PDBsum entry 6cpm

Signaling protein

PDB id: 6cpm

Contents

Protein chains

339 a.a.

79 a.a.

Ligands

GOL ×3

EDO

Metals

_CA ×5

_NA ×3

_ZN ×2

Waters ×535

PDB id:

6cpm

Name:

Signaling protein

Title:

Structure of the usp15 deubiquitinase domain in complex with a third- generation inhibitory ubv

Structure:

Ubiquitin carboxyl-terminal hydrolase 15. Chain: c, d. Synonym: deubiquitinating enzyme 15,ubiquitin thioesterase 15, ubiquitin-specific-processing protease 15,unph-2,unph4. Engineered: yes. Ubiquitin variant 15.1d. Chain: e, f. Synonym: ubv 15.1d. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: usp15, kiaa0529. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.01Å R-factor: 0.168 R-free: 0.212

Authors:

A.U.Singer,J.Teyra,G.Boehmelt,M.Lenter,F.Sicheri,S.S.Sidhu

Key ref:

J.Teyra et al. (2019). Structural and Functional Characterization of Ubiquitin Variant Inhibitors of USP15. Structure, 27, 590. PubMed id: 30713027 DOI: 10.1016/j.str.2019.01.002

Date:

13-Mar-18 Release date: 23-Jan-19

Protein chains

Q9Y4E8  (UBP15_HUMAN) -  Ubiquitin carboxyl-terminal hydrolase 15 from Homo sapiens

Seq: 981 a.a.

Struc: 339 a.a.*

Protein chains

No UniProt id for this chain

Struc: 79 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains C, D: E.C.3.4.19.12 - ubiquitinyl hydrolase 1.
• Reaction: Thiol-dependent hydrolysis of ester, thiolester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).

DOI no: 10.1016/j.str.2019.01.002

Structure 27:590 (2019)

PubMed id: 30713027

Structural and Functional Characterization of Ubiquitin Variant Inhibitors of USP15.

J.Teyra, A.U.Singer, F.W.Schmitges, P.Jaynes, S.Kit Leng Lui, M.J.Polyak, N.Fodil, J.R.Krieger, J.Tong, C.Schwerdtfeger, B.B.Brasher, D.F.J.Ceccarelli, J.Moffat, F.Sicheri, M.F.Moran, P.Gros, P.J.A.Eichhorn, M.Lenter, G.Boehmelt, S.S.Sidhu.

ABSTRACT

The multi-domain deubiquitinase USP15 regulates diverse eukaryotic processes and has been implicated in numerous diseases. We developed ubiquitin variants (UbVs) that targeted either the catalytic domain or each of three adaptor domains in USP15, including the N-terminal DUSP domain. We also designed a linear dimer (diUbV), which targeted the DUSP and catalytic domains, and exhibited enhanced specificity and more potent inhibition of catalytic activity than either UbV alone. In cells, the UbVs inhibited the deubiquitination of two USP15 substrates, SMURF2 and TRIM25, and the diUbV inhibited the effects of USP15 on the transforming growth factor β pathway. Structural analyses revealed that three distinct UbVs bound to the catalytic domain and locked the active site in a closed, inactive conformation, and one UbV formed an unusual strand-swapped dimer and bound two DUSP domains simultaneously. These inhibitors will enable the study of USP15 function in oncology, neurology, immunology, and inflammation.