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Published October 2019 | Published
Journal Article Open

Structures of the Neisseria meningitides methionine‐binding protein MetQ in substrate-free form and bound to L- and D-methionine isomers

Abstract

The bacterial periplasmic methionine‐binding protein MetQ is involved in the import of methionine by the cognate MetNI methionine ABC transporter. The MetNIQ system is one of the few members of the ABC importer family that has been structurally characterized in multiple conformational states. Critical missing elements in the structural analysis of MetNIQ are the structure of the substrate‐free form of MetQ, and detailing how MetQ binds multiple methionine derivatives, including both L‐ and D‐methionine isomers. In this study, we report the structures of the Neisseria meningitides MetQ in substrate‐free form and in complexes with L‐methionine and with D‐methionine, along with the associated binding constants determined by isothermal titration calorimetry. Structures of the substrate‐free (N238A) and substrate‐bound N. meningitides MetQ are related by a "Venus‐fly trap" hinge‐type movement of the two domains accompanying methionine binding and dissociation. L‐methionine and D‐methionine bind to the same site on MetQ, and this study emphasizes the important role of asparagine 238 in ligand binding and affinity. A thermodynamic analysis demonstrates that ligand‐free MetQ associates with the ATP bound form of MetNI ~40 times more tightly than does liganded MetQ, consistent with the necessity of dissociating methionine from MetQ for transport to occur.

Additional Information

© 2019 The Authors. Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. Accepted manuscript online: 26 July 2019; Manuscript accepted: 18 July 2019; Manuscript revised: 17 July 2019; Manuscript received: 30 June 2019. A Vietnam International Education Development scholarship from the Vietnam Ministry of Education and Training to P.T.N. is gratefully acknowledged. We thank Dr. Chad Brautigam and Dr. Shih‐chia (Scott) Tso for assistance with ITC, and Christoph Müller for his assistance in the initial phases of this project. We gratefully acknowledge the Gordon and Betty Moore Foundation and the Beckman Institute at Caltech for their generous support of the Molecular Observatory at Caltech, and the staff at Beamline 12–2, Stanford Synchrotron Radiation Lightsource (SSRL) for their assistance with data collection. SSRL is operated for the DOE and supported by its OBER and by the NIH, NIGMS (P41GM103393). We thank the Center for Environmental Microbial Interactions for their support of microbiology research at Caltech. D.C.R. is an investigator in Howard Hughes Medical Institute. Author Contributions: P.T.N. and D.C.R. designed experiments, analyzed data, and wrote the manuscript. P.T.N. performed the experiments. J.Y.L. contributed to the design and performance of experiments. J.T.K. contributed to the X‐ray crystallographic data analysis. The authors declare no conflict of interest.

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Created:
August 22, 2023
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October 18, 2023