7VW2

Structure of a dimeric periplasmic protein bound with cupric ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of copper binding by a dimeric periplasmic protein forming a six-helical bundle.

Yang, J.Gao, M.Wang, J.He, C.Wang, X.Liu, L.

(2022) J Inorg Biochem 229: 111728-111728

  • DOI: https://doi.org/10.1016/j.jinorgbio.2022.111728
  • Primary Citation of Related Structures:  
    7VW0, 7VW1, 7VW2

  • PubMed Abstract: 

    Bacteria maintain copper balance by various copper response mechanisms. A plasmid gene encoding a methionine rich protein targeted to periplasm is adjacent to the sil operon that confers heavy metal resistance. However, the gene product Orf91 has not been characterized before. Using X-ray crystallography, we solved the structures of Orf91 in apo, cuprous ion-bound, and cupric ion-bound forms. An Orf91 protomer consists of three helices of which the C-terminal two helices belong to domain of unknown function 305 (DUF305), and two Orf91s dimerize into a six-helical bundle. The MxxHH motif specific for DUF305 is critical for cuprous ion binding, and the MxxMxxMHxxMM motif in the N-terminal helix contributes to cupric ion binding. The first histidine of MxxHH shows alternative conformations related to the redox state of copper ion. We suggest that Orf91 is an adaptable copper sponge in the periplasmic space.


  • Organizational Affiliation

    School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui 230601, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DUF305 domain-containing protein
A, B
96Escherichia coliMutation(s): 0 
Gene Names: O2R_94
UniProt
Find proteins for V5J1S8 (Escherichia coli)
Explore V5J1S8 
Go to UniProtKB:  V5J1S8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV5J1S8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.446α = 90
b = 74.412β = 96.18
c = 50.786γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31870729

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-26
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description