7EV9

cryoEM structure of particulate methane monooxygenase associated with Cu(I)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Copper Centers in the Cryo-EM Structure of Particulate Methane Monooxygenase Reveal the Catalytic Machinery of Methane Oxidation.

Chang, W.H.Lin, H.H.Tsai, I.K.Huang, S.H.Chung, S.C.Tu, I.P.Yu, S.S.Chan, S.I.

(2021) J Am Chem Soc 143: 9922-9932

  • DOI: 10.1021/jacs.1c04082
  • Primary Citation of Related Structures:  
    7EV9

  • PubMed Abstract: 
  • The particulate methane monooxygenase (pMMO) is the first enzyme in the C1 metabolic pathway in methanotrophic bacteria. As this enzyme converts methane into methanol efficiently near room temperature, it has become the paradigm for developing an understanding of this difficult C1 chemistry ...

    The particulate methane monooxygenase (pMMO) is the first enzyme in the C1 metabolic pathway in methanotrophic bacteria. As this enzyme converts methane into methanol efficiently near room temperature, it has become the paradigm for developing an understanding of this difficult C1 chemistry. pMMO is a membrane-bound protein with three subunits (PmoB, PmoA, and PmoC) and 12-14 coppers distributed among different sites. X-ray crystal structures that have revealed only three mononuclear coppers at three sites have neither disclosed the location of the active site nor the catalytic mechanism of the enzyme. Here we report a cyro-EM structure of holo -pMMO from Methylococcus capsulatus (Bath) at 2.5 Å, and develop quantitative electrostatic-potential profiling to scrutinize the nonprotein densities for signatures of the copper cofactors. Our results confirm a mononuclear Cu I at the A site, resolve two Cu I s at the B site, and uncover additional Cu I clusters at the PmoA/PmoC interface within the membrane ( D site) and in the water-exposed C -terminal subdomain of the PmoB ( E clusters). These findings complete the minimal set of copper factors required for catalytic turnover of pMMO, offering a glimpse of the catalytic machinery for methane oxidation according to the chemical principles underlying the mechanism proposed earlier.


    Organizational Affiliation

    Institute of Chemistry, Academia Sinica, Nangang, Taipei 11529, Taiwan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Particulate methane monooxygenase alpha subunitA, D [auth E], G [auth I]414Methylococcus capsulatus str. BathMutation(s): 0 
Gene Names: pmoB1pmoBMCA1796pmoB2MCA2853
EC: 1.14.18.3
Membrane Entity: Yes 
UniProt
Find proteins for G1UBD1 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Explore G1UBD1 
Go to UniProtKB:  G1UBD1
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Particulate methane monooxygenase beta subunitB, E [auth F], H [auth J]247Methylococcus capsulatus str. BathMutation(s): 0 
Gene Names: pmoA1pmoAMCA1797pmoA2MCA2854
EC: 1.14.18.3
Membrane Entity: Yes 
UniProt
Find proteins for Q607G3 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Explore Q607G3 
Go to UniProtKB:  Q607G3
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ammonia monooxygenase/methane monooxygenase, subunit C family proteinC, F [auth G], I [auth K]260Methylococcus capsulatus str. BathMutation(s): 0 
Gene Names: pmoC1MCA1798MCA2855
EC: 1.14.13.25
Membrane Entity: Yes 
UniProt
Find proteins for Q603F1 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Explore Q603F1 
Go to UniProtKB:  Q603F1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU1
Query on CU1

Download Ideal Coordinates CCD File 
AA [auth I] , BA [auth I] , CA [auth I] , DA [auth I] , EA [auth I] , FA [auth J] , GA [auth J] , J [auth A] , 
AA [auth I],  BA [auth I],  CA [auth I],  DA [auth I],  EA [auth I],  FA [auth J],  GA [auth J],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  N [auth A],  O [auth A],  P [auth B],  Q [auth B],  R [auth E],  S [auth E],  T [auth E],  U [auth E],  V [auth E],  W [auth E],  X [auth F],  Y [auth F],  Z [auth I]
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-21
    Type: Initial release