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 6CPD | pdb_00006cpd

Crystal structure of PmoD soluble domain from Methylocystis sp. ATCC 49242 (Rockwell)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.209 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6CPD

This is version 1.2 of the entry. See complete history. 

Literature

Characterization of a long overlooked copper protein from methane- and ammonia-oxidizing bacteria.

Fisher, O.S., Kenney, G.E., Ross, M.O., Ro, S.Y., Lemma, B.E., Batelu, S., Thomas, P.M., Sosnowski, V.C., DeHart, C.J., Kelleher, N.L., Stemmler, T.L., Hoffman, B.M., Rosenzweig, A.C.

(2018) Nat Commun 9: 4276-4276

  • DOI: https://doi.org/10.1038/s41467-018-06681-5
  • Primary Citation Related Structures: 
    6CPD

  • PubMed Abstract: 

    Methane-oxidizing microbes catalyze the oxidation of the greenhouse gas methane using the copper-dependent enzyme particulate methane monooxygenase (pMMO). Isolated pMMO exhibits lower activity than whole cells, however, suggesting that additional components may be required. A pMMO homolog, ammonia monooxygenase (AMO), converts ammonia to hydroxylamine in ammonia-oxidizing bacteria (AOB) which produce another potent greenhouse gas, nitrous oxide. Here we show that PmoD, a protein encoded within many pmo operons that is homologous to the AmoD proteins encoded within AOB amo operons, forms a copper center that exhibits the features of a well-defined Cu A site using a previously unobserved ligand set derived from a cupredoxin homodimer. PmoD is critical for copper-dependent growth on methane, and genetic analyses strongly support a role directly related to pMMO and AMO. These findings identify a copper-binding protein that may represent a missing link in the function of enzymes critical to the global carbon and nitrogen cycles.


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

Macromolecule Content 

  • Total Structure Weight: 29.14 kDa 
  • Atom Count: 2,138 
  • Modeled Residue Count: 253 
  • Deposited Residue Count: 256 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PmoD
A, B
128Methylocystis sp. ATCC 49242Mutation(s): 0 
Gene Names: Met49242_1452
UniProt
Find proteins for A0ACD6BAU2 (Methylocystis sp. ATCC 49242)
Explore A0ACD6BAU2 
Go to UniProtKB:  A0ACD6BAU2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6BAU2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.209 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.255α = 90
b = 83.255β = 90
c = 70.963γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-SC0016284
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118035
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM119191

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary