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Visualizing molecular juggling within a B12-dependent methyltransferase complex

Abstract

Derivatives of vitamin B12 are used in methyl group transfer in biological processes as diverse as methionine synthesis in humans and CO2 fixation in acetogenic bacteria1,2,3. This seemingly straightforward reaction requires large, multimodular enzyme complexes that adopt multiple conformations to alternately activate, protect and perform catalysis on the reactive B12 cofactor. Crystal structures determined thus far have provided structural information for only fragments of these complexes4,5,6,7,8,9,10,11,12, inspiring speculation about the overall protein assembly and conformational movements inherent to activity. Here we present X-ray crystal structures of a complete 220 kDa complex that contains all enzymes responsible for B12-dependent methyl transfer, namely the corrinoid iron–sulphur protein and its methyltransferase from the model acetogen Moorella thermoacetica. These structures provide the first three-dimensional depiction of all protein modules required for the activation, protection and catalytic steps of B12-dependent methyl transfer. In addition, the structures capture B12 at multiple locations between its ‘resting’ and catalytic positions, allowing visualization of the dramatic protein rearrangements that enable methyl transfer and identification of the trajectory for B12 movement within the large enzyme scaffold. The structures are also presented alongside in crystallo spectroscopic data, which confirm enzymatic activity within crystals and demonstrate the largest known conformational movements of proteins in a crystalline state. Taken together, this work provides a model for the molecular juggling that accompanies turnover and helps explain why such an elaborate protein framework is required for such a simple, yet biologically essential reaction.

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Figure 1: The overall CFeSP/MeTr complex.
Figure 2: Comparison of B 12 positions in ‘resting’ ChCFeSP, folate-free and folate-bound CFeSP/MeTr.
Figure 3: Methyl transfer activity of CFeSP/MeTr crystals by ultraviolet–visible absorption spectroscopy.
Figure 4: Cartoon model of B 12 -dependent methyl transfer in CFeSP/MeTr.

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Protein Data Bank

Data deposits

Atomic coordinates are deposited in the Protein Data Bank under accession codes 4DJD, 4DJE and 4DJF.

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Acknowledgements

We thank J. E. Darty for his assistance with the purification of CFeSP. This work was supported by National Institutes of Health grants GM69857 (to C.L.D.) and GM39451 (to S.W.R.) and the MIT Energy Initiative (to C.L.D.). C.L.D. is a Howard Hughes Medical Institute Investigator. This work is based upon research conducted at the Advanced Photon Source on the Northeastern Collaborative Access Team beamlines, which are supported by award RR-15301 from the National Center for Research Resources at the National Institutes of Health. Use of the Advanced Photon Source is supported by the US Department of Energy, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the US Department of Energy under Contract No. DE-AC02-05CH11231.

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Contributions

Y.K. performed crystallization and data collection, processing and refinement that gave the folate-free and folate-bound CFeSP/MeTr structures. N.A. built the microspectrophotometer and performed in crystallo spectroscopic experiments with the aid of Y.K., who performed the parallel solution spectroscopic experiments. T.I.D. determined initial crystallization conditions and performed initial data collection, and L.C.B. processed and refined these data. G.B. and J.S. expressed and purified protein samples, and S.W.R. and C.L.D. were involved in study design. Y.K. and C.L.D. wrote the manuscript.

Corresponding author

Correspondence to Catherine L. Drennan.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Tables 1-2, containing X-ray data collection and refinement statistics and B-factor information, Supplementary Figures 1-21, a Supplementary Discussion and additional references. (PDF 21726 kb)

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Kung, Y., Ando, N., Doukov, T. et al. Visualizing molecular juggling within a B12-dependent methyltransferase complex. Nature 484, 265–269 (2012). https://doi.org/10.1038/nature10916

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