3CHX

Crystal structure of Methylosinus trichosporium OB3b particulate methane monooxygenase (pMMO)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.377 
  • R-Value Work: 0.342 

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Literature

The metal centers of particulate methane monooxygenase from Methylosinus trichosporium OB3b.

Hakemian, A.S.Kondapalli, K.C.Telser, J.Hoffman, B.M.Stemmler, T.L.Rosenzweig, A.C.

(2008) Biochemistry 47: 6793-6801

  • DOI: 10.1021/bi800598h
  • Primary Citation of Related Structures:  
    3CHX

  • PubMed Abstract: 
  • Particulate methane monooxygenase (pMMO) is a membrane-bound metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. The nature of the pMMO active site and the overall metal content are controversial, with spectroscopic and crystallographic data suggesting the presence of a mononuclear copper center, a dinuclear copper center, a trinuclear center, and a diiron center or combinations thereof ...

    Particulate methane monooxygenase (pMMO) is a membrane-bound metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. The nature of the pMMO active site and the overall metal content are controversial, with spectroscopic and crystallographic data suggesting the presence of a mononuclear copper center, a dinuclear copper center, a trinuclear center, and a diiron center or combinations thereof. Most studies have focused on pMMO from Methylococcus capsulatus (Bath). pMMO from a second organism, Methylosinus trichosporium OB3b, has been purified and characterized by spectroscopic and crystallographic methods. Purified M. trichosporium OB3b pMMO contains approximately 2 copper ions per 100 kDa protomer. Electron paramagnetic resonance (EPR) spectroscopic parameters indicate that type 2 Cu(II) is present as two distinct species. Extended X-ray absorption fine structure (EXAFS) data are best fit with oxygen/nitrogen ligands and reveal a Cu-Cu interaction at 2.52 A. Correspondingly, X-ray crystallography of M. trichosporium OB3b pMMO shows a dinuclear copper center, similar to that observed previously in the crystal structure of M. capsulatus (Bath) pMMO. There are, however, significant differences between the pMMO structures from the two organisms. A mononuclear copper center present in M. capsulatus (Bath) pMMO is absent in M. trichosporium OB3b pMMO, whereas a metal center occupied by zinc in the M. capsulatus (Bath) pMMO structure is occupied by copper in M. trichosporium OB3b pMMO. These findings extend previous work on pMMO from M. capsulatus (Bath) and provide new insight into the functional importance of the different metal centers.


    Organizational Affiliation

    Department of Biochemistry, Northwestern University, Evanston, Illinois 60208, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PmoBA, F [auth E], K [auth I]392Methylosinus trichosporiumMutation(s): 0 
Gene Names: pmoB
Membrane Entity: Yes 
UniProt
Find proteins for Q9KX50 (Methylosinus trichosporium)
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Go to UniProtKB:  Q9KX50
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PmoAB, G [auth F], L [auth J]252Methylosinus trichosporiumMutation(s): 0 
Gene Names: pmoA
Membrane Entity: Yes 
UniProt
Find proteins for Q50541 (Methylosinus trichosporium)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PmoCC, H [auth G], M [auth K]256Methylosinus trichosporiumMutation(s): 0 
Gene Names: pmoC
Membrane Entity: Yes 
UniProt
Find proteins for Q9KX51 (Methylosinus trichosporium)
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Go to UniProtKB:  Q9KX51
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
20-residue peptideD, I [auth H], N [auth L]20Methylosinus trichosporiumMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
26-residue peptideE [auth M], J [auth N], O26Methylosinus trichosporiumMutation(s): 0 
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.377 
  • R-Value Work: 0.342 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.81α = 90
b = 184.07β = 90
c = 203.9γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2008-03-10 
  • Released Date: 2008-07-15 
  • Deposition Author(s): Hakemian, A.S.

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance