3RFR

Crystal Structure of particulate methane monooxygenase (pMMO) from Methylocystis sp. strain M


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure and Characterization of Particulate Methane Monooxygenase from Methylocystis species Strain M.

Smith, S.M.Rawat, S.Telser, J.Hoffman, B.M.Stemmler, T.L.Rosenzweig, A.C.

(2011) Biochemistry 50: 10231-10240

  • DOI: 10.1021/bi200801z
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. Previous biochemical and structural studies of pMMO have focused on preparations from Methylococcus capsulatu ...

    Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. Previous biochemical and structural studies of pMMO have focused on preparations from Methylococcus capsulatus (Bath) and Methylosinus trichosporium OB3b. A pMMO from a third organism, Methylocystis species strain M, has been isolated and characterized. Both membrane-bound and solubilized Methylocystis sp. strain M pMMO contain ~2 copper ions per 100 kDa protomer and exhibit copper-dependent propylene epoxidation activity. Spectroscopic data indicate that Methylocystis sp. strain M pMMO contains a mixture of Cu(I) and Cu(II), of which the latter exhibits two distinct type 2 Cu(II) electron paramagnetic resonance (EPR) signals. Extended X-ray absorption fine structure (EXAFS) data are best fit with a mixture of Cu-O/N and Cu-Cu ligand environments with a Cu-Cu interaction at 2.52-2.64 Å. The crystal structure of Methylocystis sp. strain M pMMO was determined to 2.68 Å resolution and is the best quality pMMO structure obtained to date. It provides a revised model for the pmoA and pmoC subunits and has led to an improved model of M. capsulatus (Bath) pMMO. In these new structures, the intramembrane zinc/copper binding site has a different coordination environment from that in previous models.


    Organizational Affiliation

    Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PmoB
A, E, I
419Methylocystis sp. MMutation(s): 0 
Gene Names: pmoB
Find proteins for Q9KX36 (Methylocystis sp. M)
Go to UniProtKB:  Q9KX36
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
peptide
D, H
19N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PmoA
J, B, F
252Methylocystis sp. MMutation(s): 0 
Gene Names: pmoA
Find proteins for O06122 (Methylocystis sp. M)
Go to UniProtKB:  O06122
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PmoC
C, G, K
256Methylocystis sp. MMutation(s): 0 
Gene Names: pmoC
Find proteins for Q9KX37 (Methylocystis sp. M)
Go to UniProtKB:  Q9KX37
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, I, K
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CUA
Query on CUA

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.249 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 107.718α = 90.00
b = 178.310β = 90.00
c = 183.147γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-23
    Type: Initial release
  • Version 1.1: 2011-12-07
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description