2XJI

Structure and Copper-binding Properties of Methanobactins from Methylosinus trichosporium OB3b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.129 
  • R-Value Observed: 0.114 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Copper-Binding Properties and Structures of Methanobactins from Methylosinus Trichosporium Ob3B.

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

(2011) Inorg Chem 50: 1378

  • DOI: 10.1021/ic101965j
  • Primary Citation of Related Structures:  
    2XJH, 2XJI

  • PubMed Abstract: 
  • Methanobactins (mbs) are a class of copper-binding peptides produced by aerobic methane oxidizing bacteria (methanotrophs) that have been linked to the substantial copper needs of these environmentally important microorganisms. The only characterized mbs are those from Methylosinus trichosporium OB3b and Methylocystis strain SB2 ...

    Methanobactins (mbs) are a class of copper-binding peptides produced by aerobic methane oxidizing bacteria (methanotrophs) that have been linked to the substantial copper needs of these environmentally important microorganisms. The only characterized mbs are those from Methylosinus trichosporium OB3b and Methylocystis strain SB2. M. trichosporium OB3b produces a second mb (mb-Met), which is missing the C-terminal Met residue from the full-length form (FL-mb). The as-isolated copper-loaded mbs bind Cu(I). The absence of the Met has little influence on the structure of the Cu(I) site, and both molecules mediate switchover from the soluble iron methane mono-oxygenase to the particulate copper-containing enzyme in M. trichosporium OB3b cells. Cu(II) is reduced in the presence of the mbs under our experimental conditions, and the disulfide plays no role in this process. The Cu(I) affinities of these molecules are extremely high with values of (6-7) × 10(20) M(-1) determined at pH ≥ 8.0. The affinity for Cu(I) is 1 order of magnitude lower at pH 6.0. The reduction potentials of copper-loaded FL-mb and mb-Met are 640 and 590 mV respectively, highlighting the strong preference for Cu(I) and indicating different Cu(II) affinities for the two forms. Cleavage of the disulfide bridge results in a decrease in the Cu(I) affinity to ∼9 × 10(18) M(-1) at pH 7.5. The two thiolates can also bind Cu(I), albeit with much lower affinity (∼ 3 × 10(15) M(-1) at pH 7.5). The high affinity of mbs for Cu(I) is consistent with a physiological role in copper uptake and protection.


    Related Citations: 
    • Methanobactin, a Copper-Acquisition Compound from Methane-Oxidizing Bacteria.
      Kim, H.J., Graham, D.W., Dispirito, A.A., Alterman, M.A., Galeva, N., Larive, C.K., Asunskis, D., Sherwood, P.M.A.
      (2004) Science 305: 1612
    • NMR, Mass Spectrometry and Chemical Evidence Reveal a Different Chemical Structure for Methanobactin that Contains Oxazolone Rings.
      Behling, L.A., Hartsel, S.C., Lewis, D.E., Dispirito, A.A., Choi, D.W., Masterson, L.R., Veglia, G., Gallagher, W.H.
      (2008) J Am Chem Soc 130: 12604

    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   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
METHANOBACTIN MB-OB3BA, B, C, D, E, F11Methylosinus trichosporium OB3bMutation(s): 0 
EC: 1.11.1 (PDB Primary Data), 1.15.1.1 (PDB Primary Data)
UniProt
Find proteins for E3YBA4 (Methylosinus trichosporium)
Explore E3YBA4 
Go to UniProtKB:  E3YBA4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BB9
Query on BB9
A, B, C, D, E, FPEPTIDE LINKINGC3 H5 N O2 SCYS
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 1
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000762
Query on PRD_000762
A, B, C, D, E, FMETHANOBACTINChalkophore, Polypeptide /  Metal transport Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.129 
  • R-Value Observed: 0.114 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.71α = 90
b = 39.57β = 90
c = 85.05γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
iMOSFLMdata reduction
SCALAdata scaling
SHELXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-02
    Type: Initial release
  • Version 1.1: 2012-03-28
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2012-05-09
    Changes: Other
  • Version 1.3: 2012-11-30
    Changes: Other
  • Version 1.4: 2013-07-24
    Changes: Non-polymer description
  • Version 2.0: 2019-05-22
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Refinement description
  • Version 2.1: 2019-07-10
    Changes: Data collection