Relief of autoinhibition by conformational switch explains enzyme activation by a catalytically dead paralog.

Oleg A Volkov,Xiaoyi Deng,Diana R Tomchick,Zhe Chen,Margaret A Phillips,Shihua Zhong,Lisa Kinch,Nick Grishin,Carson Ariagno

doi:10.7554/elife.20198

Oleg A Volkov, Xiaoyi Deng + Show 7 more

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https://doi.org/10.7554/elife.20198

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Abstract

Catalytically inactive enzyme paralogs occur in many genomes. Some regulate their active counterparts but the structural principles of this regulation remain largely unknown. We report X-ray structures of Trypanosoma brucei S-adenosylmethionine decarboxylase alone and in functional complex with its catalytically dead paralogous partner, prozyme. We show monomeric TbAdoMetDC is inactive because of autoinhibition by its N-terminal sequence. Heterodimerization with prozyme displaces this sequence from the active site through a complex mechanism involving a cis-to-trans proline isomerization, reorganization of a β-sheet, and insertion of the N-terminal α-helix into the heterodimer interface, leading to enzyme activation. We propose that the evolution of this intricate regulatory mechanism was facilitated by the acquisition of the dimerization domain, a single step that can in principle account for the divergence of regulatory schemes in the AdoMetDC enzyme family. These studies elucidate an allosteric mechanism in an enzyme and a plausible scheme by which such complex cooperativity evolved.

Highlights

The availability of numerous sequenced eukaryotic genomes has uncovered enzyme paralogs across diverse gene families that are predicted to be enzymatically inactive because they lack essential catalytic residues (Adrain and Freeman, 2012; Pils and Schultz, 2004; Todd et al, 2002; Reynolds and Fischer, 2015; Reiterer et al, 2014; Kung and Jura, 2016)
Deletion or mutation of these residues led to loss of prozyme-mediated activation of TbAdoMetDC despite competent heterodimer formation implicating the N-terminus in the activation mechanism (Velez et al, 2013)
A single TbAdoMetDCD26 ab-monomer was found in the asymmetric unit composed of a four-layer sandwich with two central b-sheets positioned between outer a-helices (Figure 2C)

Summary

Introduction

The availability of numerous sequenced eukaryotic genomes has uncovered enzyme paralogs across diverse gene families that are predicted to be enzymatically inactive because they lack essential catalytic residues (Adrain and Freeman, 2012; Pils and Schultz, 2004; Todd et al, 2002; Reynolds and Fischer, 2015; Reiterer et al, 2014; Kung and Jura, 2016) These ‘pseudoenzymes’ are estimated to represent up to 10% of human encoded proteins, and are abundant within the protease and kinase families. An interesting hypothesis emerges from the fact that many enzymes form functional oligomers (Goodsell and Olson, 2000; Marianayagam et al, 2004) This property leads to the idea that pseudoenzymes might generally evolve to serve as regulators of enzymes, directly interacting with their cognate active homolog to exert regulatory control.

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