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

Oriana S. Fisher; Grace E. Kenney; Matthew O. Ross; Soo Y. Ro; Betelehem E. Lemma; Sharon Batelu; Paul M. Thomas; Victoria C. Sosnowski; Caroline J. DeHart; Neil L. Kelleher; Timothy L. Stemmler; Brian M. Hoffman; Amy C. Rosenzweig

doi:10.1038/s41467-018-06681-5

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

Oriana S. Fisher, Grace E. Kenney, Matthew O. Ross, Soo Y. Ro, Betelehem E. Lemma, Sharon Batelu, Paul M. Thomas, Victoria C. Sosnowski, Caroline J. DeHart, Neil L. Kelleher, Timothy L. Stemmler, Brian M. Hoffman, Amy C. Rosenzweig^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

49 Scopus citations

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.

Original language	English (US)
Article number	4276
Journal	Nature communications
Volume	9
Issue number	1
DOIs	https://doi.org/10.1038/s41467-018-06681-5
State	Published - Dec 1 2018

Funding

This work was funded by the Department of Energy grant DE-SC0016284 (A.C.R.), National Institutes of Health grants GM118035 (A.C.R.), GM111097 (B.M.H.), DK068139 (T.L.S.), R01AT009143 (N.L.K.) and F32GM119191 (O.S.F.), and American Heart Association grant 14PRE20460104 (G.E.K.). We thank the staff of the GM/CA and LS-CAT beamlines of the Advanced Photon Source, which is a DOE Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11356. Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-76SF00515. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research, and by the National Institutes of Health, National Institute of General Medical Sciences (including P41GM103393). The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of NIGMS or NIH. Steven Almo and Anthony Gizzi at Albert Einstein College of Medicine produced the wild-type His6-PmoDMet49242_1452 soluble domain construct. The Quantitative Bio-element Imaging Center at Northwestern is supported by NASA Ames Research Center NNA06CB93G. The Proteomics Center for Excellence at Northwestern is supported by National Resource for Translational and Developmental Proteomics under NIH grant P41 GM108569 and NCI CCSG P30 CA060553. The Keck Biophysics Facility at Northwestern is supported in part by NCI CCSG P30 CA060553. We thank Laura M. K. Dassama and Thomas J. Lawton for discussions.

ASJC Scopus subject areas

General Physics and Astronomy
General Chemistry
General Biochemistry, Genetics and Molecular Biology

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10.1038/s41467-018-06681-5

Cite this

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). Characterization of a long overlooked copper protein from methane- and ammonia-oxidizing bacteria. Nature communications, 9(1), Article 4276. https://doi.org/10.1038/s41467-018-06681-5

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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.",

author = "Fisher, {Oriana S.} and Kenney, {Grace E.} and Ross, {Matthew O.} and Ro, {Soo Y.} and Lemma, {Betelehem E.} and Sharon Batelu 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.}",

note = "Funding Information: This work was funded by the Department of Energy grant DE-SC0016284 (A.C.R.), National Institutes of Health grants GM118035 (A.C.R.), GM111097 (B.M.H.), DK068139 (T.L.S.), R01AT009143 (N.L.K.) and F32GM119191 (O.S.F.), and American Heart Association grant 14PRE20460104 (G.E.K.). We thank the staff of the GM/CA and LS-CAT beamlines of the Advanced Photon Source, which is a DOE Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11356. Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-76SF00515. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research, and by the National Institutes of Health, National Institute of General Medical Sciences (including P41GM103393). The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of NIGMS or NIH. Steven Almo and Anthony Gizzi at Albert Einstein College of Medicine produced the wild-type His6-PmoDMet49242_1452 soluble domain construct. The Quantitative Bio-element Imaging Center at Northwestern is supported by NASA Ames Research Center NNA06CB93G. The Proteomics Center for Excellence at Northwestern is supported by National Resource for Translational and Developmental Proteomics under NIH grant P41 GM108569 and NCI CCSG P30 CA060553. The Keck Biophysics Facility at Northwestern is supported in part by NCI CCSG P30 CA060553. We thank Laura M. K. Dassama and Thomas J. Lawton for discussions. Publisher Copyright: {\textcopyright} 2018, The Author(s).",

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AU - Ross, Matthew O.

AU - Ro, Soo Y.

AU - Lemma, Betelehem E.

AU - Batelu, Sharon

AU - Thomas, Paul M.

AU - Sosnowski, Victoria C.

AU - DeHart, Caroline J.

AU - Kelleher, Neil L.

AU - Stemmler, Timothy L.

AU - Hoffman, Brian M.

AU - Rosenzweig, Amy C.

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N2 - 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.

AB - 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.

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

Abstract

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

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

Abstract

Funding

ASJC Scopus subject areas

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Datasets

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

Cite this