6Y6R image
Entry Detail
PDB ID:
6Y6R
Keywords:
Title:
Crystal structure of MINDY1 T335D mutant
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2020-02-27
Release Date:
2021-03-31
Method Details:
Experimental Method:
Resolution:
3.32 Å
R-Value Free:
0.24
R-Value Work:
0.19
R-Value Observed:
0.20
Space Group:
P 41 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Ubiquitin carboxyl-terminal hydrolase MINDY-1
Mutations:T335D
Chain IDs:A
Chain Length:289
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2.
Mol.Cell 81 4176 4190.e6 (2021)
PMID: 34529927 DOI: 10.1016/j.molcel.2021.08.024

Abstact

Of 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.

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Primary Citation of related structures