8YTR | pdb_00008ytr

The structure of Cu(II)-CopC from Thioalkalivibrio paradoxus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.230 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

CopC as a potential metallochaperone delivering copper ions to the active site of a thiocyanate dehydrogenase.

Solovieva, A.Y.Kulikova, O.G.Varfolomeeva, L.A.Dergousova, N.I.Boyko, K.M.Khrenova, M.G.Tikhonova, T.V.Popov, V.O.

(2025) Int J Biol Macromol 322: 146801-146801

  • DOI: https://doi.org/10.1016/j.ijbiomac.2025.146801
  • Primary Citation of Related Structures:  
    8YTR

  • PubMed Abstract: 

    The CopC proteins are periplasmic copper binding proteins involved in bacterial copper homeostasis. One of the supposed functions of СopСs is to deliver copper ions for incorporation into the active sites of copper-containing oxidoreductases. In the sulfur oxidizing bacterium Thiolkalivibrio paradoxus, the genes encoding the CopCD proteins are located near the gene encoding the enzyme thiocyanate dehydrogenase (TcDH) containing three copper ions in the active site. The biochemical characterization demonstrated that CopC from Tv. paradoxus (tpCopC) has a high affinity for copper ions in both oxidation states (log K D  = -16.3 ± 0.6 for Cu(II) and -11.1 ± 0.2 for Cu(I)). The protein Cu(II)-tpCopC forms a transient complex with TcDH, in which a copper ion could be transferred from tpCopC to the active site of TcDH. In the absence of a reducing agent, the transfer of 0.5 ± 0.2 copper ions is observed; under reducing conditions, the transfer of 2.4 ± 0.1 copper ions takes place followed by the activation of TcDH. Thus, CopC can act as a metallochaperone, providing the incorporation of copper ions into the active site of TcDH. The mechanism is proposed for the copper ion transfer from Cu(II)-tpCopC to TcDH through the intermediate reduction to form Cu(I)-tpCopC.


  • Organizational Affiliation
    • Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Leninsky prospect, 33, build. 2, Moscow 119071, Russian Federation. Electronic address: nastya.soloveva1@yandex.ru.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CopC domain-containing protein
A, B
130Thioalkalivibrio paradoxus ARh 1Mutation(s): 0 
Gene Names: THITH_13340
UniProt
Find proteins for W0DSL1 (Thioalkalivibrio paradoxus ARh 1)
Explore W0DSL1 
Go to UniProtKB:  W0DSL1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW0DSL1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.230 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.241α = 90
b = 38.275β = 90.33
c = 104.666γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release
  • Version 1.1: 2025-08-27
    Changes: Database references, Structure summary
  • Version 1.2: 2025-09-03
    Changes: Database references