3CHX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.377 
  • R-Value Work: 0.342 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • 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 crysta ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PmoB
A, E, I
392Methylosinus trichosporiumMutation(s): 0 
Gene Names: pmoB
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxygenases
Protein: 
Particulate methane monooxgenase (pMMO)
Find proteins for Q9KX50 (Methylosinus trichosporium)
Go to UniProtKB:  Q9KX50
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PmoA
B, F, J
252Methylosinus trichosporiumMutation(s): 0 
Gene Names: pmoA
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxygenases
Protein: 
Particulate methane monooxgenase (pMMO)
Find proteins for Q50541 (Methylosinus trichosporium)
Go to UniProtKB:  Q50541
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PmoC
C, G, K
256Methylosinus trichosporiumMutation(s): 0 
Gene Names: pmoC
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxygenases
Protein: 
Particulate methane monooxgenase (pMMO)
Find proteins for Q9KX51 (Methylosinus trichosporium)
Go to UniProtKB:  Q9KX51
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
20-residue peptide
D, H, L
20N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
26-residue peptide
M, N, O
26N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download SDF File 
Download CCD File 
A, C, E, G, I, K
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
D, H, L, M, N, O
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.377 
  • R-Value Work: 0.342 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 113.810α = 90.00
b = 184.070β = 90.00
c = 203.900γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
CNSrefinement
Blu-Icedata collection
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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