5MN9

Crystal structure of MINDY-1 tMIU in complex with K48-diUb

Summary for 5MN9

• Entry DOI: 10.2210/pdb5mn9/pdb
• Descriptor: Ubiquitin-40S ribosomal protein S27a, Ubiquitin carboxyl-terminal hydrolase MINDY-1 (3 entities in total)
• Functional Keywords: motif interacting with ubiquitin, ubiquitin binding domain, hydrolase and cysteine protease, hydrolase
• Biological source: Homo sapiens (Human); More
• Cellular location: Ubiquitin: Cytoplasm : P62992
• Total number of polymer chains: 3
• Total formula weight: 22093.04

Authors

Kristariyanto, Y.A.,Abdul Rehman, S.A.,Kulathu, Y. (deposition date: 2016-12-13, release date: 2017-01-25, Last modification date: 2024-01-17)

Primary citation

Kristariyanto, Y.A.,Abdul Rehman, S.A.,Weidlich, S.,Knebel, A.,Kulathu, Y.
A single MIU motif of MINDY-1 recognizes K48-linked polyubiquitin chains.
EMBO Rep., 18:392-402, 2017

PubMed Abstract: The eight different types of ubiquitin (Ub) chains that can be formed play important roles in diverse cellular processes. Linkage-selective recognition of Ub chains by Ub-binding domain (UBD)-containing proteins is central to coupling different Ub signals to specific cellular responses. The motif interacting with ubiquitin (MIU) is a small UBD that has been characterized for its binding to monoUb. The recently discovered deubiquitinase MINDY-1/FAM63A contains a tandem MIU repeat (tMIU) that is highly selective at binding to K48-linked polyUb. We here identify that this linkage-selective binding is mediated by a single MIU motif (MIU2) in MINDY-1. The crystal structure of MIU2 in complex with K48-linked polyubiquitin chains reveals that MIU2 on its own binds to all three Ub moieties in an open conformation that can only be accommodated by K48-linked triUb. The weak Ub binder MIU1 increases overall affinity of the tMIU for polyUb chains without affecting its linkage selectivity. Our analyses reveal new concepts for linkage selectivity and polyUb recognition by UBDs.

PubMed: 28082312
DOI: 10.15252/embr.201643205

Experimental method

X-RAY DIFFRACTION (2.05 Å)