Universität zu Köln

Minges, Alexander ORCID: 0000-0001-7760-2753, Ciupka, Daniel, Winkler, Christian, Hoeppner, Astrid ORCID: 0000-0002-7076-5936, Gohlke, Holger and Groth, Georg (2017). Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase. Sci Rep, 7. LONDON: NATURE PUBLISHING GROUP. ISSN 2045-2322

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Abstract

Pyruvate phosphate dikinase (PPDK) is a vital enzyme in cellular energy metabolism catalyzing the ATP-and P-i-dependent formation of phosphoenolpyruvate from pyruvate in C-4-plants, but the reverse reaction forming ATP in bacteria and protozoa. The multi-domain enzyme is considered an efficient molecular machine that performs one of the largest single domain movements in proteins. However, a comprehensive understanding of the proposed swiveling domain motion has been limited by not knowing structural intermediates or molecular dynamics of the catalytic process. Here, we present crystal structures of PPDKs from Flaveria, a model genus for studying the evolution of C-4-enzymes from phylogenetic ancestors. These structures resolve yet unknown conformational intermediates and provide the first detailed view on the large conformational transitions of the protein in the catalytic cycle. Independently performed unrestrained MD simulations and configurational free energy calculations also identified these intermediates. In all, our experimental and computational data reveal strict coupling of the CD swiveling motion to the conformational state of the NBD. Moreover, structural asymmetries and nucleotide binding states in the PPDK dimer support an alternate binding change mechanism for this intriguing bioenergetic enzyme.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Minges, Alexander UNSPECIFIED orcid.org/0000-0001-7760-2753 UNSPECIFIED Ciupka, Daniel UNSPECIFIED UNSPECIFIED UNSPECIFIED Winkler, Christian UNSPECIFIED UNSPECIFIED UNSPECIFIED Hoeppner, Astrid UNSPECIFIED orcid.org/0000-0002-7076-5936 UNSPECIFIED Gohlke, Holger UNSPECIFIED UNSPECIFIED UNSPECIFIED Groth, Georg UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-236229
DOI:	10.1038/srep45389
Journal or Publication Title:	Sci Rep
Volume:	7
Date:	2017
Publisher:	NATURE PUBLISHING GROUP
Place of Publication:	LONDON
ISSN:	2045-2322
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language MOLECULAR-DYNAMICS SIMULATIONS; ORTHOPHOSPHATE DIKINASE; C-4 PHOTOSYNTHESIS; CRYSTAL-STRUCTURES; DOMAIN MECHANISM; SOFTWARE; SYSTEM; SITE; DNA; RESOLUTION Multiple languages Multidisciplinary Sciences Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/23622