Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2

Syed Arif Abdul Rehman,Lee A Armstrong,Sven M Lange,Yosua Adi Kristariyanto,Tobias W Gräwert,Axel Knebel,Dmitri I Svergun,Yogesh Kulathu

doi:10.1016/j.molcel.2021.08.024

Syed Arif Abdul Rehman, Lee A Armstrong + Show 6 more

Open Access

https://doi.org/10.1016/j.molcel.2021.08.024

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Abstract

SummaryOf the eight distinct polyubiquitin (polyUb) linkages that can be assembled, the roles of K48-linked polyUb (K48-polyUb) are the most established, with K48-polyUb modified proteins being targeted for degradation. MINDY1 and MINDY2 are members of the MINDY family of deubiquitinases (DUBs) that have exquisite specificity for cleaving K48-polyUb, yet we have a poor understanding of their catalytic mechanism. Here, we analyze the crystal structures of MINDY1 and MINDY2 alone and in complex with monoUb, di-, and penta-K48-polyUb, identifying 5 distinct Ub binding sites in the catalytic domain that explain how these DUBs sense both Ub chain length and linkage type to cleave K48-polyUb chains. The activity of MINDY1/2 is inhibited by the Cys-loop, and we find that substrate interaction relieves autoinhibition to activate these DUBs. We also find that MINDY1/2 use a non-canonical catalytic triad composed of Cys-His-Thr. Our findings highlight multiple layers of regulation modulating DUB activity in MINDY1 and MINDY2.

Highlights

Most aspects of eukaryotic cell biology are influenced by the posttranslational modification (PTM) of proteins with ubiquitin (Ub)
The crystal structures of MINDY2cat and MINDY1cat closely resemble one another, and both DUBs bind to K48 chains in a similar way (Figure S1C)
We found MINDY1 and MINDY2 to use analogous mechanisms and, to simplify our description, we focus on MINDY1, highlighting any differences observed with MINDY2

Summary

Introduction

Most aspects of eukaryotic cell biology are influenced by the posttranslational modification (PTM) of proteins with ubiquitin (Ub). M1-, K33-, and K63-linked chains can exist in an open extended conformation with accessible I44 binding patches that can be recognized by DUBs (Kristariyanto et al, 2015; Ronau et al, 2016) Other linkage types, such as K6-, K11-, and K48-linked chains, adopt compact conformations and must undergo significant conformational changes to be recognized by a DUB (Bekes et al, 2016; Gersch et al, 2017; Mevissen et al, 2016; Sato et al, 2017; Ye et al, 2012). Despite it being the most abundant linkage type, we do not know how K48-linked polyUb is recognized by DUBs, as there are no available structures of DUBs bound to K48-linked chains

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