9C14 | pdb_00009c14

Structure of the CopC-like domain of YcnJ


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.233 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

Starting Model: in silico
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Literature

Copper acquisition in Bacillus subtilis involves Cu(II) exchange between YcnI and YcnJ.

de Oliveira Silva, Y.R.Barnes, G.Zheng, D.Zhitnitsky, D.Geathers, S.J.Peters, S.C.Szalai, V.A.Helmann, J.D.Fisher, O.S.

(2025) J Biological Chem 301: 110480-110480

  • DOI: https://doi.org/10.1016/j.jbc.2025.110480
  • Primary Citation of Related Structures:  
    9C14

  • PubMed Abstract: 

    The transition metal copper is biologically essential across all three domains of life. Several copper-dependent proteins and enzymes produced by the Gram-positive bacterium Bacillus subtilis have been characterized. However, many questions remain about how copper is recognized and trafficked to metalate cuproproteins. The ycnKJI operon in B. subtilis encodes a suite of proteins implicated in copper uptake and regulation, including the copper-binding protein YcnI and the putative copper importer YcnJ. Here, we demonstrate that one of the extracellular domains within YcnJ (YcnJ CopC ) binds Cu(II) in 1:1 stoichiometry with high affinity using a histidine brace motif. Biochemical results reveal that YcnJ CopC and YcnI can exchange Cu(II). Genetic studies reveal that loss of either YcnI or YcnJ, or mutation of the key residues required for Cu(II)-binding, leads to a growth defect under conditions of copper limitation. Together, these data suggest that the Cu(II)-binding sites in both YcnI and YcnJ may contribute to efficient import under Cu limited conditions. Our results support a model in which YcnI may sequester Cu(II) from YcnJ, serving a regulatory role to limit the amount of copper that enters the cytoplasm and allowing Cu(II) to be stored for later import on the outer face of the membrane. This transfer of Cu(II) between extracellular domains of membrane-bound proteins represents a potential new paradigm in bacterial copper usage.


  • Organizational Affiliation
    • Department of Chemistry, Lehigh University, 6 E Packer Ave, Bethlehem, PA, USA, 18015.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Copper transport protein YcnJ97Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: ycnJBSU03950
UniProt
Find proteins for C0SP95 (Bacillus subtilis (strain 168))
Explore C0SP95 
Go to UniProtKB:  C0SP95
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC0SP95
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.233 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.957α = 90
b = 35.957β = 90
c = 165.762γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States2137107

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release
  • Version 1.1: 2025-08-20
    Changes: Database references