, 9CSU, 9CSV, 9CSW, 9E6Z

  • PubMed Abstract: 

    Recent studies have revealed critical roles for the local environments surrounding metallocofactors, such as the newly identified Cu D site in particulate methane monooxygenases (pMMOs) and the second sphere aromatic residues in lytic polysaccharide monooxygenases (LPMOs), implicated in the protection against oxidative damage. However, these features are subjects of continued debate. Our work utilizes biotin-streptavidin (Sav) technology to develop artificial metalloproteins (ArMs) that mimic the active sites of natural copper metalloenzymes. By engineering ArMs with aromatic residues within their secondary coordination spheres, we systematically investigate the influence of these residues on Cu reactivity and oxidant activation. We demonstrate that the placement and orientation of tyrosine relative to the Cu cofactor critically affect the oxidation outcomes upon exposure to hydrogen peroxide. A key finding is the interplay between the coordination of an active site asparagine and the incorporation of aromatic residues proximal to the artificial Cu cofactor, which are the only variants where oxidation of an engineered residues is observed. These findings underscore the importance of the secondary coordination sphere in modulating Cu center reactivity, suggest a role for amide coordination in C-H bond activation by pMMOs, and potential inactivation pathways in natural copper enzymes like LPMOs.


  • Organizational Affiliation

    Department of Chemistry, University of California-Irvine Irvine CA 92697 USA afollmer@uci.edu aborovik@uci.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Streptavidin159Streptomyces avidiniiMutation(s): 3 
UniProt
Find proteins for P22629 (Streptomyces avidinii)
Explore P22629 
Go to UniProtKB:  P22629
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22629
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.77α = 90
b = 57.77β = 90
c = 184.25γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHENIXrefinement
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM120349

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release
  • Version 1.1: 2024-12-18
    Changes: Database references