Seeing but not believing: the structure of glycerol dehydrogenase initially assumed to be the structure of a survival protein fromSalmonella typhimurium

Hatti, Kaushik and Mathiharan, Yamuna Kalyani and Srinivasan, Narayanaswamy and Murthy, Mathur RN (2017) Seeing but not believing: the structure of glycerol dehydrogenase initially assumed to be the structure of a survival protein fromSalmonella typhimurium. In: Acta Crystallographica Section D Structural Biology, 73 (7). pp. 609-617. ISSN 2059-7983

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Abstract

The determination of the crystal structure of a mutant protein using phases based on a previously determined crystal structure of the wild-type protein is often a straightforward molecular-replacement protocol. Such a structure determination may be difficult if there are large-scale structural differences between the wild-type and mutant proteins. In this manuscript, an interesting case is presented of the unintentional crystallization of a contaminant protein which shared some structural features with the presumed target protein, leading to difficulties in obtaining a completely satisfactory molecular-replacement structure solution. It was not immediately evident that the initial structure solution was incorrect owing to the poor quality of the X-ray diffraction data and low resolution. The structure was subsequently determined by improving the quality of the data and following a sequence-independent MarathonMR protocol. The structure corresponded to that of glycerol dehydrogenase, which crystallized as a contaminant, instead of the presumed mutant of a survival protein encoded by Salmonella typhimurium. The reasons why a solution that appeared to be reasonable was obtained with an incorrect protein model are discussed. The results presented here show that a degree of caution is warranted when handling large-scale structure-determination projects.A seemingly reasonable solution was obtained for the structure of a presumed mutant of an S. typhimurium survival protein (SurE) by molecular replacement using the wild-type SurE structure as the phasing model. Although the crystal was of glycerol dehydrogenase, as subsequently demonstrated using the MarathonMR protocol, the initial structure appeared to be reasonable because of a partial similarity in the arrangement of secondary-structural elements in the two proteins.

Item Type:	Journal Article
Publication:	Acta Crystallographica Section D Structural Biology
Publisher:	International Union of Crystallography
Additional Information:	The copyright for this article belongs to the International Union of Crystallography.
Keywords:	contaminant; glycerol dehydrogenase; MarathonMR; molecular replacement; serendipity
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	08 Jun 2022 05:25
Last Modified:	08 Jun 2022 05:25
URI:	https://eprints.iisc.ac.in/id/eprint/73157

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