9CL6 | pdb_00009cl6

Ammonia monooxygenase in native membranes

  • Classification: OXIDOREDUCTASE
  • Organism(s): Nitrosomonas europaea ATCC 19718
  • Mutation(s): No 

  • Deposited: 2024-07-10 Released: 2025-01-08 
  • Deposition Author(s): Tucci, F.J., Rosenzweig, A.C.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.77 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures of methane and ammonia monooxygenases in native membranes.

Tucci, F.J.Rosenzweig, A.C.

(2025) Proc Natl Acad Sci U S A 122: e2417993121-e2417993121

  • DOI: https://doi.org/10.1073/pnas.2417993121
  • Primary Citation of Related Structures:  
    9CL1, 9CL2, 9CL3, 9CL4, 9CL5, 9CL6

  • PubMed Abstract: 

    Methane- and ammonia-oxidizing bacteria play key roles in the global carbon and nitrogen cycles, respectively. These bacteria use homologous copper membrane monooxygenases to accomplish the defining chemical transformations of their metabolisms: the oxidations of methane to methanol by particulate methane monooxygenase (pMMO) and ammonia to hydroxylamine by ammonia monooxygenase (AMO), enzymes of prime interest for applications in mitigating climate change. However, investigations of these enzymes have been hindered by the need for disruptive detergent solubilization prior to structure determination, confounding studies of pMMO and precluding studies of AMO. Here, we overcome these challenges by using cryoEM to visualize pMMO and AMO directly in their native membrane arrays at 2.4 to 2.8 Å resolution. These structures reveal details of the copper centers, numerous bound lipids, and previously unobserved components, including identifiable and distinct supernumerary helices interacting with pMMO and AMO, suggesting a widespread role for these helices in copper membrane monooxygenases. Comparisons between these structures, their metallocofactors, and their unexpected protein-protein interactions highlight features that may govern activity or the formation of higher-order arrays in native membranes. The ability to obtain molecular insights within the native membrane will enable further understanding of these environmentally important enzymes.


  • Organizational Affiliation
    • Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ammonia monooxygenase subunit CA [auth C],
I [auth J],
J [auth G]
254Nitrosomonas europaea ATCC 19718Mutation(s): 0 
UniProt
Find proteins for Q82T63 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298))
Explore Q82T63 
Go to UniProtKB:  Q82T63
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ82T63
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ammonia monooxygenase beta subunitB [auth A],
K [auth H],
L [auth E]
383Nitrosomonas europaea ATCC 19718Mutation(s): 0 
EC: 1.14.99.39
UniProt
Find proteins for Q04508 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298))
Explore Q04508 
Go to UniProtKB:  Q04508
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04508
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ammonia monooxygenase alpha subunitC [auth B],
G [auth I],
H [auth F]
274Nitrosomonas europaea ATCC 19718Mutation(s): 0 
EC: 1.14.99.39
UniProt
Find proteins for Q04507 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298))
Explore Q04507 
Go to UniProtKB:  Q04507
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04507
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ammonia monooxygenase supernumerary helixD [auth Da],
E [auth Db],
F [auth Dc]
39Nitrosomonas europaea ATCC 19718Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.77 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207:

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 StatesR35GM118035
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM105538
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesF31ES034283

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-08
    Type: Initial release
  • Version 1.1: 2025-01-15
    Changes: Data collection, Database references