Apo PCuAC domain from PmoF1

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


PCuAC domains from methane-oxidizing bacteria use a histidine brace to bind copper.

Fisher, O.S.Sendzik, M.R.Ross, M.O.Lawton, T.J.Hoffman, B.M.Rosenzweig, A.C.

(2019) J Biol Chem 294: 16351-16363

  • DOI: https://doi.org/10.1074/jbc.RA119.010093
  • Primary Citation of Related Structures:  
    6P16, 6P17, 6P1E, 6P1F, 6P1G

  • PubMed Abstract: 

    Copper is critically important for methanotrophic bacteria because their primary metabolic enzyme, particulate methane monooxygenase (pMMO), is copper-dependent. In addition to pMMO, many other copper proteins are encoded in the genomes of methanotrophs, including proteins that contain p eriplasmic c opper- A c haperone (PCu A C) domains. Using bioinformatics analyses, we identified three distinct classes of PCu A C domain-containing proteins in methanotrophs, termed PmoF1, PmoF2, and PmoF3. PCu A C domains from other types of bacteria bind a single Cu(I) ion via an H X n M X 21/22 H X M motif, which is also present in PmoF3, but PmoF1 and PmoF2 lack this motif entirely. Instead, the PCu A C domains of PmoF1 and PmoF2 bind only Cu(II), and PmoF1 binds additional Cu(II) ions in a His-rich extension to its PCu A C domain. Crystal structures of the PmoF1 and PmoF2 PCu A C domains reveal that Cu(II) is coordinated by an N-terminal histidine brace H X 10 H motif. This binding site is distinct from those of previously characterized PCu A C domains but resembles copper centers in CopC proteins and lytic polysaccharide monooxygenase (LPMO) enzymes. Bioinformatics analysis of the entire PCu A C family reveals previously unappreciated diversity, including sequences that contain both the H X n M X 21/22 H X M and H X 10 H motifs, and sequences that lack either set of copper-binding ligands. These findings provide the first characterization of an additional class of copper proteins from methanotrophs, further expand the PCu A C family, and afford new insight into the biological significance of histidine brace-mediated copper coordination.

  • Organizational Affiliation

    Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PmoF1A [auth B],
B [auth A]
123Methylocystis sp. ATCC 49242Mutation(s): 0 
Gene Names: Met49242_1449
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.642α = 90
b = 60.579β = 90
c = 85.1γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesF32GM119191
Department of Energy (DOE, United States)United StatesDE-SC0016284

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-13
    Changes: Database references
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description