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

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 CuA 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.

Authors:
 [1]; ORCiD logo [1];  [1];  [1];  [1];  [2]; ORCiD logo [1];  [1];  [1]; ORCiD logo [1];  [2];  [1]; ORCiD logo [1]
  1. Northwestern Univ., Evanston, IL (United States)
  2. Wayne State Univ., Detroit, MI (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
NIHAHA; USDOE
OSTI Identifier:
1479027
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Fisher, Oriana S., Kenney, Grace E., Ross, Matthew O., Ro, Soo Y., Lemma, Betelehem E., Batelu, Sharon, Thomas, Paul M., Sosnowski, Victoria C., DeHart, Caroline J., Kelleher, Neil L., Stemmler, Timothy L., Hoffman, Brian M., and Rosenzweig, Amy C.. Characterization of a long overlooked copper protein from methane- and ammonia-oxidizing bacteria. United States: N. p., 2018. Web. doi:10.1038/s41467-018-06681-5.
Fisher, Oriana S., Kenney, Grace E., Ross, Matthew O., Ro, Soo Y., Lemma, Betelehem E., Batelu, Sharon, Thomas, Paul M., Sosnowski, Victoria C., DeHart, Caroline J., Kelleher, Neil L., Stemmler, Timothy L., Hoffman, Brian M., & Rosenzweig, Amy C.. Characterization of a long overlooked copper protein from methane- and ammonia-oxidizing bacteria. United States. doi:10.1038/s41467-018-06681-5.
Fisher, Oriana S., Kenney, Grace E., Ross, Matthew O., Ro, Soo Y., Lemma, Betelehem E., Batelu, Sharon, Thomas, Paul M., Sosnowski, Victoria C., DeHart, Caroline J., Kelleher, Neil L., Stemmler, Timothy L., Hoffman, Brian M., and Rosenzweig, Amy C.. Mon . "Characterization of a long overlooked copper protein from methane- and ammonia-oxidizing bacteria". United States. doi:10.1038/s41467-018-06681-5. https://www.osti.gov/servlets/purl/1479027.
@article{osti_1479027,
title = {Characterization of a long overlooked copper protein from methane- and ammonia-oxidizing bacteria},
author = {Fisher, Oriana S. and Kenney, Grace E. and Ross, Matthew O. and Ro, Soo Y. and Lemma, Betelehem E. and Batelu, Sharon and Thomas, Paul M. and Sosnowski, Victoria C. and DeHart, Caroline J. and Kelleher, Neil L. and Stemmler, Timothy L. and Hoffman, Brian M. and Rosenzweig, Amy C.},
abstractNote = {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 CuA 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.},
doi = {10.1038/s41467-018-06681-5},
journal = {Nature Communications},
issn = {2041-1723},
number = 1,
volume = 9,
place = {United States},
year = {2018},
month = {10}
}

Journal Article:
Free Publicly Available Full Text
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