4PI0

Crystal structure of particulate methane monooxygenase from Methylocystis sp. ATCC 49242 (Rockwell) soaked in copper

  • Classification: OXIDOREDUCTASE

  • Deposited: 2014-05-07 Released: 2014-06-25 
  • Deposition Author(s): Sirajuddin, S., Rosenzweig, A.C.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Effects of zinc on particulate methane monooxygenase activity and structure.

Sirajuddin, S.Barupala, D.Helling, S.Marcus, K.Stemmler, T.L.Rosenzweig, A.C.

(2014) J.Biol.Chem. 289: 21782-21794

  • DOI: 10.1074/jbc.M114.581363
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Particulate methane monooxygenase (pMMO) is a membrane-bound metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. Zinc is a known inhibitor of pMMO, but the details of zinc binding and the mechanism of inhibition are not unders ...

    Particulate methane monooxygenase (pMMO) is a membrane-bound metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. Zinc is a known inhibitor of pMMO, but the details of zinc binding and the mechanism of inhibition are not understood. Metal binding and activity assays on membrane-bound pMMO from Methylococcus capsulatus (Bath) reveal that zinc inhibits pMMO at two sites that are distinct from the copper active site. The 2.6 Å resolution crystal structure of Methylocystis species strain Rockwell pMMO reveals two previously undetected bound lipids, and metal soaking experiments identify likely locations for the two zinc inhibition sites. The first is the crystallographic zinc site in the pmoC subunit, and zinc binding here leads to the ordering of 10 previously unobserved residues. A second zinc site is present on the cytoplasmic side of the pmoC subunit. Parallels between these results and zinc inhibition studies of several respiratory complexes suggest that zinc might inhibit proton transfer in pMMO.


    Organizational Affiliation

    From the Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
unknown peptide
D, H, N
25N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Particulate methane monooxygenase subunit A
F, J, B
252N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Particulate methane monooxygenase subunit C
K, C, G
256N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Particulate methane monooxygenase subunit B
E, A, I
420N/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, N
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 116.361α = 90.00
b = 184.739β = 90.00
c = 188.637γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM070473

Revision History 

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2014-07-09
    Type: Database references
  • Version 1.2: 2014-10-01
    Type: Database references
  • Version 1.3: 2016-04-06
    Type: Source and taxonomy
  • Version 1.4: 2017-09-06
    Type: Author supporting evidence, Derived calculations