7L97

Crystal structure of STAMBPL1 in complex with an engineered binder

Summary for 7L97

• Entry DOI: 10.2210/pdb7l97/pdb
• Descriptor: AMSH-like protease, Ubiquitin variant, ZINC ION, ... (7 entities in total)
• Functional Keywords: stambp1, ubv, structural genomics, structural genomics consortium, sgc, protein binding
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 2
• Total formula weight: 28877.83

Authors

Guo, Y.,Dong, A.,Hou, F.,Li, Y.,Zhang, W.,Arrowsmith, C.H.,Edwards, A.M.,Tong, Y.,Structural Genomics Consortium (SGC) (deposition date: 2021-01-02, release date: 2021-08-25, Last modification date: 2023-10-18)

Primary citation

Guo, Y.,Liu, Q.,Mallette, E.,Caba, C.,Hou, F.,Fux, J.,LaPlante, G.,Dong, A.,Zhang, Q.,Zheng, H.,Tong, Y.,Zhang, W.
Structural and functional characterization of ubiquitin variant inhibitors for the JAMM-family deubiquitinases STAMBP and STAMBPL1.
J.Biol.Chem., 297:101107-101107, 2021

PubMed Abstract: Ubiquitination is a crucial posttranslational protein modification involved in a myriad of biological pathways. This modification is reversed by deubiquitinases (DUBs) that deconjugate the single ubiquitin (Ub) moiety or poly-Ub chains from substrates. In the past decade, tremendous efforts have been focused on targeting DUBs for drug discovery. However, most chemical compounds with inhibitory activity for DUBs suffer from mild potency and low selectivity. To overcome these obstacles, we developed a phage display-based protein engineering strategy for generating Ub variant (UbV) inhibitors, which was previously successfully applied to the Ub-specific protease (USP) family of cysteine proteases. In this work, we leveraged the UbV platform to selectively target STAMBP, a member of the JAB1/MPN/MOV34 (JAMM) metalloprotease family of DUB enzymes. We identified two UbVs (UbV and UbV) that bind to STAMBP with high affinity but differ in their selectivity for the closely related paralog STAMBPL1. We determined the STAMBPL1-UbV complex structure by X-ray crystallography, revealing hotspots of the JAMM-UbV interaction. Finally, we show that UbV and UbV are potent inhibitors of STAMBP isopeptidase activity, far exceeding the reported small-molecule inhibitor BC-1471. This work demonstrates that UbV technology is suitable to develop molecules as tools to target metalloproteases, which can be used to further understand the cellular function of JAMM family DUBs.

PubMed: 34425109
DOI: 10.1016/j.jbc.2021.101107

Experimental method

X-RAY DIFFRACTION (2.01 Å)