1YEW

Crystal structure of particulate methane monooxygenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.801 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.272 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane.

Lieberman, R.L.Rosenzweig, A.C.

(2005) Nature 434: 177-182

  • DOI: 10.1038/nature03311

  • PubMed Abstract: 
  • Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that catalyses the conversion of methane to methanol. Knowledge of how pMMO performs this extremely challenging chemistry may have an impact on the use of methane as an al ...

    Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that catalyses the conversion of methane to methanol. Knowledge of how pMMO performs this extremely challenging chemistry may have an impact on the use of methane as an alternative energy source by facilitating the development of new synthetic catalysts. We have determined the structure of pMMO from the methanotroph Methylococcus capsulatus (Bath) to a resolution of 2.8 A. The enzyme is a trimer with an alpha3beta3gamma3 polypeptide arrangement. Two metal centres, modelled as mononuclear copper and dinuclear copper, are located in soluble regions of each pmoB subunit, which resembles cytochrome c oxidase subunit II. A third metal centre, occupied by zinc in the crystal, is located within the membrane. The structure provides new insight into the molecular details of biological methane oxidation.


    Organizational Affiliation

    Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois 60208, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
particulate methane monooxygenase, B subunit
A, E, I
382Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)Mutation(s): 0 
Gene Names: pmoB1, pmoB2 (pmoB)
EC: 1.14.18.3
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxygenases
Protein: 
Particulate methane monooxgenase (pMMO)
Find proteins for G1UBD1 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Go to UniProtKB:  G1UBD1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
particulate methane monooxygenase, A subunit
B, F, J
247Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)Mutation(s): 0 
Gene Names: pmoA1, pmoA2 (pmoA)
EC: 1.14.18.3
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxygenases
Protein: 
Particulate methane monooxgenase (pMMO)
Find proteins for Q607G3 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Go to UniProtKB:  Q607G3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
particulate methane monooxygenase subunit C2
C, G, K
289Methylococcus capsulatusMutation(s): 0 
Gene Names: pmoC2
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxygenases
Protein: 
Particulate methane monooxgenase (pMMO)
Find proteins for O05111 (Methylococcus capsulatus)
Go to UniProtKB:  O05111
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, C, E, G, K
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CUA
Query on CUA

Download SDF File 
Download CCD File 
A, E, I
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A, E, I
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.801 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.272 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 264.140α = 90.00
b = 264.140β = 90.00
c = 150.005γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
MAR345data collection
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-08
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description