2YGJ

Methanobactin MB4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.80 Å
  • R-Value Free: 0.109 
  • R-Value Observed: 0.086 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Variations in Methanobactin Structure Influences Copper Utilization by Methane-Oxidizing Bacteria.

El Ghazouani, A.Basle, A.Gray, J.Graham, D.W.Firbank, S.J.Dennison, C.

(2012) Proc Natl Acad Sci U S A 109: 8400

  • DOI: https://doi.org/10.1073/pnas.1112921109
  • Primary Citation of Related Structures:  
    2YGI, 2YGJ

  • PubMed Abstract: 

    Methane-oxidizing bacteria are nature's primary biological mechanism for suppressing atmospheric levels of the second-most important greenhouse gas via methane monooxygenases (MMOs). The copper-containing particulate enzyme is the most widespread and efficient MMO. Under low-copper conditions methane-oxidizing bacteria secrete the small copper-binding peptide methanobactin (mbtin) to acquire copper, but how variations in the structures of mbtins influence copper metabolism and species selection are unknown. Methanobactins have been isolated from Methylocystis strains M and hirsuta CSC1, organisms that can switch to using an iron-containing soluble MMO when copper is limiting, and the nonswitchover Methylocystis rosea. These mbtins are shorter, and have different amino acid compositions, than the characterized mbtin from Methylosinus trichosporium OB3b. A coordinating pyrazinedione ring in the Methylocystis mbtins has little influence on the Cu(I) site structure. The Methylocystis mbtins have a sulfate group that helps stabilize the Cu(I) forms, resulting in affinities of approximately 10(21) M(-1). The Cu(II) affinities vary over three orders of magnitude with reduction potentials covering approximately 250 mV, which may dictate the mechanism of intracellular copper release. Copper uptake and the switchover from using the iron-containing soluble MMO to the copper-containing particulate enzyme is faster when mediated by the native mbtin, suggesting that the amino acid sequence is important for the interaction of mbtins with receptors. The differences in structures and properties of mbtins, and their influence on copper utilization by methane-oxidizing bacteria, have important implications for the ecology and global function of these environmentally vital organisms.


  • Organizational Affiliation

    Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
METHANOBACTIN MB46Methylocystis sp. MMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.80 Å
  • R-Value Free: 0.109 
  • R-Value Observed: 0.086 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 9.06α = 90
b = 13.32β = 90
c = 42.65γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
XDSdata reduction
SCALAdata scaling
SHELXCDEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2012-05-23
    Changes: Other
  • Version 1.2: 2012-10-03
    Changes: Database references
  • Version 1.3: 2019-05-22
    Changes: Data collection, Derived calculations, Other, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other