Mechanism and evolutionary origins of alanine-tail C-degron recognition by E3 ligases Pirh2 and CRL2-KLHDC10
Pratik Rajendra Patil,
A. Maxwell Burroughs,
Mohit Misra,
Federico Cerullo,
Carlos Costas Insua,
Hao-Chih Hung,
Ivan Dikic,
L. Aravind,
Claudio A.P. Joazeiro
Affiliations
Pratik Rajendra Patil
Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, 69120 Heidelberg, Germany
A. Maxwell Burroughs
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Mohit Misra
Institute of Biochemistry II, Goethe University Faculty of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
Federico Cerullo
Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, 69120 Heidelberg, Germany
Carlos Costas Insua
Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, 69120 Heidelberg, Germany
Hao-Chih Hung
Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, 69120 Heidelberg, Germany
Ivan Dikic
Institute of Biochemistry II, Goethe University Faculty of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
L. Aravind
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Claudio A.P. Joazeiro
Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, 69120 Heidelberg, Germany; Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL 33458, USA; Corresponding author
Summary: In ribosome-associated quality control (RQC), nascent polypeptides produced by interrupted translation are modified with C-terminal polyalanine tails (“Ala-tails”) that function outside ribosomes to induce ubiquitylation by E3 ligases Pirh2 (p53-induced RING-H2 domain-containing) or CRL2 (Cullin-2 RING ligase2)-KLHDC10. Here, we investigate the molecular basis of Ala-tail function using biochemical and in silico approaches. We show that Pirh2 and KLHDC10 directly bind to Ala-tails and that structural predictions identify candidate Ala-tail-binding sites, which we experimentally validate. The degron-binding pockets and specific pocket residues implicated in Ala-tail recognition are conserved among Pirh2 and KLHDC10 homologs, suggesting that an important function of these ligases across eukaryotes is in targeting Ala-tailed substrates. Moreover, we establish that the two Ala-tail-binding pockets have convergently evolved, either from an ancient module of bacterial provenance (Pirh2) or via tinkering of a widespread C-degron-recognition element (KLHDC10). These results shed light on the recognition of a simple degron sequence and the evolution of Ala-tail proteolytic signaling.
