4PHZ | pdb_00004phz

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

• PDB DOI: https://doi.org/10.2210/pdb4PHZ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Methylocystis sp. ATCC 49242
• Mutation(s): No 


• 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 (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 
  0.289 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

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 Biological Chem 289: 21782-21794

• PubMed: 24942740 
• DOI: https://doi.org/10.1074/jbc.M114.581363
• Primary Citation 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. 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.

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Organizational Affiliation: 
• From the Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208.
the Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201, and.
the Medical Proteome Center, Department of Functional Proteomics, Ruhr-Universität Bochum, 44801 Bochum, Germany.
the Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201, and [e-mail].
From the Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer - A3B3C3D2E1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 320.16 kDa 
• Atom Count: 20,853 
• Modeled Residue Count: 2,598 
• Deposited Residue Count: 2,856 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
unknown peptide	A [auth D], B [auth H], D [auth N]	24	Methylocystis sp. ATCC 49242	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Particulate methane monooxygenase subunit C	C [auth K], K [auth C], L [auth G]	256	Methylocystis sp. ATCC 49242	Mutation(s): 0  EC: 1.14.18.3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Particulate methane monooxygenase subunit B	E [auth A], G [auth E], H [auth I]	420	Methylocystis sp. ATCC 49242	Mutation(s): 0  EC: 1.14.18.3

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Particulate methane monooxygenase subunit A	F [auth B], I [auth F], J	252	Methylocystis sp. ATCC 49242	Mutation(s): 0  EC: 1.14.18.3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGT	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
CU	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free:  0.289 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.462	α = 90
b = 184.531	β = 90
c = 189.417	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-06-25 
Deposition Author(s): Sirajuddin, S., Rosenzweig, A.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM070473

Revision History  

• 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
• Version 1.6: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.7: 2024-10-23
  Changes: Structure summary