4PHZ

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

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This is version 1.5 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: https://doi.org/10.1074/jbc.M114.581363
  • Primary Citation of Related Structures:  
    4PHZ, 4PI0, 4PI2

  • 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 understood ...

    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, amyr@northwestern.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
unknown peptideA [auth D],
B [auth H],
D [auth N]		24Methylocystis sp. ATCC 49242Mutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Particulate methane monooxygenase subunit CC [auth K],
K [auth C],
L [auth G]		256Methylocystis sp. ATCC 49242Mutation(s): 0 
EC: 1.14.18.3
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Particulate methane monooxygenase subunit BE [auth A],
G [auth E],
H [auth I]		420Methylocystis sp. ATCC 49242Mutation(s): 0 
EC: 1.14.18.3
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Particulate methane monooxygenase subunit AF [auth B],
I [auth F],
J		252Methylocystis sp. ATCC 49242Mutation(s): 0 
EC: 1.14.18.3
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGT
Query on PGT
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N [auth K],
S [auth C],
U [auth G],
V [auth G]		(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C40 H79 O10 P
KBPVYRBBONZJHF-AMAPPZPBSA-N		 Ligand Interaction
CU
Query on CU
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M [auth K]
O [auth A]
P [auth E]
Q [auth I]
R [auth C]
M [auth K],
O [auth A],
P [auth E],
Q [auth I],
R [auth C],
T [auth G]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.462α = 90
b = 184.531β = 90
c = 189.417γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM070473

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2014-07-09
    Changes: Database references
  • Version 1.2: 2014-10-01
    Changes: Database references
  • Version 1.3: 2016-04-06
    Changes: Source and taxonomy
  • Version 1.4: 2017-09-06
    Changes: Author supporting evidence, Derived calculations
  • Version 1.5: 2019-12-25
    Changes: Author supporting evidence