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Structure and function of the lanthanide-dependent methanol dehydrogenase XoxF from the methanotroph Methylomicrobium buryatense 5GB1C

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Abstract

In methylotrophic bacteria, which use one-carbon (C1) compounds as a carbon source, methanol is oxidized by pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH) enzymes. Methylotrophic genomes generally encode two distinct MDHs, MxaF and XoxF. MxaF is a well-studied, calcium-dependent heterotetrameric enzyme whereas XoxF is a lanthanide-dependent homodimer. Recent studies suggest that XoxFs are likely the functional MDHs in many environments. In methanotrophs, methylotrophs that utilize methane, interactions between particulate methane monooxygenase (pMMO) and MxaF have been detected. To investigate the possibility of interactions between pMMO and XoxF, XoxF was isolated from the methanotroph Methylomicrobium buryatense 5GB1C (5G-XoxF). Purified 5G-XoxF exhibits a specific activity of 0.16 μmol DCPIP reduced min−1 mg−1. The 1.85 Å resolution crystal structure reveals a La(III) ion in the active site, in contrast to the calcium ion in MxaF. The overall fold is similar to other MDH structures, but 5G-XoxF is a monomer in solution. An interaction between 5G-XoxF and its cognate pMMO was detected by biolayer interferometry, with a KD value of 50 ± 17 μM. These results suggest an alternative model of MDH-pMMO association, in which a XoxF monomer may bind to pMMO, and underscore the potential importance of lanthanide-dependent MDHs in biological methane oxidation.

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Abbreviations

ICP-MS:

Inductively coupled plasma mass spectrometry

ICP-OES:

Inductively coupled plasma optical emission spectrometry

Mc.:

Methylococcus

MDH:

Methanol dehydrogenase

Mm.:

Methylomicrobium

MMO:

Methane monooxygenase

pMMO:

Particulate methane monooxygenase

PQQ:

Pyrroloquinoline quinone

REE:

Rare earth element

SEC-MALS:

Size exclusion chromatography with multi-angle light scattering

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Acknowledgements

This work was supported by NIH Grant GM118035 (A.C.R.) and a grant from the Undergraduate Research Grant Program which is administered by Northwestern University’s Office of Undergraduate Research. The authors thank Dr. Mary Lidstrom at Washington University for providing Mm. buryatense 5GB1C cultures and Theint Aung from the Northwestern Keck Biophysics Facility for assistance with BLItz instrumentation, data collection, and data interpretation. This work used the Advanced Photon Source, a US Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. Use of the LS-CAT Sector 21 was supported by the Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor (Grant 085P1000817). Data were collected at the LS-CAT beamlines 21-ID-D/F/G. Use of GM/CA has been funded in whole or in part with Federal funds from the National Cancer Institute (ACB-12002) and the National Institute of General Medical Sciences (AGM-12006). The GM/CA Eiger 16 M detector at beamline 23ID-B was funded by an NIH-Office of Research Infrastructure Programs, High-End Instrumentation Grant (1S10OD012289-01A1).

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Author notes

  1. Yue Wen Deng and Soo Y. Ro contributed equally to this work.

Authors and Affiliations

  1. Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA

    Yue Wen Deng, Soo Y. Ro & Amy C. Rosenzweig

  2. Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA

    Yue Wen Deng, Soo Y. Ro & Amy C. Rosenzweig

Authors
  1. Yue Wen Deng
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  2. Soo Y. Ro
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  3. Amy C. Rosenzweig
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Correspondence to Amy C. Rosenzweig.

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PDB accession code: 6DAM.

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Deng, Y.W., Ro, S.Y. & Rosenzweig, A.C. Structure and function of the lanthanide-dependent methanol dehydrogenase XoxF from the methanotroph Methylomicrobium buryatense 5GB1C. J Biol Inorg Chem 23, 1037–1047 (2018). https://doi.org/10.1007/s00775-018-1604-2

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