Methanobactin periplasmic binding protein

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Methanobactin transport machinery.

Dassama, L.M.Kenney, G.E.Ro, S.Y.Zielazinski, E.L.Rosenzweig, A.C.

(2016) Proc Natl Acad Sci U S A 113: 13027-13032

  • DOI: https://doi.org/10.1073/pnas.1603578113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Methanotrophic bacteria use methane, a potent greenhouse gas, as their primary source of carbon and energy. The first step in methane metabolism is its oxidation to methanol. In almost all methanotrophs, this chemically challenging reaction is catalyzed by particulate methane monooxygenase (pMMO), a copper-dependent integral membrane enzyme. Methanotrophs acquire copper (Cu) for pMMO by secreting a small ribosomally produced, posttranslationally modified natural product called methanobactin (Mbn). Mbn chelates Cu with high affinity, and the Cu-loaded form (CuMbn) is reinternalized into the cell via an active transport process. Bioinformatic and gene regulation studies suggest that two proteins might play a role in CuMbn handling: the TonB-dependent transporter MbnT and the periplasmic binding protein MbnE. Disruption of the gene that encodes MbnT abolishes CuMbn uptake, as reported previously, and expression of MbnT in Escherichia coli confers the ability to take up CuMbn. Biophysical studies of MbnT and MbnE reveal specific interactions with CuMbn, and a crystal structure of apo MbnE is consistent with MbnE's proposed role as a periplasmic CuMbn transporter. Notably, MbnT and MbnE exhibit different levels of discrimination between cognate and noncognate CuMbns. These findings provide evidence for CuMbn-protein interactions and begin to elucidate the molecular mechanisms of its recognition and transport.

  • Organizational Affiliation

    Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methylocystis parvus OBBP MbnE610Methylocystis parvus OBBPMutation(s): 0 
Find proteins for A0A1L1QK06 (Methylocystis parvus OBBP)
Explore A0A1L1QK06 
Go to UniProtKB:  A0A1L1QK06
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1L1QK06
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.2α = 90
b = 141.5β = 90
c = 83.1γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesF32GM110934
National Science Foundation (NSF, United States)United StatesMCB0842366

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-11-30
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Database references
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description